Contacts of the helix formed by residues 22 - 41 (chain B) in PDB entry 2GTL
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 22 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR 3.7 1.2 + - - -
21B GLY* 1.3 76.9 - - - -
23B GLY* 1.3 68.8 + - - +
24B HIS 3.3 3.1 + - - -
25B ASP* 3.3 21.0 + - - +
26B ARG* 3.9 21.1 - - - +
20C ASP* 3.7 25.1 + - - -
23C TRP* 6.3 2.2 - - - -
83C ASN* 4.3 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 1.3 74.7 - - - +
24B HIS* 1.3 64.8 + - - -
26B ARG* 3.5 5.3 - - - +
27B GLU* 3.3 18.4 + - - +
66B ASP* 5.2 0.7 - - - +
16C GLN* 5.6 7.4 - - - -
83C ASN* 3.4 33.1 + - - +
84C LEU* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER 3.3 1.0 + - - -
23B GLY* 1.3 70.5 - - - -
25B ASP* 1.3 71.3 + - - +
26B ARG 2.8 3.1 + - - -
27B GLU* 2.9 24.4 + - - +
28B ALA* 2.9 24.5 + - - +
86C ASP* 4.0 36.1 + - + +
63M ASP* 5.7 5.2 - - - +
66M GLU* 3.9 22.7 - - - +
78M HIS* 4.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR 4.6 4.7 - - - +
21B GLY* 5.1 2.7 - - - -
22B SER 3.5 18.1 - - - +
24B HIS* 1.3 78.7 + - - +
26B ARG* 1.3 51.1 + - - +
28B ALA* 3.4 1.6 + - - +
29B PHE* 2.7 37.3 + - - +
120B GLN* 4.7 6.6 - - - +
63M ASP* 5.1 6.9 - - - +
64M GLU 4.3 7.2 - - - +
65M HIS* 3.2 37.4 + - - +
66M GLU* 5.2 3.1 - - - +
78M HIS* 3.6 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.2 56.8 + - + +
21B GLY 3.1 20.4 + - - -
22B SER* 3.6 17.9 + - - +
23B GLY 3.5 11.6 + - - +
24B HIS 2.8 0.6 + - - -
25B ASP* 1.3 75.9 - - - +
27B GLU* 1.3 56.5 + - - +
28B ALA 2.7 15.1 + - - -
29B PHE* 3.0 7.4 + - + +
30B SER* 2.9 27.1 + - - +
66B ASP* 3.2 29.2 + - - +
69B LEU* 5.8 0.2 - - + -
23C TRP* 5.7 4.6 - - - -
32C LYS* 6.1 0.4 - - - +
76C ASN* 6.0 1.8 - - - +
79C ASP* 3.4 27.7 + - - +
80C LEU* 5.2 3.8 - - - +
83C ASN* 3.5 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY 3.3 9.6 + - - +
24B HIS* 2.9 30.6 + - - +
26B ARG* 1.3 76.2 - - - +
28B ALA* 1.3 54.9 + - - +
30B SER* 3.1 10.0 + - - -
31B GLN* 3.0 24.6 - - + +
62B ILE* 4.0 34.6 - - + +
66B ASP* 3.7 14.7 + - - +
83C ASN 5.3 1.4 - - - +
84C LEU* 4.3 15.2 - - + +
86C ASP 5.0 0.3 - - - +
87C ASP* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS 2.9 12.2 + - - +
25B ASP 3.6 3.1 - - - +
26B ARG 2.7 4.6 + - - -
27B GLU* 1.3 72.9 - - - +
29B PHE* 1.3 66.6 + - - +
30B SER 3.0 1.6 - - - -
31B GLN* 2.6 20.6 + - - -
32B ALA* 2.6 17.4 + - - +
78M HIS* 3.7 35.0 - - + +
80M LEU* 4.9 0.9 - - + -
81M LEU* 4.2 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 3.7 28.7 - + - -
19B ALA* 3.6 29.2 - - + +
20B TYR* 4.2 19.3 - + - +
25B ASP 2.7 23.4 + - - +
26B ARG* 3.5 7.6 - - - +
28B ALA* 1.3 71.8 - - - +
30B SER* 1.3 63.6 + - - +
32B ALA* 3.4 2.6 + - - +
33B ILE* 3.0 46.0 + - + +
69B LEU* 3.9 8.5 - - + -
116B VAL* 3.6 26.4 - - + +
117B VAL* 3.7 30.1 - - + -
120B GLN* 4.0 12.6 - - + +
80M LEU* 4.0 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 2.9 17.8 + - - -
27B GLU* 3.1 11.8 + - - -
29B PHE* 1.3 75.6 - - - +
31B GLN* 1.3 74.7 + - - +
33B ILE* 3.0 6.3 + - - +
34B TRP* 2.9 27.5 + - - -
62B ILE* 5.2 1.9 + - - +
65B ALA* 3.9 21.1 - - - +
66B ASP* 4.3 7.1 + - - -
69B LEU* 3.6 35.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 3.0 19.7 - - + +
28B ALA* 2.6 17.7 + - - +
30B SER* 1.3 79.5 + - - +
32B ALA* 1.3 64.2 + - - +
34B TRP* 3.2 4.9 + - - +
35B ARG* 3.0 43.9 + - - +
56B THR* 2.6 27.6 + - - +
57B SER* 3.5 22.6 + - - +
61B PHE* 5.2 1.8 - - - -
62B ILE* 3.6 29.0 - - + +
65B ALA* 5.1 3.1 - - + +
81M LEU* 4.6 12.8 - - + +
88M ASP* 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 2.6 13.4 + - - +
29B PHE 3.6 7.9 - - - +
31B GLN* 1.3 72.4 - - - +
33B ILE* 1.3 65.3 + - - +
35B ARG* 3.2 11.2 + - - +
36B ALA* 2.9 22.7 + - - +
116B VAL* 3.9 12.5 - - + +
80M LEU* 3.9 38.6 - - + +
81M LEU* 4.8 4.8 - - + +
141M PHE* 4.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 5.6 0.2 - - + -
29B PHE* 3.0 44.6 + - + +
30B SER* 3.0 9.3 + - - +
32B ALA* 1.3 77.5 - - - +
34B TRP* 1.3 67.3 + - + +
36B ALA* 3.1 6.7 + - - +
37B THR* 2.9 20.1 + - - +
69B LEU* 4.0 15.0 - - + -
109B PHE* 4.2 19.5 - - + -
112B ALA* 3.4 13.8 - - + +
113B ILE* 4.0 33.4 - - + -
116B VAL* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER 2.9 18.2 + - - -
31B GLN* 3.8 6.3 - - - +
33B ILE* 1.3 76.9 - - + +
35B ARG* 1.3 65.1 + - + +
37B THR* 2.9 20.8 + - + -
38B PHE* 2.8 67.6 + + + +
48B PHE* 3.5 21.8 - + - -
56B THR* 5.6 0.9 - - - +
61B PHE* 3.7 25.4 - + + -
64B HIS* 4.1 6.7 - - - -
65B ALA* 3.5 37.9 - - + +
68B VAL* 4.2 4.3 - - + +
69B LEU* 4.4 10.6 - - + +
109B PHE* 3.4 29.4 - + - -
160B HEM 4.9 4.7 - + + -
161B CMO 3.2 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN* 3.0 49.3 + - - +
32B ALA* 3.5 10.1 - - - +
34B TRP* 1.3 75.0 - - - +
36B ALA* 1.3 57.5 + - - +
38B PHE* 4.0 6.3 - - - +
39B ALA* 3.0 31.6 + - - +
45B ARG* 6.0 1.3 - - - +
56B THR* 3.7 13.4 + - + +
57B SER* 3.6 12.3 + - - -
81M LEU* 4.0 7.4 - - - +
84M ASP* 3.0 31.1 + - + +
86M GLU* 3.4 41.8 + - - +
88M ASP* 2.8 41.8 + - - -
140M PHE 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 2.9 12.6 + - - +
33B ILE* 3.3 10.3 - - - +
35B ARG* 1.3 75.9 - - - +
37B THR* 1.3 65.4 + - - +
39B ALA* 3.6 2.5 + - - +
40B GLN* 3.3 24.8 + - - +
112B ALA* 3.8 19.7 - - + +
115B HIS* 5.9 0.4 - - + -
116B VAL* 4.7 2.7 - - + -
140M PHE* 3.8 28.6 - - + +
141M PHE* 4.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE 2.9 10.1 + - - -
34B TRP* 2.9 32.4 + - + -
36B ALA* 1.3 76.8 - - - +
38B PHE* 1.3 66.2 + - + +
40B GLN* 2.9 25.4 + - - +
41B VAL* 3.1 21.9 + - + +
44B SER* 4.6 1.3 - - - +
105B TYR* 5.5 1.3 - - + +
108B ALA* 4.8 0.7 - - + -
109B PHE* 3.3 34.0 - - + +
112B ALA* 3.2 21.5 - - - +
160B HEM 5.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TRP* 2.8 44.2 + + - +
35B ARG* 4.2 3.4 - - - +
37B THR* 1.3 77.8 - - + +
39B ALA* 1.3 64.2 + - - +
41B VAL 4.3 3.6 - - - -
42B PRO* 3.0 28.1 - - - +
44B SER* 3.4 22.9 - - - -
45B ARG* 3.7 52.9 + - + +
48B PHE* 3.6 31.9 - + + -
53B GLY* 4.0 15.5 - - - -
56B THR* 5.3 4.0 - - - -
61B PHE* 3.6 29.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG 3.0 20.4 + - - +
36B ALA 3.8 5.4 - - - +
37B THR 3.1 0.2 - - - -
38B PHE* 1.3 78.2 - - - +
40B GLN* 1.3 61.7 + - - +
42B PRO* 4.1 5.7 - - - +
45B ARG* 5.8 0.7 - - - +
140M PHE* 4.0 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA 3.3 15.2 + - - +
37B THR* 2.9 8.8 + - - +
39B ALA* 1.3 81.5 - - - +
41B VAL* 1.3 65.1 + - + +
42B PRO* 3.5 7.0 - - - +
108B ALA* 2.9 41.3 - - + +
111B THR* 3.7 31.1 + - - +
112B ALA 3.9 3.6 + - - -
140M PHE* 3.8 29.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 3.1 16.0 + - + +
38B PHE 3.3 3.2 - - - +
40B GLN* 1.3 83.4 - - + +
42B PRO* 1.3 63.1 - - - +
43B GLU* 2.8 10.2 + - + +
44B SER* 2.7 47.5 + - - +
104B ASN* 4.2 24.2 - - - +
105B TYR* 4.0 19.7 - - + -
108B ALA* 4.0 23.8 - - + -
----------------------------------------------------------
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