Contacts of the helix formed by residues 21 - 38 (chain A) in PDB entry 2GVI
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 PRO 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A CYS* 1.3 88.9 - - + +
22A TYR* 1.3 63.7 + - + +
23A MSE 3.6 0.2 - - - -
24A PRO* 3.5 5.9 - - - +
25A MSE 3.2 31.2 + - - +
111A LEU* 4.1 22.0 - - + -
115A ALA* 4.7 1.3 - - + -
118A PHE* 3.5 27.4 - - + -
119A PHE* 4.2 14.4 - - + -
136A ILE* 3.8 13.2 - - + -
139A VAL* 4.3 12.8 - - + -
140A LEU* 4.0 10.1 - - + -
143A ILE* 4.0 4.8 - - + +
400A UNL 4.3 5.6 - - + -
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Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS* 3.4 2.0 - - - -
21A PRO* 1.3 78.8 - - + +
23A MSE 1.3 62.1 + - - +
25A MSE 3.3 30.5 + - + +
26A GLY 2.9 23.4 + - - -
59A ASN* 3.2 49.1 + - + +
61A CYS* 4.2 7.4 - - + -
62A PHE* 3.3 24.8 - - + +
87A LEU* 4.0 21.6 - - + +
108A MSE 4.6 6.6 - - - -
111A LEU* 4.4 10.2 - - + +
119A PHE* 3.9 31.2 - + - -
400A UNL 3.5 20.6 - - + -
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Residues in contact with MSE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.4 5.8 - - + -
12A ALA* 3.6 38.8 - - + +
13A PHE* 3.4 43.1 - - + +
16A HIS* 3.9 37.0 - - + +
18A HIS 4.9 1.1 - - - +
20A CYS* 3.8 5.3 - - - -
22A TYR* 1.3 76.2 - - - +
24A PRO* 1.3 69.5 - - + +
26A GLY 3.1 2.1 + - - -
27A TYR* 2.8 27.2 + - - -
61A CYS 3.4 16.2 + - - +
64A ASP* 4.4 1.8 - - + -
65A GLY* 3.4 27.6 - - - +
68A ALA* 5.5 0.4 - - - -
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Residues in contact with PRO 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 6.5 0.2 - - + -
8A ILE* 4.0 16.3 - - + +
13A PHE* 4.2 22.4 - - + -
20A CYS 3.1 27.8 - - - +
21A PRO 3.5 7.2 - - - +
23A MSE 1.3 97.2 - - + +
25A MSE 1.3 55.4 + - - +
27A TYR* 3.2 7.9 + - + +
28A ARG* 2.8 36.0 + - - +
140A LEU* 3.8 18.8 - - + -
143A ILE* 5.1 10.1 - - + -
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Residues in contact with MSE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 3.2 20.7 + - - +
22A TYR* 3.5 33.0 - - + +
23A MSE 3.2 0.6 - - - -
24A PRO* 1.3 78.7 - - - +
26A GLY* 1.3 57.3 + - - +
28A ARG* 3.4 6.6 + - - +
29A ALA* 2.9 28.2 + - - +
62A PHE* 4.0 7.9 - - + -
87A LEU* 4.3 7.6 - - + -
103A VAL* 4.3 13.9 - - + -
107A PHE* 3.9 16.8 - - + -
108A MSE 3.3 26.9 - - + -
111A LEU* 3.6 26.9 - - - -
143A ILE* 4.2 14.6 - - + -
151A ILE* 5.4 3.1 - - + -
152A PHE* 3.7 6.6 - - + -
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR 2.9 10.7 + - - -
23A MSE 3.5 1.3 - - - -
25A MSE 1.3 73.2 - - - +
27A TYR* 1.3 60.8 + - - +
29A ALA* 3.3 2.5 + - - +
30A GLY 2.9 24.1 + - - -
62A PHE* 3.3 38.7 - - - -
66A ALA* 3.3 17.8 - - - +
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.8 23.8 - - + -
9A PRO* 3.2 37.4 - - + +
11A TRP* 4.3 8.6 - + - -
12A ALA* 4.2 14.4 - - + -
23A MSE 2.8 16.5 + - - +
24A PRO* 3.2 9.2 + - + +
26A GLY* 1.3 76.9 - - - +
28A ARG* 1.3 58.9 + - - +
31A SER* 2.9 46.5 + - - -
41A LYS* 5.5 1.0 + - - +
65A GLY* 3.3 22.1 - - - +
68A ALA* 3.7 16.4 + - + -
69A ALA* 3.1 31.5 + - + +
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY 5.4 2.9 - - - -
8A ILE* 4.2 17.5 - - + -
24A PRO 2.8 21.4 + - - +
25A MSE 3.6 6.5 - - - +
27A TYR* 1.3 78.2 - - - +
29A ALA* 1.3 57.2 + - - +
31A SER* 3.5 5.9 + - - -
32A TYR* 2.9 30.0 + - - +
143A ILE* 3.0 40.2 + - + +
144A SER* 4.0 9.5 + - - +
146A LEU 3.0 21.6 + - - -
147A GLU 3.7 1.4 - - - -
148A ASP* 2.9 40.6 + - - +
151A ILE* 3.9 12.2 - - + +
152A PHE* 3.7 14.3 - - + -
413A ACY 3.6 25.0 + - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A MSE 2.9 17.8 + - - +
26A GLY 3.6 4.7 - - - +
27A TYR 3.2 0.2 - - - -
28A ARG* 1.3 76.0 - - - +
30A GLY* 1.3 58.1 + - - +
32A TYR* 3.3 3.6 + - - +
33A ALA* 2.9 28.8 + - - +
62A PHE* 4.1 12.8 - - + -
89A LEU* 3.7 18.0 - - + +
101A VAL* 4.3 10.4 - - + +
152A PHE* 3.3 26.4 - - + -
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Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY 2.9 14.7 + - - -
27A TYR 3.8 2.5 - - - -
29A ALA* 1.3 72.1 - - - +
31A SER* 1.3 65.6 + - - +
33A ALA* 3.3 6.1 + - - +
34A LEU* 3.2 25.7 + - - +
66A ALA 4.5 1.8 - - - -
69A ALA* 4.0 4.3 - - - -
70A THR* 3.6 24.2 - - - +
89A LEU* 3.7 11.5 - - - +
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A TYR* 2.9 40.5 + - - -
28A ARG* 3.7 8.3 - - - -
30A GLY* 1.3 73.5 - - - +
32A TYR* 1.3 57.5 + - - +
34A LEU* 3.3 12.8 + - - +
35A LYS* 3.0 28.2 + - - +
69A ALA* 3.6 7.8 + - - +
148A ASP* 6.1 0.2 - - - -
413A ACY 5.0 11.4 - - - -
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG 2.9 18.6 + - - +
29A ALA 3.6 4.7 - - - +
31A SER* 1.3 75.3 - - - +
33A ALA* 1.3 64.2 + - - +
35A LYS* 3.3 14.2 + - + -
36A ILE* 2.9 58.1 + - + +
101A VAL* 4.2 6.3 - - + -
148A ASP* 3.2 43.4 + - + +
149A GLU* 4.5 12.3 + - - +
152A PHE* 3.6 41.0 + + + -
154A TYR* 3.6 25.5 - + + -
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA 2.9 14.2 + - - +
30A GLY* 3.3 11.6 + - - +
32A TYR* 1.3 76.2 - - - +
34A LEU* 1.3 55.1 + - - +
36A ILE* 3.7 5.3 - - - +
37A ALA* 3.0 29.3 + - - +
49A LEU* 5.3 5.6 - - + -
70A THR* 5.5 0.2 - - + -
89A LEU* 5.5 3.6 - - + -
91A LEU* 3.5 30.3 - - + +
99A ILE* 4.7 5.6 - - + +
101A VAL* 3.9 21.2 - - + +
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 3.2 16.3 + - - +
31A SER* 3.5 10.1 - - - +
33A ALA* 1.3 74.5 - - - +
35A LYS* 1.3 54.1 + - - +
37A ALA* 3.2 2.2 + - - -
38A GLY 2.8 30.5 + - - -
39A LEU* 2.9 30.4 + - + +
40A GLU* 3.7 17.0 - - - +
41A LYS* 4.0 22.2 - - + +
42A GLU* 5.3 1.1 - - + +
47A THR* 5.7 2.0 - - + -
69A ALA 3.5 24.7 - - - +
70A THR* 4.0 17.3 - - + +
72A CYS* 6.0 0.4 - - - -
91A LEU* 4.0 22.0 - - + -
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER 3.0 14.1 + - - +
32A TYR* 3.6 17.3 - - + +
34A LEU* 1.3 73.5 - - - +
36A ILE* 1.3 63.1 + - + +
38A GLY* 3.1 10.5 + - - -
39A LEU 5.2 0.9 - - - -
148A ASP* 4.2 19.3 - - - +
404A EDO 3.1 31.6 + - - +
413A ACY 4.4 8.7 - - - +
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 2.9 51.1 + - + +
33A ALA 3.7 3.4 - - - +
35A LYS* 1.3 73.7 - - + +
37A ALA* 1.3 61.6 + - - +
99A ILE* 3.8 22.8 - - + +
101A VAL* 4.1 8.3 - - + -
154A TYR* 3.5 63.7 - - + -
156A GLU* 5.9 0.4 - - + -
404A EDO 3.1 25.1 + - - -
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA 3.0 19.3 + - - +
34A LEU 3.7 2.9 - - - +
36A ILE* 1.3 75.4 - - - +
38A GLY* 1.3 62.0 + - - +
39A LEU* 3.6 31.0 - - + +
91A LEU* 3.9 8.1 - - + -
96A ARG* 4.2 10.2 + - - +
99A ILE* 4.4 15.5 - - + -
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 2.8 8.5 + - - -
35A LYS* 3.1 12.2 + - - -
36A ILE 3.2 1.5 - - - -
37A ALA* 1.3 76.0 - - - +
39A LEU* 1.3 63.5 + - - +
96A ARG* 5.3 0.7 + - - -
404A EDO 4.5 4.3 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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