Contacts of the strand formed by residues 4 - 12 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3F ALA* 1.3 80.3 - - - +
5F ARG* 1.3 58.9 + - - +
6F LYS* 3.9 22.4 - - + +
51F LYS* 6.2 1.6 - - + +
52F GLN 3.6 21.6 + - - +
53F VAL* 3.3 12.5 - - + +
54F GLU 2.9 24.1 + - - -
179F LEU* 3.6 30.5 - - + -
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Residues in contact with ARG 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868E ARG 3.3 23.8 + - - -
869E LEU* 4.4 0.4 - - - +
870E GLN* 3.3 35.6 + - - +
873E ASP* 4.0 11.9 + - - -
3F ALA* 3.9 9.4 + - + +
4F ILE* 1.3 75.3 - - - +
6F LYS* 1.3 71.5 + - - +
43F VAL* 4.0 7.7 - - - +
54F GLU* 3.3 37.8 + - + +
56F ALA* 3.9 25.9 - - - +
78F ASP* 4.3 2.9 - - - +
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Residues in contact with LYS 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ILE* 3.9 27.2 + - + +
5F ARG* 1.3 80.3 + - - +
7F LYS* 1.3 62.6 + - - +
53F VAL* 4.1 11.8 - - + +
54F GLU 3.1 8.7 + - - +
55F LEU* 3.6 9.9 - - + -
56F ALA* 2.9 25.7 + - - +
78F ASP* 3.3 38.0 + - + +
178F ALA* 3.6 36.5 + - + +
179F LEU* 3.9 11.2 - - + +
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Residues in contact with LYS 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873E ASP* 5.5 2.5 - - - +
6F LYS* 1.3 76.6 - - - +
8F LEU* 1.3 60.6 + - - +
9F VAL* 3.9 6.5 - - + -
55F LEU* 4.3 0.9 - - - -
56F ALA* 3.6 14.6 - - + -
58F TRP* 3.0 53.3 - - + +
73F SER 3.1 18.9 + - - -
75F PRO* 3.4 17.4 + - - +
76F ASP* 3.2 20.6 - - + +
77F THR* 3.2 23.2 - - - +
78F ASP* 2.9 29.8 + - - +
79F VAL* 3.4 6.8 + - - +
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Residues in contact with LEU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F LYS* 1.3 73.7 - - - +
9F VAL* 1.3 63.0 + - - +
10F ILE* 4.6 9.2 - - + +
22F LEU* 5.0 2.7 - - + -
55F LEU* 3.6 21.0 - - + +
56F ALA 2.9 9.0 + - - +
57F LEU* 3.7 24.7 - - + -
58F TRP* 3.0 29.1 + - - +
79F VAL* 3.2 24.0 - - + +
81F LEU* 3.8 26.0 - - + -
171F PHE* 4.1 13.2 - - + -
174F ALA* 3.4 33.7 - - + -
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Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F LYS* 3.9 8.7 - - - -
8F LEU* 1.3 78.7 - - - +
10F ILE* 1.3 62.8 + - - +
11F VAL* 3.6 17.9 + - + +
58F TRP* 3.7 12.6 - - + +
60F THR* 3.8 28.0 - - + -
73F SER* 3.8 18.2 - - - +
74F TYR* 4.3 13.0 - - + -
77F THR* 3.3 31.4 - - + +
79F VAL 3.2 6.5 + - - -
80F ILE* 3.5 9.0 - - + -
81F LEU 3.2 19.8 + - - -
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Residues in contact with ILE 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 4.1 5.5 - - + +
9F VAL* 1.3 71.8 - - - +
11F VAL* 1.3 58.9 + - - +
18F LYS* 3.7 34.6 - - + +
21F LEU* 4.3 8.1 - - + -
22F LEU* 3.7 26.9 - - + -
58F TRP 3.2 17.9 + - - +
59F ASP* 3.9 8.7 - - - +
60F THR* 2.9 18.5 + - - -
81F LEU* 3.3 31.0 - - + +
83F CYS* 3.7 30.5 - - - -
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Residues in contact with VAL 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.8 25.6 - - + +
10F ILE* 1.3 78.2 - - - +
12F GLY* 1.3 60.1 + - - +
18F LYS* 3.9 3.8 - - - -
60F THR* 3.7 9.0 - - + +
74F TYR* 4.2 17.9 - - + +
80F ILE* 4.1 10.3 - - + -
81F LEU 2.8 9.6 + - - +
82F MET* 4.0 22.7 - - + -
83F CYS* 2.9 28.2 + - - -
99F TRP* 3.7 27.4 - - + -
103F VAL* 4.3 13.5 - - + -
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Residues in contact with GLY 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 1.3 82.1 - - - +
13F ASP* 1.3 58.6 + - - -
16F CYS* 4.4 0.7 - - - -
18F LYS* 2.6 34.3 + - - -
60F THR* 4.8 0.2 + - - -
64F GLU* 3.8 0.9 - - - +
82F MET* 5.3 0.7 - - - -
83F CYS 3.5 15.5 - - - -
99F TRP* 3.5 27.7 - - - -
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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