Contacts of the strand formed by residues 1 - 9 (chain B) in PDB entry 3VF1
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 MET 1 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0B HIS* 1.3 80.0 + - - +
2B LYS* 1.3 89.8 + - + +
3B TYR* 3.3 31.6 + - + +
57B SER* 3.1 6.4 - - - -
58B GLY 3.0 41.6 + - - +
60B ASP* 3.1 41.3 - - + +
89B LYS* 4.0 6.3 - - + -
90B ILE* 3.3 50.3 - - + +
92B GLU* 5.5 1.6 - - - -
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Residues in contact with LYS 2 (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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0B HIS 3.9 3.4 + - - -
1B MET* 1.3 93.6 - - + +
3B TYR* 1.3 65.3 + - - +
4B LYS* 5.1 7.2 - - + +
56B GLN 3.3 8.7 - - - +
57B SER* 4.5 2.5 - - - +
88B GLU* 4.3 15.7 + - - +
89B LYS* 3.8 17.6 + - - +
90B ILE* 3.7 45.0 - - + +
97B SER* 5.5 1.6 - - - -
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Residues in contact with TYR 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.3 33.1 - - + +
2B LYS* 1.3 80.8 - - - +
4B LYS* 1.3 59.8 + - - +
5B ILE* 3.6 13.0 + - + -
25B LEU* 3.5 30.7 - - + -
33B THR* 3.8 14.4 - - + -
36B PHE* 3.8 19.5 - + - -
54B TYR 3.5 3.1 - - - +
55B ASP* 3.6 0.8 - - - -
56B GLN* 2.7 48.9 + - + +
58B GLY 4.7 2.7 - - - -
59B VAL 3.1 19.1 + - - -
61B VAL* 3.3 25.7 + - + +
64B ILE* 4.9 0.7 - - + -
87B ILE* 4.5 4.5 - - + -
88B GLU 3.8 2.0 - - - -
89B LYS* 3.6 30.3 - - + -
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Residues in contact with LYS 4 (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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2B LYS* 4.3 6.8 - - + +
3B TYR* 1.3 70.5 - - - +
5B ILE* 1.3 58.5 + - - +
6B THR* 3.7 7.4 + - - +
53B THR* 3.6 29.4 - - + -
54B TYR 3.4 3.6 - - - -
55B ASP* 3.8 18.8 - - - +
86B ILE 3.3 5.4 - - - +
87B ILE* 4.4 0.4 - - - +
88B GLU* 2.9 61.8 + - + +
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Residues in contact with ILE 5 (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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3B TYR* 4.3 13.0 - - + +
4B LYS* 1.3 72.8 - - - +
6B THR* 1.3 59.9 + - - +
7B VAL* 4.3 11.2 - - + -
23B ILE* 3.8 37.5 - - + -
25B LEU* 4.6 6.5 - - + -
36B PHE* 4.3 10.1 - - + -
38B LEU* 4.7 8.3 - - + -
54B TYR* 2.7 51.4 + - + +
56B GLN* 4.2 19.1 - - + -
85B VAL* 3.8 24.5 - - + -
86B ILE 3.6 2.9 - - - -
87B ILE* 4.1 17.9 - - + +
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Residues in contact with THR 6 (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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4B LYS* 4.3 9.9 + - - +
5B ILE* 1.3 71.9 - - - +
7B VAL* 1.3 63.6 + - - +
8B GLU* 4.1 7.8 + - + +
51B THR* 3.3 32.5 - - + -
52B ASP 3.5 2.9 - - - -
53B THR* 3.5 22.0 + - - +
85B VAL* 3.4 4.2 - - - +
86B ILE* 2.7 61.6 + - + +
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Residues in contact with VAL 7 (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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5B ILE* 4.3 9.6 - - + -
6B THR* 1.3 76.8 - - - +
8B GLU* 1.3 65.2 + - - +
9B THR* 3.8 1.2 + - - -
38B LEU* 4.0 26.2 - - + -
51B THR* 3.5 3.3 - - - -
52B ASP* 2.9 37.9 + - + +
54B TYR* 4.2 11.9 - - + -
69B LEU* 6.5 0.4 - - + -
80B TRP* 3.5 34.1 - - + -
82B ILE* 3.9 28.9 - - + -
84B LYS 4.0 2.0 - - - -
85B VAL* 4.5 9.2 - - + +
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Residues in contact with GLU 8 (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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6B THR* 4.9 5.0 - - + +
7B VAL* 1.3 75.0 - - - +
9B THR* 1.3 62.8 + - - +
50B GLY 3.7 6.3 - - - +
51B THR* 4.0 18.6 + - + +
82B ILE* 3.6 3.8 - - - +
83B ALA* 2.8 33.7 + - + +
84B LYS* 3.0 46.8 + - + +
86B ILE* 3.8 21.5 - - + +
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Residues in contact with THR 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL 3.8 1.1 + - - -
8B GLU* 1.3 74.9 - - - +
10B GLY* 1.3 76.3 + - - +
12B LEU 4.6 6.7 - - - +
13B ARG* 6.4 0.2 - - - -
40B LYS* 4.1 8.7 - - - -
42B PHE* 4.5 13.5 - - + -
48B SER* 5.5 0.2 - - - -
49B GLY* 3.4 36.1 + - - +
50B GLY 3.1 10.3 + - - +
52B ASP* 4.3 2.9 + - - -
80B TRP* 3.0 36.2 + - + +
81B TYR 3.4 13.9 - - - +
82B ILE* 4.5 0.4 - - - +
83B ALA* 4.1 3.3 - - - +
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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