Contacts of the strand formed by residues 30 - 39 (chain B) in PDB entry 6GR2
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 LEU 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLU* 1.3 93.5 - - + +
31B ALA* 1.3 60.7 + - - +
63B LEU 4.4 0.2 - - - -
64B VAL* 3.2 5.4 - - - -
65B GLY 2.8 32.0 + - - +
67B PRO* 4.0 13.9 - - + -
152B PHE* 3.6 20.4 - - + -
155B GLN* 4.1 29.6 - - + +
156B LEU* 3.4 33.2 - - + +
390B LEU 5.2 0.2 - - - -
392B LEU* 3.7 6.5 - - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.8 20.0 - - + -
30B LEU* 1.3 77.9 - - - +
32B VAL* 1.3 70.1 + - - +
63B LEU 3.3 7.4 - - - +
64B VAL* 4.3 0.9 - - + -
152B PHE* 5.5 0.4 - - - -
155B GLN* 5.0 0.9 - - - +
389B VAL* 3.7 6.3 - - - +
390B LEU* 3.0 51.3 + - + +
392B LEU* 3.8 16.8 - - + +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 1.3 81.9 - - - +
33B SER* 1.3 64.3 + - - +
62B VAL* 3.3 7.3 - - - +
63B LEU* 2.9 36.5 + - + +
148B ALA* 3.2 37.0 - - + +
151B THR* 3.5 46.2 - - + +
152B PHE* 3.8 10.1 - - + +
155B GLN* 4.2 9.4 - - + -
388B LYS 3.7 7.9 - - - +
389B VAL* 4.3 4.0 - - - -
390B LEU* 4.2 5.3 - - - +
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Residues in contact with SER 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.1 1.3 - - - +
32B VAL* 1.3 83.9 - - - +
34B ALA* 1.3 61.7 + - - +
35B PRO* 4.9 0.2 - - - -
60B MET* 4.1 23.8 - - - -
61B THR 3.2 10.3 - - - -
62B VAL* 4.2 0.7 - - - -
386B GLY 5.1 0.9 + - - -
387B ALA* 3.2 5.5 - - - +
388B LYS* 3.0 52.4 + - - +
390B LEU* 3.9 17.2 - - - +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER* 1.3 76.6 - - - +
35B PRO* 1.3 67.1 - - + +
60B MET* 4.5 2.9 - - - -
61B THR 2.9 20.2 + - - -
144B SER* 2.7 42.1 + - - +
147B VAL* 4.0 10.1 - - + -
148B ALA* 3.5 18.8 - - + +
190B SER* 3.8 9.0 - - - +
387B ALA* 4.1 1.8 - - + +
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Residues in contact with PRO 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ALA* 1.3 86.7 - - - +
36B GLY* 1.3 66.9 + - - +
56B ALA* 3.8 12.8 - - + -
57B LEU 3.5 21.8 - - - +
59B LEU 3.5 7.2 - - - +
60B MET* 4.2 6.3 - - + -
140B SER* 5.9 0.2 - - - -
144B SER* 3.4 10.6 + - - -
190B SER* 2.8 53.5 + - - +
384B ALA* 5.1 0.2 - - + -
385B ASP 3.0 21.8 - - - +
386B GLY* 3.6 12.3 - - - +
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PRO* 1.3 76.8 - - - +
37B ARG* 1.3 61.5 + - - +
56B ALA* 3.6 7.6 - - - +
57B LEU* 3.1 25.7 + - - -
59B LEU* 3.0 16.2 + - - -
133B VAL* 4.0 12.4 - - - +
139B LEU 3.3 11.7 - - - -
140B SER* 4.0 9.4 - - - -
144B SER* 3.8 2.4 + - - -
189B ILE* 5.5 0.2 - - - +
190B SER* 5.4 1.7 - - - -
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY* 1.3 76.3 - - - +
38B VAL* 1.3 75.2 + - - +
39B ASN* 3.8 7.6 - - - +
43B GLU* 6.0 0.2 - - - -
54B PRO* 4.1 3.6 - - + -
55B MET 3.7 7.4 - - - +
57B LEU* 3.8 6.5 - - - +
138B GLY* 2.8 27.0 + - - -
139B LEU* 2.7 30.6 + - - +
140B SER* 2.7 25.6 + - - +
185B MET* 3.9 18.2 - - - -
186B ASP* 2.3 36.3 + - - +
189B ILE* 3.8 31.6 - - + -
190B SER* 6.1 0.7 - - - -
344B THR* 4.9 0.4 + - - +
345B GLY* 3.9 18.3 - - - +
346B GLY 5.1 1.0 - - - +
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 1.3 81.6 - - - +
39B ASN* 1.3 62.1 + - - +
40B LEU* 3.6 9.6 + - + -
54B PRO* 3.3 1.0 - - - +
55B MET* 3.0 45.1 + - + -
57B LEU* 3.5 20.6 - - + +
139B LEU* 4.3 1.8 - - + -
222B ILE* 3.9 24.5 - - + -
344B THR* 3.7 21.1 - - + +
353B VAL* 3.8 27.6 - - + -
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Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ARG* 3.8 7.9 - - - +
38B VAL* 1.3 71.4 - - - +
40B LEU* 1.3 64.5 + - - +
41B ILE 2.9 18.1 - - - +
42B GLY 3.2 28.5 + - - -
43B GLU* 3.0 29.2 + - - +
52B VAL* 4.6 0.2 - - - +
53B LEU 3.3 8.5 + - - -
54B PRO* 4.0 3.8 - - - -
185B MET* 3.0 32.4 - - + +
342B ARG* 2.9 13.2 + - - -
344B THR* 2.8 29.4 + - - +
345B GLY 4.9 0.7 - - - +
353B VAL* 3.8 6.1 - - - +
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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