Contacts of the helix formed by residues 39 - 59 (chain B) in PDB entry 2P1A
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 SER 39 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU 3.9 11.4 - - - -
30B LYS* 4.0 18.0 - - - +
32B ALA 5.4 2.5 - - - -
34B ILE* 4.7 6.3 - - - -
38B ARG* 1.3 76.2 - - - +
40B LEU* 1.3 61.0 + - - +
41B PHE* 3.7 6.4 + - - +
42B GLU* 3.0 34.2 + - - +
43B MSE 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.4 24.6 + - + +
32B ALA* 3.8 15.5 - - + -
34B ILE* 3.5 29.5 - - + +
39B SER* 1.3 73.8 - - - +
41B PHE* 1.3 61.4 + - - +
43B MSE 3.9 11.5 - - - +
44B TYR* 3.1 28.6 + - - +
136B ILE* 3.9 28.9 - - + +
139B LEU* 3.5 35.0 - - + +
140B LEU* 3.5 24.7 - - + -
144B MSE 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU* 3.8 28.9 - - + -
29B LEU* 3.4 23.3 + - + +
30B LYS* 3.7 42.4 - - + +
39B SER* 3.7 6.7 - - - +
40B LEU* 1.3 77.9 - - - +
42B GLU* 1.3 65.5 + - + +
44B TYR 3.1 1.6 + - - -
45B ALA* 2.9 26.0 + - + +
75B PRO 4.1 13.2 - - - -
76B GLU* 3.5 31.6 - - - -
77B THR* 3.9 1.6 - - - -
78B ILE* 4.4 11.4 - - + -
81B MSE 3.1 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS 4.7 0.7 - - - +
38B ARG* 3.1 50.3 + - + +
39B SER* 3.0 35.2 + - - +
41B PHE* 1.3 85.0 - - + +
43B MSE 1.3 56.9 + - - +
45B ALA* 3.5 8.0 + - - +
46B HIS* 3.0 26.5 + - - +
74B THR* 5.2 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 3.9 17.9 - - + -
34B ILE* 5.3 5.4 - - - -
36B SER* 5.6 2.9 - - - -
38B ARG* 4.4 21.3 - - + +
39B SER 3.0 16.4 + - - +
40B LEU* 3.9 19.1 - - - +
42B GLU* 1.3 74.7 - - - +
44B TYR* 1.3 60.1 + - - +
46B HIS* 3.6 9.9 + - - +
47B LEU* 3.0 21.0 + - - +
132B HIS* 5.0 1.9 - - + +
135B GLN* 3.7 42.2 - - + +
136B ILE* 3.4 28.5 - - + +
139B LEU* 4.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 2.8 31.3 + - - -
20B MSE 3.0 25.6 - - + +
21B LEU* 3.4 47.6 + - + -
24B TYR* 5.8 0.7 - + - -
29B LEU* 4.6 12.6 - - + -
40B LEU* 3.1 18.9 + - + +
41B PHE* 3.1 5.8 + - - +
43B MSE 1.3 73.6 - - - +
45B ALA* 1.3 61.6 + - - +
47B LEU* 3.3 20.0 + - + +
48B SER* 3.0 28.1 + - - -
81B MSE 3.9 11.8 - - + +
85B MSE 4.5 4.7 - - + -
136B ILE* 3.4 35.9 - - + +
140B LEU* 4.4 9.2 - - + -
----------------------------------------------------------
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 PHE* 2.9 12.8 + - + +
42B GLU* 3.7 7.6 - - - +
44B TYR* 1.3 76.7 - - - +
46B HIS* 1.4 60.0 + - - +
48B SER* 2.6 26.1 + - - -
49B LEU* 3.4 11.3 + - - +
74B THR* 3.4 28.7 - - + -
75B PRO* 3.6 12.9 - - + +
81B MSE 3.3 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 3.0 18.6 + - - +
43B MSE 3.6 9.4 - - - +
45B ALA* 1.4 72.4 - - - +
47B LEU* 1.3 67.7 + - - +
49B LEU* 3.1 18.1 + - - +
50B ILE* 3.4 12.1 + - + +
70B TYR* 3.7 36.4 + + + -
74B THR* 4.7 2.4 - - - +
128B HIS* 4.1 11.9 + + - -
132B HIS* 3.5 38.4 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 3.7 30.7 - - - +
20B MSE 5.3 0.7 - - + -
43B MSE 3.0 16.0 + - - +
44B TYR* 3.4 21.5 - - + +
46B HIS* 1.3 77.5 - - - +
48B SER* 1.3 61.8 + - - +
49B LEU 3.3 0.9 + - - -
50B ILE* 3.3 29.8 + - + +
51B CYS 4.9 0.2 + - - -
85B MSE 4.3 2.7 - - + -
129B PHE* 3.7 31.3 - - + +
132B HIS* 3.8 14.4 - - + +
133B ARG* 3.6 30.7 - - + +
136B ILE* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR 3.0 9.9 + - - -
45B ALA* 2.6 19.9 + - - -
47B LEU* 1.3 76.3 - - - +
49B LEU* 1.3 57.9 + - - +
50B ILE 3.5 0.4 + - - -
51B CYS* 4.8 4.0 + - - +
52B HIS* 4.7 1.9 + - - -
75B PRO* 3.3 21.5 - - - +
81B MSE 3.3 30.3 - - - -
84B THR* 3.5 16.5 - - - +
85B MSE 3.4 34.1 - - - +
88B GLY* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA 3.7 11.7 - - - +
46B HIS* 3.1 11.2 + - - +
48B SER* 1.3 76.6 + - - +
50B ILE* 1.3 56.7 + - - +
51B CYS 3.4 1.6 - - - -
52B HIS* 3.3 5.3 + - - +
53B ALA* 2.9 31.7 + - - +
69B PHE* 4.0 27.8 - - + -
70B TYR* 3.4 38.8 - - + -
73B GLN* 3.8 16.8 - - + +
74B THR* 3.5 28.0 - - + +
75B PRO* 4.1 3.8 - - + -
84B THR* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 3.4 13.9 + - + +
47B LEU* 3.3 42.4 + - + +
49B LEU* 1.3 75.2 - - - +
51B CYS* 1.3 64.8 + - - +
53B ALA* 4.6 3.6 - - - -
54B ASP* 3.0 45.0 + - - +
70B TYR* 4.7 2.9 - - - +
125B ILE* 4.1 12.1 - - + -
128B HIS* 3.5 34.1 - - + +
129B PHE* 3.9 27.4 - - + -
132B HIS* 4.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.9 36.3 - - - -
14B VAL* 4.7 3.4 - - - -
47B LEU 4.9 0.6 + - - -
48B SER 4.8 3.8 + - - +
49B LEU 3.4 0.6 - - - -
50B ILE* 1.3 81.5 - - - +
52B HIS* 1.3 62.1 + - - +
54B ASP* 4.5 0.3 - - - +
55B LEU* 3.2 21.5 + - - +
85B MSE 4.8 5.2 - - + +
88B GLY* 3.4 29.4 - - - +
89B TYR* 3.7 13.2 - - - +
92B LEU* 4.0 16.5 - - + +
125B ILE* 4.7 2.7 - - - -
129B PHE* 4.5 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER 4.7 2.0 + - - -
49B LEU* 3.3 5.5 + - - +
50B ILE 3.3 0.6 - - - -
51B CYS* 1.3 76.5 - - - +
53B ALA* 1.3 60.7 + - - +
55B LEU* 3.3 7.7 + - - +
56B LEU* 3.0 34.4 + - + +
69B PHE* 3.5 26.6 - + + -
84B THR* 3.3 43.1 + - + +
87B GLN* 3.9 16.1 + - + +
88B GLY* 3.3 24.3 + - - -
91B LEU* 4.3 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU 2.9 16.9 + - - +
50B ILE 4.0 2.2 - - - +
52B HIS* 1.3 74.3 - - - +
54B ASP* 1.3 63.1 + - - +
56B LEU* 3.0 7.3 + - - +
57B ILE* 2.8 31.2 + - + +
66B LEU* 3.8 19.8 - - + +
69B PHE* 4.0 8.7 - - + -
70B TYR* 3.2 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.0 25.4 + - - +
51B CYS 4.5 0.4 - - - +
53B ALA* 1.3 85.2 - - - +
55B LEU* 1.3 55.9 + - - +
57B ILE* 3.5 17.6 + - - +
58B LEU* 3.1 15.4 + - - +
70B TYR* 5.1 1.0 + - - -
92B LEU* 6.2 0.2 - - + -
121B TRP* 3.0 29.3 + - + +
124B GLU 4.9 0.2 - - - +
125B ILE* 3.2 34.0 - - + +
128B HIS* 2.9 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS 3.2 20.5 + - - +
52B HIS* 3.5 6.7 - - - +
53B ALA 3.2 0.8 - - - -
54B ASP* 1.3 75.2 - - - +
56B LEU* 1.3 65.0 + - + +
58B LEU* 3.4 18.3 + - + +
59B ASN* 3.0 41.3 + - - +
88B GLY 5.4 0.2 - - - +
91B LEU* 3.5 45.8 - - + +
92B LEU* 4.0 23.9 - - + +
95B THR* 3.9 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B HIS* 3.0 22.0 + - + +
53B ALA* 3.0 8.0 + - - +
55B LEU* 1.3 74.8 - - + +
57B ILE* 1.3 63.5 + - - +
59B ASN* 3.1 13.7 + - + +
61B SER* 3.0 43.3 + - - +
65B GLU* 4.4 14.1 - - + +
66B LEU* 4.4 6.7 - - + -
69B PHE* 3.8 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 2.8 17.2 + - + +
54B ASP* 3.6 24.7 - - - +
55B LEU 3.3 0.2 - - - -
56B LEU* 1.3 75.7 - - - +
58B LEU* 1.3 62.9 + - - +
60B GLY* 3.2 14.0 + - - -
61B SER* 4.0 8.1 + - - +
66B LEU* 4.0 24.0 - - + -
108B LYS* 6.0 0.2 - - - +
109B THR 4.6 2.3 - - - +
110B ALA* 3.8 35.4 - - + -
111B TYR* 4.2 13.6 + - + +
112B TRP* 3.6 25.1 - - + -
121B TRP* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP 3.1 13.4 + - - +
55B LEU* 3.5 22.9 - - + +
56B LEU 3.3 0.2 - - - -
57B ILE* 1.3 77.0 - - - +
59B ASN* 1.3 62.6 + - - +
60B GLY 3.3 3.5 + - - -
92B LEU* 5.3 0.7 - - + -
96B PHE* 3.5 36.6 - - + -
99B TYR* 4.2 9.9 - - - +
108B LYS* 3.9 46.6 - - + +
109B THR 5.7 0.7 - - - +
116B TYR 6.0 0.2 - - - +
118B ARG* 4.1 16.3 + - + +
121B TRP* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.0 41.6 + - - +
56B LEU* 3.1 9.5 + - + +
58B LEU* 1.3 79.1 - - - +
60B GLY* 1.3 59.4 + - - +
61B SER* 3.6 2.8 + - - +
95B THR* 5.2 3.2 + - - +
99B TYR* 4.0 15.9 + - - -
108B LYS* 5.9 2.3 - - - +
118B ARG* 5.3 4.0 + - - -
----------------------------------------------------------
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