Contacts of the helix formed by residues 18 - 47 (chain B) in PDB entry 2IB0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 18 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 1.3 98.4 + - - +
19B GLY* 1.3 64.1 + - - +
20B SER* 3.6 26.7 + - - -
21B ALA* 3.4 14.5 + - + +
22B ASP* 3.2 20.1 + - - +
120B HIS 4.6 0.7 - - - +
122B GLU* 3.8 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 1.3 75.1 + - - +
20B SER* 1.3 57.5 + - - +
21B ALA 3.4 0.2 - - - -
22B ASP* 3.5 5.4 - - - +
23B ASN* 3.0 39.7 + - - +
122B GLU* 3.5 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 3.1 27.1 + - - -
19B GLY* 1.3 76.2 - - - +
21B ALA* 1.3 63.7 + - - +
23B ASN* 3.7 6.4 + - - +
24B ALA* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 4.0 11.7 - - - +
18B GLU* 3.4 16.8 + - + +
20B SER* 1.3 76.3 - - - +
22B ASP* 1.3 62.3 + - - +
24B ALA* 4.1 4.6 - - - +
25B ALA* 3.2 25.3 + - - +
120B HIS* 3.8 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU 3.2 9.3 + - - +
19B GLY* 3.5 12.3 - - - +
20B SER 3.3 0.2 - - - -
21B ALA* 1.3 76.0 - - - +
23B ASN* 1.3 65.6 + - - +
25B ALA* 3.4 4.2 + - - +
26B LEU* 3.1 19.2 + - - +
76B ARG* 2.8 39.8 + - - +
117B VAL* 5.0 3.5 - - - +
120B HIS* 3.5 15.7 + - - +
121B ALA* 3.4 19.9 + - - +
122B GLU* 2.8 29.1 + - + +
123B THR* 4.6 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY* 3.0 24.8 + - - +
20B SER* 4.0 6.4 - - - +
22B ASP* 1.3 77.3 - - - +
24B ALA* 1.3 56.7 + - - +
26B LEU* 3.3 1.7 + - - +
27B CYS* 2.9 38.8 + - - -
73B LEU* 4.5 1.9 - - - +
76B ARG* 3.1 32.5 + - - +
78B VAL* 3.5 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER 3.2 16.0 + - - +
21B ALA* 4.1 6.5 - - - +
23B ASN* 1.3 74.6 - - - +
25B ALA* 1.3 65.3 + - - +
27B CYS* 3.9 5.9 - - - +
28B ASP* 3.0 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA 3.2 17.2 + - - +
22B ASP 3.8 3.6 - - - +
24B ALA* 1.3 78.9 - - - +
26B LEU* 1.4 57.4 + - - +
28B ASP* 3.4 10.9 + - - +
29B ALA* 3.0 22.0 + - - +
113B ALA 4.7 1.9 - - - +
116B ALA* 3.8 29.8 - - + +
117B VAL* 3.4 19.2 - - + +
120B HIS* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP 3.1 16.6 + - - +
23B ASN 3.8 3.1 - - - +
24B ALA 3.3 0.2 - - - -
25B ALA* 1.4 74.1 - - - +
27B CYS* 1.4 58.5 - - - +
29B ALA* 3.2 2.8 + - - +
30B LEU* 2.9 28.1 + - - +
69B VAL* 3.8 17.9 - - + -
72B MET* 4.1 29.2 - - + -
73B LEU* 3.9 20.2 - - + -
76B ARG* 3.5 35.7 - - - +
114B TRP* 3.7 28.7 - - + -
117B VAL* 3.9 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN* 2.9 25.5 + - - +
24B ALA* 3.9 6.3 - - - +
26B LEU* 1.4 71.8 - - - +
28B ASP* 1.3 62.1 + - - +
30B LEU 3.3 1.0 + - - -
31B ALA* 2.9 27.1 + - - +
73B LEU* 3.8 21.8 - - - -
78B VAL* 3.8 18.4 - - - -
79B THR 5.0 0.7 - - - -
81B PRO* 3.5 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 3.0 29.3 + - - +
25B ALA* 3.5 9.2 - - - +
27B CYS* 1.3 76.7 - - - +
29B ALA* 1.3 58.6 + - - +
31B ALA* 3.3 7.6 + - - +
32B VAL* 3.0 33.9 + - + +
113B ALA* 5.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 3.0 14.3 + - - +
26B LEU 3.6 7.6 - - - +
27B CYS 3.2 0.2 - - - -
28B ASP* 1.3 74.7 - - - +
30B LEU* 1.3 59.2 + - - +
32B VAL* 3.3 4.7 + - - +
33B GLU* 2.9 33.3 + - - +
113B ALA* 4.1 18.8 - - + -
114B TRP* 3.7 34.8 + - + -
117B VAL* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU 2.9 13.5 + - - +
27B CYS* 3.7 8.1 - - - +
29B ALA* 1.3 74.1 - - - +
31B ALA* 1.3 58.9 + - - +
33B GLU* 3.1 7.1 + - + +
34B HIS* 2.9 39.0 + - + +
66B ARG* 3.7 46.4 - - + +
69B VAL* 3.8 15.4 - - + +
70B ILE* 4.0 6.7 - - + -
73B LEU* 3.8 7.2 - - + -
80B ALA* 3.5 23.8 - - + -
81B PRO* 3.4 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B CYS 2.9 13.9 + - - +
28B ASP* 3.3 11.4 + - - +
30B LEU* 1.3 75.6 - - - +
32B VAL* 1.3 64.5 + - + +
34B HIS* 3.4 12.1 + - - +
35B ALA* 3.1 22.7 + - - +
81B PRO* 4.5 10.5 - - + +
87B TYR* 4.6 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASP* 3.0 18.9 + - + +
29B ALA 3.5 8.5 - - - +
30B LEU 3.2 0.2 - - - -
31B ALA* 1.3 75.8 - - + +
33B GLU* 1.3 66.6 + - - +
35B ALA* 3.2 7.8 + - + +
36B THR* 2.9 35.3 + - - +
109B ASP* 4.1 11.2 - - + +
110B GLY* 3.9 32.8 - - - +
113B ALA* 4.1 14.8 - - + -
114B TRP* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 2.9 19.3 + - - +
30B LEU* 3.1 11.4 + - + +
32B VAL* 1.3 77.7 - - - +
34B HIS* 1.3 62.7 + - - +
36B THR* 3.3 3.9 + - - -
37B ILE* 3.0 31.2 + - + +
62B HIS* 2.6 39.9 + - - +
65B ARG* 2.8 35.8 + - + -
66B ARG* 4.5 19.7 - - + +
69B VAL* 5.5 0.7 - - + -
110B GLY* 5.1 4.7 - - - -
114B TRP* 2.8 29.4 + - + -
137B SER* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 2.9 32.2 + - + +
31B ALA* 3.6 9.9 - - - +
33B GLU* 1.3 76.5 - - - +
35B ALA* 1.3 62.3 + - - +
37B ILE* 3.5 7.1 + - - +
38B TYR* 3.2 21.7 + - - +
66B ARG* 3.6 36.0 + - + -
70B ILE* 4.7 7.6 - - + -
81B PRO* 2.9 25.8 + - + -
82B ILE* 3.5 8.3 - - - -
83B ALA* 3.5 35.8 + - + +
87B TYR* 3.4 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA 3.1 9.9 + - - +
32B VAL* 3.6 9.6 - - + +
34B HIS* 1.3 78.9 - - - +
36B THR* 1.3 55.7 + - - +
38B TYR* 3.3 6.6 + - - +
39B GLY* 2.9 25.3 + - - -
87B TYR* 3.8 34.9 + - + +
106B MET* 4.5 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 2.9 31.4 + - - +
33B GLU* 3.3 6.2 + - - -
35B ALA* 1.3 69.1 - - - +
37B ILE* 1.3 59.3 + - - +
39B GLY* 3.1 1.4 + - - -
40B TYR* 2.8 48.4 + - + -
62B HIS* 3.6 32.6 - - + +
106B MET* 3.9 35.1 + - + +
107B GLU* 4.7 0.9 - - - +
110B GLY* 5.6 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU 3.0 26.6 + - - +
34B HIS* 3.8 6.1 - - - +
36B THR* 1.3 71.7 - - - +
38B TYR* 1.3 69.7 + - - +
40B TYR* 3.3 13.3 + - - +
41B GLY* 3.4 7.4 + - - -
59B LEU* 3.9 21.0 - - + +
62B HIS* 3.7 41.3 - - + +
63B ARG* 4.2 20.9 - - + +
66B ARG* 3.8 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B HIS 3.2 8.9 + - - +
35B ALA 3.4 8.5 - - - +
37B ILE* 1.3 79.8 - - - +
39B GLY* 1.3 65.3 + - - +
41B GLY* 3.1 14.4 + - - -
42B ILE* 3.5 33.8 - - + +
84B ALA 5.4 0.7 - - - -
85B ALA 4.1 8.3 - - - -
86B GLY* 3.9 16.3 - - - -
87B TYR* 3.6 64.3 + + + -
89B LEU* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA 2.9 12.3 + - - -
36B THR 3.1 4.2 + - - -
38B TYR* 1.3 76.4 - - - +
40B TYR* 1.3 57.2 + - - +
42B ILE* 3.1 8.5 + - - +
43B VAL* 3.0 26.9 + - - +
89B LEU* 4.3 19.7 - - - -
102B LEU* 4.1 1.5 - - - +
106B MET* 3.6 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B THR* 2.8 41.4 + - + +
37B ILE* 3.7 1.1 - - - +
38B TYR 3.2 0.8 - - - -
39B GLY* 1.3 72.4 - - - +
41B GLY* 1.3 58.6 + - - +
43B VAL* 3.7 16.2 - - + +
44B SER* 2.8 30.1 + - - -
55B VAL* 4.2 10.7 - - + +
58B ALA* 3.4 22.1 - - + +
59B LEU* 3.7 28.4 - - + +
62B HIS* 3.7 13.9 - + - -
103B ALA* 3.9 13.4 - - + +
106B MET* 4.0 5.6 - - + -
107B GLU* 2.6 36.5 + - + +
140B MET* 3.8 0.2 - - - +
144B TRP* 3.0 40.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE 3.4 5.9 + - - -
38B TYR 3.1 11.0 + - - -
40B TYR* 1.3 77.9 - - - +
42B ILE* 1.3 58.8 + - - +
44B SER* 3.6 6.2 - - - -
45B ALA* 3.1 26.5 + - - +
59B LEU* 4.9 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 3.5 44.9 - - + +
39B GLY 3.1 8.5 + - - +
41B GLY* 1.3 76.2 - - - +
43B VAL* 1.3 64.9 + - - +
45B ALA* 3.3 6.7 + - + +
46B LEU* 3.1 44.5 + - + +
89B LEU* 4.2 21.3 - - + -
93B VAL* 4.0 16.8 - - + -
102B LEU* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLY 3.0 15.2 + - - +
40B TYR* 3.7 17.0 - - + +
41B GLY 3.5 0.2 - - - -
42B ILE* 1.3 73.4 - - - +
44B SER* 1.3 63.9 + - - +
46B LEU* 3.4 1.2 + - - -
47B SER* 2.7 34.4 + - - +
55B VAL* 4.4 1.6 - - + -
99B ALA* 3.6 31.9 - - - +
102B LEU* 4.1 9.2 - - + -
103B ALA* 4.2 2.5 - - + -
106B MET* 3.8 20.9 - - + -
144B TRP* 3.4 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR 2.8 22.6 + - - -
41B GLY* 3.6 7.2 - - - -
43B VAL* 1.3 75.8 - - - +
45B ALA* 1.3 64.6 + - - +
46B LEU 3.2 1.2 + - - -
47B SER* 3.3 15.6 + - - +
52B ASN* 5.5 5.2 + - - +
55B VAL* 3.7 28.1 - - - +
59B LEU* 5.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY 3.1 14.9 + - - +
42B ILE* 3.3 8.5 + - - +
44B SER* 1.3 79.6 - - - +
46B LEU* 1.3 61.5 + - + +
47B SER 3.8 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.1 26.1 + - + +
45B ALA* 1.3 78.0 - - + +
47B SER* 1.3 62.7 + - - +
93B VAL* 3.8 33.2 - - + -
94B SER* 4.0 7.6 - - - +
95B SER* 3.5 37.9 - - - +
96B ALA* 3.4 19.5 + - - +
99B ALA* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 2.7 33.6 + - - +
44B SER 3.3 12.4 + - - +
45B ALA 4.4 2.1 - - - +
46B LEU* 1.3 79.4 - - - +
48B PRO* 1.4 69.7 - - - +
49B PRO* 4.6 0.9 - - - +
51B VAL* 3.3 25.7 - - - +
52B ASN* 5.1 2.6 - - - +
55B VAL* 4.6 5.8 - - - -
96B ALA* 4.4 3.4 + - - -
99B ALA* 3.8 8.8 - - - +
144B TRP* 3.9 5.2 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il