Contacts of the strand formed by residues 30 - 39 (chain B) in PDB entry 3VKO
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 GLY 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PRO* 1.3 72.7 - - - +
31B THR* 1.3 61.7 - - - -
32B LEU* 3.7 11.3 + - - +
108B MET* 4.8 10.7 - - - +
109B VAL 2.6 16.4 + - - -
110B LEU* 4.7 4.8 - - - +
152B SER* 4.1 3.5 + - - +
153B PHE* 4.7 6.2 - - - +
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Residues in contact with THR 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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26B GLN 3.7 3.5 + - - -
27B LEU* 3.8 22.7 - - + -
28B ASP* 2.6 37.8 + - - +
29B PRO 4.7 0.2 + - - -
30B GLY* 1.3 79.9 - - - +
32B LEU* 1.3 69.6 + - - +
33B ILE* 4.9 0.7 - - + -
108B MET* 3.3 3.6 - - - -
109B VAL* 2.8 40.5 + - + +
152B SER 3.3 13.0 + - - +
153B PHE* 3.7 27.2 - - + +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 5.6 2.0 - - + -
30B GLY 4.2 7.4 - - - +
31B THR* 1.3 80.5 - - - +
33B ILE* 1.3 65.1 + - - +
34B VAL* 4.1 13.0 - - + -
106B VAL* 4.2 18.2 - - + -
107B ILE 3.2 4.3 - - - +
108B MET* 3.5 40.8 - - + -
151B PHE* 3.3 6.1 - - - +
152B SER* 2.8 57.9 + - - +
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Residues in contact with ILE 33 (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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23B ILE* 4.6 3.4 - - + -
27B LEU* 4.2 30.1 - - + -
31B THR* 4.9 1.1 - - + -
32B LEU* 1.3 78.2 - - - +
34B VAL* 1.3 63.5 + - - +
35B ILE* 4.1 23.0 + - + +
50B LEU* 3.8 31.0 - - + -
105B ILE 3.6 1.6 - - - +
106B VAL* 3.5 2.3 - - - -
107B ILE* 2.8 51.5 + - + +
109B VAL* 5.1 2.9 - - + -
138B LEU* 4.7 11.7 - - + -
149B ILE* 5.3 0.9 - - + -
150B GLY 3.6 4.5 - - - +
151B PHE* 4.1 28.9 - - + -
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Residues in contact with VAL 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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8B LEU* 4.1 31.0 - - + -
32B LEU* 4.6 8.1 - - + -
33B ILE* 1.3 79.0 - - - +
35B ILE* 1.3 66.6 + - - +
36B ARG* 4.1 25.9 + - + +
104B GLU* 4.0 23.1 - - + +
105B ILE 3.3 8.5 - - - +
106B VAL* 4.3 18.8 - - + -
148B SER 3.9 0.7 - - - +
149B ILE* 3.3 5.0 - - - +
150B GLY 2.8 40.7 + - - +
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Residues in contact with ILE 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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33B ILE* 4.3 20.2 - - + +
34B VAL* 1.3 80.5 - - - +
36B ARG* 1.3 65.7 + - - +
48B VAL* 3.9 32.8 - - + -
103B PHE* 3.9 9.0 - - + -
104B GLU* 3.4 1.2 - - - -
105B ILE* 2.8 51.8 + - + +
107B ILE* 5.2 4.7 - - + -
138B LEU* 4.5 5.2 - - + -
140B ILE* 4.1 15.9 - - + -
146B ILE* 3.7 32.5 - - + -
148B SER 3.5 7.6 - - - +
149B ILE* 4.5 9.6 - - + -
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Residues in contact with ARG 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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8B LEU* 4.1 23.4 - - - +
11B ILE* 5.7 4.8 - - - +
13B TYR* 5.8 1.8 + - - -
34B VAL* 4.1 14.7 + - + +
35B ILE* 1.3 78.5 - - - +
37B GLY* 1.3 52.3 + - - +
103B PHE* 3.4 8.5 - - - +
104B GLU* 2.5 47.0 + - + +
146B ILE* 3.5 4.5 - - - +
147B HIS* 2.6 36.0 + - + -
148B SER* 3.0 42.2 + - - +
149B ILE 6.1 0.2 - - - -
150B GLY 5.8 1.4 - - - +
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Residues in contact with GLY 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 ARG* 1.3 76.0 - - - +
38B HIS* 1.3 56.8 + - - -
102B SER* 3.2 5.7 - - - -
103B PHE* 2.7 48.1 + - - +
145B ASN 3.0 13.9 - - - -
146B ILE* 4.1 0.7 - - - -
147B HIS* 3.3 16.9 + - - -
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Residues in contact with HIS 38 (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 GLY* 1.3 74.8 - - - +
39B VAL* 1.3 77.2 + - - +
40B PRO* 4.5 5.8 - - + +
100B GLU* 5.3 8.5 - - - -
101B LYS 3.4 12.6 - - - +
102B SER* 3.4 18.8 - - - +
103B PHE* 3.7 9.3 - - - -
144B VAL* 3.6 3.3 - - - +
145B ASN* 2.9 66.0 + - + +
147B HIS* 3.2 24.7 - + - +
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Residues in contact with VAL 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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38B HIS* 1.3 79.6 - - - +
40B PRO* 1.3 66.1 - - + +
43B ALA* 3.3 28.5 - - + -
46B PHE* 4.1 5.8 - - + -
70B PHE* 3.4 33.2 - - + -
97B PHE* 4.6 2.2 - - + -
98B LYS 3.8 20.4 - - - +
99B ARG* 3.8 8.7 - - - -
100B GLU* 2.7 31.7 + - - +
101B LYS 3.1 11.4 + - - +
103B PHE* 3.9 20.2 - - + -
143B LYS 4.7 2.0 - - - +
144B VAL* 5.0 0.9 - - - -
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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