Contacts of the strand formed by residues 30 - 39 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PRO* 1.3 72.8 - - - +
31A THR* 1.3 62.6 + - - +
32A LEU* 3.6 14.5 + - - +
108A MET* 6.3 2.9 - - - -
109A VAL 2.8 11.8 + - - -
110A LEU* 4.9 4.7 - - - +
152A SER 4.2 2.8 - - - +
153A PHE 5.1 4.9 - - - +
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Residues in contact with THR 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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26A GLN 3.8 0.2 + - - -
27A LEU* 3.7 18.6 - - + -
28A ASP* 2.7 35.3 + - - +
29A PRO 4.8 0.2 + - - -
30A GLY* 1.3 77.8 - - - +
32A LEU* 1.3 71.6 + - - +
33A ILE* 4.9 0.9 - - + -
107A ILE 3.7 0.2 - - - +
108A MET* 3.8 1.2 - - - -
109A VAL* 2.9 34.7 + - + +
151A PHE* 5.0 0.2 - - + -
152A SER 3.3 9.4 - - - +
153A PHE* 3.6 44.2 + - + +
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Residues in contact with LEU 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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30A GLY 4.1 10.5 - - - +
31A THR* 1.3 81.9 - - - +
33A ILE* 1.3 65.2 + - - +
34A VAL* 4.1 12.1 - - + -
106A VAL* 4.6 12.6 - - + -
107A ILE 3.4 2.7 - - - +
108A MET* 3.4 39.0 - - + -
151A PHE* 3.4 4.5 - - - -
152A SER* 2.9 52.0 + - - +
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Residues in contact with ILE 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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27A LEU* 4.1 20.6 - - + -
31A THR* 4.9 1.1 - - + -
32A LEU* 1.3 77.4 - - - +
34A VAL* 1.3 62.6 + - - +
35A ILE* 4.1 17.4 - - + +
50A LEU* 4.1 33.7 - - + -
105A ILE 3.3 4.7 - - - +
106A VAL* 3.4 1.6 - - - -
107A ILE* 2.9 53.6 + - + +
109A VAL* 4.7 4.3 - - + -
138A LEU* 4.0 21.3 - - + -
149A ILE* 5.3 0.7 - - + -
150A GLY 3.6 5.6 - - - +
151A PHE* 3.7 26.9 - - + -
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Residues in contact with VAL 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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8A LEU* 3.7 35.2 - - + -
10A ASN* 4.9 1.4 + - - +
32A LEU* 4.8 10.3 - - + -
33A ILE* 1.3 77.7 - - - +
35A ILE* 1.3 66.5 + - - +
36A ARG* 4.2 8.2 + - + -
104A GLU* 3.9 32.5 - - + +
105A ILE 3.3 2.2 - - - +
106A VAL* 4.1 18.2 - - + -
148A SER* 3.8 2.4 + - - +
149A ILE* 3.5 3.1 - - - -
150A GLY 2.9 38.1 + - - +
152A SER* 5.9 0.2 - - - -
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Residues in contact with ILE 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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33A ILE* 4.1 22.4 - - + +
34A VAL* 1.3 79.6 - - - +
36A ARG* 1.3 63.0 + - - +
48A VAL* 3.8 33.0 - - + -
103A PHE* 3.9 9.4 - - + -
104A GLU* 3.4 0.9 - - - -
105A ILE* 2.6 53.1 + - + +
107A ILE* 4.8 6.7 - - + -
138A LEU* 4.4 6.3 - - + -
140A ILE* 4.1 15.7 - - + -
146A ILE* 3.8 26.9 - - + -
148A SER 3.3 8.7 - - - +
149A ILE* 4.4 10.1 - - + -
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Residues in contact with ARG 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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34A VAL* 4.4 7.2 - - + -
35A ILE* 1.3 76.8 - - - +
37A GLY* 1.3 52.9 + - - +
103A PHE* 3.4 8.1 - - - +
104A GLU* 3.4 34.5 - - + +
146A ILE* 3.6 4.2 - - - +
147A HIS* 2.6 55.2 + - + +
148A SER* 2.9 30.5 + - - +
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Residues in contact with GLY 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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36A ARG* 1.3 74.8 - - - +
38A HIS* 1.3 62.3 + - - +
102A SER* 3.3 5.2 - - - -
103A PHE* 2.8 47.3 + - - +
145A ASN 3.0 13.0 - - - -
146A ILE* 4.0 0.9 - - - -
147A HIS* 3.5 16.9 + - - -
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Residues in contact with HIS 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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37A GLY* 1.3 74.6 - - - +
39A VAL* 1.3 81.6 + - - +
40A PRO* 3.5 6.7 - - + +
100A GLU* 3.3 35.1 + - + +
101A LYS 3.5 16.6 - - - -
102A SER* 3.1 21.3 - - - -
103A PHE* 3.4 4.4 - - - -
144A VAL* 3.6 2.3 - - - +
145A ASN* 2.7 46.2 + - + +
147A HIS* 3.7 18.4 - + + +
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Residues in contact with VAL 39 (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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38A HIS* 1.3 76.9 + - - +
40A PRO* 1.3 60.0 - - + +
43A ALA* 3.4 28.0 - - + -
46A PHE* 4.0 9.9 - - + -
70A PHE* 3.6 30.3 - - + -
97A PHE* 4.5 5.4 - - + -
98A LYS 3.3 17.3 - - - +
99A ARG* 3.8 11.2 - - - -
100A GLU* 2.6 35.5 + - - -
101A LYS 3.2 7.5 + - - +
103A PHE* 3.9 22.7 - - + -
143A LYS 4.7 1.6 - - - +
144A VAL* 4.9 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