Contacts of the helix formed by residues 34 - 44 (chain H) in PDB entry 3G5G
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 ASP 34 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H ALA* 3.9 1.1 - - - -
33H LEU* 1.3 77.3 - - - +
35H ARG* 1.3 79.8 + - - +
36H THR* 3.5 26.5 + - - +
37H TYR* 3.2 20.3 + - + +
38H ILE* 3.2 14.2 + - - +
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Residues in contact with ARG 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H GLN* 5.0 5.1 - - + +
25H GLU* 3.3 46.8 + - + +
28H ALA* 3.7 21.6 - - + +
34H ASP* 1.3 78.2 + - - +
36H THR* 1.3 65.6 + - + +
38H ILE* 3.2 5.5 + - - +
39H SER* 3.0 28.7 + - - -
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Residues in contact with THR 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ASP* 3.5 18.9 + - - +
35H ARG* 1.3 80.1 - - + +
37H TYR* 1.3 59.0 + - - +
39H SER* 3.6 7.4 - - - -
40H GLY* 2.8 31.2 + - - -
43H ARG* 5.6 0.3 + - - -
46H ARG* 4.2 15.3 + - - -
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Residues in contact with TYR 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU* 3.8 35.9 - - + -
34H ASP* 3.2 21.4 + - + +
36H THR* 1.3 83.5 + - - +
38H ILE* 1.3 57.0 + - + +
40H GLY* 3.3 1.0 + - - -
41H ILE* 2.9 57.9 + - + +
46H ARG* 4.3 35.4 - - + +
47H ASN 3.1 24.8 + - - -
48H LEU* 3.5 13.2 - - - -
49H THR* 4.2 2.4 + - - +
52H SER* 3.7 21.0 + - - -
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Residues in contact with ILE 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H ILE* 5.9 1.6 - - + -
24H GLN* 4.0 32.5 - - + +
27H LEU* 4.2 26.0 - - + -
28H ALA* 4.0 20.2 - - - +
31H SER* 4.7 2.5 - - - +
33H LEU* 4.2 15.9 - - + -
34H ASP 3.2 12.5 + - - +
35H ARG 3.6 6.7 - - - +
37H TYR* 1.3 76.1 - - + +
39H SER* 1.3 66.1 + - - +
41H ILE* 3.2 7.1 + - + +
42H GLU* 3.1 30.8 + - + +
56H ILE* 4.0 32.3 - - + -
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Residues in contact with SER 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLN* 3.5 27.5 + - - +
35H ARG* 3.0 17.6 + - - -
36H THR* 3.6 9.6 - - - -
38H ILE* 1.3 78.4 - - - +
40H GLY* 1.3 60.7 + - - -
42H GLU* 3.4 2.4 + - - +
43H ARG* 3.1 34.7 + - - +
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Residues in contact with GLY 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H THR 2.8 21.1 + - - -
37H TYR 3.7 1.6 - - - -
39H SER* 1.3 72.5 - - - +
41H ILE* 1.3 61.9 + - - +
43H ARG* 3.2 13.8 + - - +
44H ASN 3.1 5.2 + - - -
45H SER* 3.0 32.5 + - - -
46H ARG* 3.8 19.7 - - - -
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Residues in contact with ILE 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H LEU* 5.5 3.6 - - + +
10H SER* 3.1 32.5 - - - -
13H ILE* 4.0 21.8 - - + -
37H TYR* 2.9 60.7 + - + +
38H ILE* 3.2 8.5 + - + +
40H GLY* 1.3 75.7 - - - +
42H GLU* 1.3 66.2 + - + +
44H ASN* 3.1 11.1 + - - +
45H SER 5.0 0.2 - - - +
46H ARG* 4.7 14.8 - - + +
48H LEU* 3.9 20.4 - - + -
56H ILE* 3.9 19.1 - - + -
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Residues in contact with GLU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H SER* 4.0 18.5 + - - +
13H ILE* 4.1 13.1 - - + +
14H LYS* 3.5 38.9 + - + +
17H ARG* 2.8 42.3 + - - -
24H GLN* 2.7 33.4 + - - +
38H ILE* 3.1 19.0 + - + +
39H SER 3.4 1.1 + - - +
40H GLY 3.3 0.2 - - - -
41H ILE* 1.3 78.4 - - + +
43H ARG* 1.3 59.0 + - + +
44H ASN* 3.2 4.2 + - - -
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Residues in contact with ARG 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H THR 5.6 0.4 + - - -
39H SER* 3.1 25.2 + - - +
40H GLY* 3.2 13.4 + - - +
42H GLU* 1.3 74.1 - - + +
44H ASN* 1.3 71.1 + - - +
45H SER* 2.7 41.5 + - - -
46H ARG* 5.7 1.4 - - - +
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Residues in contact with ASN 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H SER 5.7 0.4 - - - -
6H LEU* 3.6 24.5 - - + +
7H SER* 3.3 46.2 + - - +
10H SER* 3.5 16.5 + - - -
40H GLY 3.1 2.8 + - - -
41H ILE* 3.1 9.0 + - - +
42H GLU 3.2 4.6 + - - -
43H ARG* 1.3 82.5 - - - +
45H SER* 1.3 60.1 + - - +
46H ARG 3.9 0.4 - - - -
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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