Contacts of the strand formed by residues 4 - 12 (chain B) in PDB entry 3T06
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 ILE 4 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B ALA* 1.3 74.3 - - - +
5B ARG* 1.3 62.1 + - - +
6B LYS* 4.3 24.7 - - + -
51B LYS* 4.8 20.4 - - + +
52B GLN 3.5 24.4 + - - +
53B VAL* 3.7 4.7 - - + +
54B GLU* 2.8 29.9 + - - +
179B LEU* 4.4 25.4 - - + -
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Residues in contact with ARG 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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868A ARG* 2.9 31.2 + - - -
869A LEU* 4.0 0.8 - - - +
870A GLN* 3.3 35.0 + - - +
873A ASP* 3.9 15.8 + - - -
3B ALA* 3.5 9.6 + - + +
4B ILE* 1.3 72.4 - - - +
6B LYS* 1.3 71.2 + - - +
43B VAL* 3.7 16.8 - - - +
54B GLU* 3.2 37.4 + - + +
56B ALA* 4.5 9.9 - - - +
78B ASP* 4.1 3.1 - - - +
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Residues in contact with LYS 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 ILE* 3.8 19.2 + - + -
5B ARG* 1.3 83.1 + - - +
7B LYS* 1.3 60.8 + - - +
53B VAL* 4.2 14.8 - - + -
54B GLU 2.9 7.8 + - - +
55B LEU* 3.5 17.7 - - + -
56B ALA* 2.8 26.7 + - - +
78B ASP* 3.0 34.4 + - + +
175B THR* 5.9 0.2 - - + -
178B ALA* 3.6 37.4 + - + -
179B LEU* 4.9 10.1 + - + +
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Residues in contact with LYS 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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872A ARG* 5.4 5.3 - - - +
873A ASP* 4.6 4.4 + - - +
6B LYS* 1.3 75.7 - - - +
8B LEU* 1.3 66.4 + - - +
9B VAL* 3.7 2.0 - - - -
55B LEU* 4.1 2.9 - - - -
56B ALA* 3.8 7.9 - - + -
58B TRP* 3.4 57.4 - - + +
72B LEU 5.7 0.2 + - - -
73B SER 3.6 12.3 + - - -
75B PRO* 2.8 21.4 + - - +
76B ASP* 3.3 27.8 - - + +
77B THR* 3.5 19.7 - - - +
78B ASP* 2.6 28.4 + - - +
79B VAL* 3.1 9.8 + - - +
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Residues in contact with LEU 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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7B LYS* 1.3 73.2 - - - +
9B VAL* 1.3 82.9 + - - +
10B ILE* 3.6 8.3 - - + +
22B LEU* 5.0 2.2 - - + -
55B LEU* 3.7 28.8 - - + +
56B ALA 2.7 18.2 + - - +
57B LEU* 4.1 10.3 - - + -
58B TRP* 3.1 27.7 + - - +
79B VAL* 3.3 18.6 - - + +
81B LEU* 3.9 21.8 - - + -
171B PHE* 3.8 24.7 - - + -
174B ALA* 3.9 18.2 - - + -
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Residues in contact with VAL 9 (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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7B LYS* 3.7 7.5 + - - -
8B LEU* 1.3 83.1 - - - +
10B ILE* 1.3 61.7 + - - +
11B VAL* 3.7 8.4 + - + -
58B TRP* 3.6 17.5 - - + +
60B THR* 3.8 25.4 - - + -
73B SER* 3.5 23.6 - - - +
74B TYR* 4.1 10.3 - - + -
77B THR* 3.5 14.8 - - - +
79B VAL 3.0 8.5 + - - -
80B ILE* 3.3 28.4 - - + +
81B LEU 3.1 18.9 + - - -
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Residues in contact with ILE 10 (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* 3.6 8.1 - - + +
9B VAL* 1.3 73.1 - - - +
11B VAL* 1.3 52.0 + - - +
18B LYS* 3.7 30.1 - - + +
21B LEU* 4.4 7.9 - - + -
22B LEU* 3.5 28.9 - - + -
58B TRP 3.2 17.0 + - - +
59B ASP* 4.0 7.9 - - - +
60B THR* 2.7 27.2 + - - -
81B LEU* 3.3 34.5 - - + +
83B CYS* 3.3 28.9 - - - -
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Residues in contact with VAL 11 (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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9B VAL* 3.7 13.0 + - + +
10B ILE* 1.3 78.6 - - - +
12B GLY* 1.3 59.0 + - - +
18B LYS* 3.7 5.2 - - - -
60B THR* 3.6 11.4 - - + +
74B TYR* 3.7 34.5 - - + +
80B ILE* 4.0 14.4 - - + -
81B LEU 2.8 14.7 + - - +
82B MET* 3.4 20.3 - - + -
83B CYS* 2.9 26.5 + - - -
99B TRP* 3.8 21.1 - - + -
103B VAL* 4.3 7.4 - - + -
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Residues in contact with GLY 12 (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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11B VAL* 1.3 78.3 - - - +
13B ASP* 1.3 70.4 + - - +
18B LYS* 3.1 20.8 + - - +
64B GLU* 3.6 1.2 - - - +
82B MET* 5.5 1.1 - - - -
83B CYS 3.4 14.4 - - - -
99B TRP* 3.2 32.8 - - - -
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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