Contacts of the strand formed by residues 101 - 110 (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 LYS 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A HIS* 3.5 5.5 + - - -
39A VAL* 3.2 23.1 + - - +
98A LYS* 3.3 57.0 + - + +
99A ARG 3.2 4.4 - - - +
100A GLU* 1.3 84.0 - - - +
102A SER* 1.3 67.4 + - - +
103A PHE* 4.2 1.7 - - - -
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Residues in contact with SER 102 (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 3.3 11.0 + - - -
38A HIS* 3.1 20.8 - - - +
101A LYS* 1.3 81.6 - - - +
103A PHE* 1.3 64.5 - - - +
119A ASN* 4.2 9.9 + - - +
147A HIS* 4.3 8.0 + - - -
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Residues in contact with PHE 103 (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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35A ILE* 3.9 10.3 - - + -
36A ARG* 3.4 4.7 - - - +
37A GLY* 2.8 55.9 + - - +
38A HIS* 3.4 15.9 - - - -
39A VAL* 3.9 20.6 - - + -
46A PHE* 3.9 11.7 - + - -
97A PHE* 3.6 23.8 - + + -
101A LYS 4.2 1.1 - - - -
102A SER* 1.3 80.7 - - - +
104A GLU* 1.3 61.8 - - - +
105A ILE* 3.7 32.3 - - + -
118A VAL* 4.3 4.7 - - + -
119A ASN* 3.2 13.7 - - - +
144A VAL* 3.8 25.8 - - + -
146A ILE* 4.2 5.4 - - + -
147A HIS* 5.5 0.2 - - - -
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Residues in contact with GLU 104 (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* 3.9 25.2 - - + +
35A ILE 3.4 3.8 - - - -
36A ARG* 3.4 28.8 - - + +
103A PHE* 1.3 74.9 - - - +
105A ILE* 1.3 63.6 + - - +
106A VAL* 4.0 16.8 - - + +
117A ALA 3.8 0.9 - - - +
118A VAL* 3.4 5.5 - - - +
119A ASN* 3.0 36.8 + - - +
120A GLY 5.7 2.6 + - - -
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Residues in contact with ILE 105 (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 3.3 1.4 - - - +
34A VAL* 3.3 6.1 - - - +
35A ILE* 2.6 51.2 + - + +
46A PHE* 4.5 6.5 - - + -
48A VAL* 4.6 12.1 - - + -
66A PHE* 4.1 17.3 - - + -
97A PHE* 3.7 27.4 - - + -
103A PHE* 3.7 32.1 - - + -
104A GLU* 1.3 73.6 - - - +
106A VAL* 1.3 64.0 + - - +
107A ILE* 3.8 27.6 - - + -
116A VAL* 4.0 17.0 - - + -
117A ALA 3.8 2.5 - - - -
118A VAL* 4.4 1.8 - - + +
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Residues in contact with VAL 106 (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 LEU* 4.6 20.2 - - + -
33A ILE 3.4 4.3 - - - +
34A VAL* 4.1 19.5 - - + -
104A GLU* 4.0 23.1 - - + +
105A ILE* 1.3 78.6 - - - +
107A ILE* 1.3 66.8 + - - +
108A MET* 4.7 6.2 - - + +
115A GLN 3.6 1.9 - - - +
116A VAL* 3.4 3.6 - - - -
117A ALA* 2.9 46.3 + - + +
120A GLY 6.4 0.2 - - - +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A THR 3.7 0.9 - - - +
32A LEU* 3.4 4.9 - - - -
33A ILE* 2.9 65.3 + - + +
35A ILE* 4.8 2.0 - - + -
48A VAL* 4.6 20.9 - - + -
50A LEU* 4.9 3.1 - - + -
64A PHE* 4.3 19.5 - - + -
66A PHE* 5.6 3.6 - - + -
105A ILE* 3.8 20.6 - - + -
106A VAL* 1.3 75.6 - - - +
108A MET* 1.3 64.5 + - - +
109A VAL* 4.8 0.8 - - + +
114A PHE* 3.9 27.6 - - + -
115A GLN 3.5 3.1 - - - +
116A VAL* 4.0 19.1 - - + -
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Residues in contact with MET 108 (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* 6.3 3.4 - - - -
31A THR 3.8 4.0 - - - -
32A LEU* 3.4 24.0 - - + -
106A VAL* 4.7 8.3 - - + +
107A ILE* 1.3 73.1 - - - +
109A VAL* 1.3 62.5 + - - +
110A LEU* 3.6 26.0 + - + -
114A PHE* 3.3 7.4 - - - +
115A GLN* 2.7 70.9 + - + +
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Residues in contact with VAL 109 (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* 3.7 41.1 - - + +
28A ASP 4.2 9.6 - - - +
29A PRO* 3.2 2.4 - - + +
30A GLY* 2.8 31.7 + - - -
31A THR* 2.9 22.4 + - - +
33A ILE* 4.7 9.0 - - + -
107A ILE 4.8 1.3 - - - +
108A MET* 1.3 75.2 - - - +
110A LEU* 1.3 70.1 + - - +
113A LYS 4.2 1.6 - - - -
114A PHE* 3.9 31.0 - - + -
128A HIS* 4.2 5.8 - - + -
132A PRO* 4.3 7.2 - - + -
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Residues in contact with LEU 110 (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 PRO* 4.2 8.8 - - - +
30A GLY* 5.4 3.6 - - - +
108A MET* 3.8 31.0 - - + +
109A VAL* 1.3 83.1 - - - +
111A LYS* 1.3 62.4 + - - +
112A ASP 3.5 0.7 - - - -
113A LYS* 2.8 41.0 + - + +
115A GLN* 3.7 26.5 - - + +
128A HIS* 2.8 23.0 + - - -
132A PRO* 5.1 1.0 - - - +
204A CL 3.8 12.8 - - + -
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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