Contacts of the strand formed by residues 2 - 9 (chain G) in PDB entry 1VCB
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 ASP 2 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET* 1.3 81.3 - - - +
3G VAL* 1.3 60.1 + - - +
4G PHE* 3.9 31.0 - - + -
17G ASP* 3.6 18.9 - - - +
18G ALA 3.3 8.1 - - - +
19G LYS* 2.9 35.7 + - - +
64G SER* 3.4 18.4 + - - -
82H ARG* 5.6 5.0 + - - +
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Residues in contact with VAL 3 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G ASP* 1.3 75.4 - - - +
4G PHE* 1.3 63.7 + - - +
5G LEU* 3.7 32.8 - - + -
17G ASP* 3.1 26.5 - - - +
18G ALA 2.7 16.2 + - - +
20G GLU* 4.5 13.9 - - + +
57G LEU* 4.2 13.2 - - + -
62G PHE* 3.3 32.1 - - + +
63G THR* 3.6 13.0 - - - -
64G SER 4.1 0.2 - - - +
67G ALA* 3.5 17.7 - - + -
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Residues in contact with PHE 4 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G ASP* 3.9 33.2 - - + -
3G VAL* 1.3 70.3 - - - +
5G LEU* 1.3 63.9 + - - +
16G THR 3.9 2.5 - - - +
17G ASP* 3.7 24.7 - - + -
67G ALA* 2.9 38.1 + - - +
68G ARG 3.9 11.7 - - - +
69G PRO* 3.5 39.7 - - + -
72G PRO* 3.1 8.2 - - + +
73G ALA 2.8 23.9 + - - -
35H HIS* 6.2 0.9 - - - -
78H THR* 4.8 14.8 - - + +
82H ARG* 4.0 26.9 - - + -
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Residues in contact with LEU 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G VAL* 3.7 25.4 - - + +
4G PHE* 1.3 81.9 - - - +
6G MET* 1.3 64.9 + - - +
7G ILE* 4.0 5.4 - - + -
14G ILE 4.1 0.7 - - - -
15G PHE* 3.5 6.8 - - - +
16G THR* 2.7 45.0 + - + +
17G ASP 5.4 0.2 - - - -
18G ALA* 4.9 5.6 - - + -
27G LEU* 4.0 26.9 - - + -
57G LEU* 4.0 18.6 - - + -
62G PHE* 3.7 33.0 - - + -
72G PRO* 4.0 5.1 - - - +
73G ALA* 3.4 12.1 - - + +
75G VAL* 4.2 7.9 - - + -
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Residues in contact with MET 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LEU* 1.3 73.6 - - - +
7G ILE* 1.3 62.1 + - - +
8G ARG* 3.4 19.3 + - + +
13G THR* 3.6 20.4 - - - +
14G ILE 3.1 5.6 - - - -
15G PHE* 3.7 30.7 - - + +
72G PRO* 4.1 17.9 - - + +
73G ALA 2.8 12.1 + - - +
74G THR* 3.3 24.7 - - - +
75G VAL 3.1 20.1 + - - -
93G PHE* 4.8 13.2 - - + -
75H MET* 3.9 22.4 - - + -
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Residues in contact with ILE 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LEU* 4.6 6.1 - - + -
6G MET* 1.3 69.6 - - - +
8G ARG* 1.3 62.6 + - - +
12G THR* 4.5 0.5 - - - +
13G THR* 3.2 2.9 - - - -
14G ILE* 2.7 56.2 + - + +
16G THR* 3.9 18.8 - - + -
27G LEU* 3.4 33.9 - - + -
30G ILE* 5.8 1.6 - - + -
31G VAL* 3.8 23.6 - - + +
34G ILE* 6.4 0.2 - - + -
44G LEU* 4.5 8.7 - - + -
75G VAL* 3.4 20.6 - - + +
77G LEU* 4.2 27.4 - - + -
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Residues in contact with ARG 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G MET* 3.5 25.2 - - - +
7G ILE* 1.3 79.8 - - - +
9G ARG* 1.3 60.0 + - - +
11G LYS 5.6 1.6 - - - +
12G THR 3.6 4.1 + - - +
13G THR* 3.5 23.1 - - - +
74G THR* 3.9 18.4 + - + +
75G VAL 2.6 16.1 + - - +
76G GLY* 3.5 5.0 - - - -
77G LEU* 3.0 26.0 + - - -
90G ILE* 3.5 36.4 - - + +
91G GLU 2.7 29.7 + - - +
92G PRO* 4.4 4.0 - - - +
93G PHE* 3.3 45.2 - - - -
27H HIS* 3.9 3.4 + - - -
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Residues in contact with ARG 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ILE 4.3 0.4 + - - -
8G ARG* 1.3 74.0 - - - +
10G HIS* 1.3 118.1 + - - +
11G LYS 3.7 0.4 - - - -
12G THR* 2.8 30.2 + - + -
35G LEU* 5.6 1.5 - - + +
77G LEU* 3.4 40.8 - - + +
79G PHE* 3.1 39.3 - - - +
86G GLU* 2.6 42.2 + - - -
89G CYS 3.9 6.3 - - - +
90G ILE* 4.7 1.8 - - - +
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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