Contacts of the strand formed by residues 2 - 11 (chain J) in PDB entry 2CHT
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 2 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3J ILE* 1.3 92.5 + - - +
4J ARG* 3.7 23.1 - - - +
96J GLN* 3.2 9.8 - - - +
97J THR 2.7 43.1 + - - +
98J ASP* 3.8 14.1 + - - +
3L ILE* 5.1 3.8 - - + -
40L GLU 3.5 20.9 - - - +
41L ASP* 3.4 26.2 - - - +
43L VAL* 4.0 11.4 - - + +
96L GLN* 3.4 48.5 - - + +
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Residues in contact with ILE 3 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J MET* 1.3 98.5 - - + +
4J ARG* 1.3 59.7 + - - +
43J VAL* 3.6 23.1 - - + -
94J THR* 3.3 33.9 - - + -
95J VAL 3.0 6.5 - - - +
96J GLN* 4.3 5.4 - - + -
2K MET* 4.3 16.8 - - - -
3K ILE* 3.8 25.4 - - + +
3L ILE* 4.3 19.5 - - + -
43L VAL* 3.2 33.2 - - + +
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Residues in contact with ARG 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J MET* 3.7 20.4 - - - +
3J ILE* 1.3 80.0 - - - +
5J GLY* 1.3 59.9 + - - +
94J THR* 3.3 3.5 - - - +
95J VAL* 2.7 35.4 + - + +
97J THR* 3.5 36.0 + - + +
99J VAL 4.2 14.0 + - - +
100J PRO* 5.0 3.6 - - - +
101J GLN* 3.4 47.6 + - - +
104J ILE* 4.1 13.2 - - + -
40L GLU* 2.8 35.0 + - - +
42L VAL 3.5 12.1 + - - -
43L VAL* 3.8 11.4 - - - -
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Residues in contact with GLY 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J ARG* 1.3 75.4 - - - +
6J ILE* 1.3 62.5 + - - -
92J MET* 4.3 2.5 - - - -
93J MET 3.2 7.4 - - - -
104J ILE* 3.8 10.4 - - - +
106J HIS* 3.6 8.3 + - - -
43L VAL* 3.0 16.4 + - - +
44L GLN* 3.7 17.9 - - - -
72L PRO* 3.4 22.8 - - - +
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Residues in contact with ILE 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J GLY* 1.3 74.9 - - - -
7J ARG* 1.3 65.0 + - - +
31J ILE* 3.9 19.0 - - + +
35J ASN* 3.4 46.0 - - + +
37J THR* 4.1 9.2 - - - +
92J MET* 3.6 2.7 + - - -
93J MET* 2.7 39.9 + - + +
95J VAL* 3.6 33.7 - - + -
104J ILE* 3.6 18.8 - - + -
105J ARG 3.4 13.5 - - - +
106J HIS* 3.8 3.1 - - + -
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Residues in contact with ARG 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J GLY 3.9 0.8 - - - -
6J ILE* 1.3 79.9 - - - +
8J GLY* 1.3 78.2 + - - +
31J ILE* 4.0 3.6 - - - +
90J ARG* 3.8 12.3 - - - +
91J VAL 2.8 24.9 + - - +
92J MET* 3.9 13.5 - - - -
106J HIS* 3.1 28.3 + - + +
107J VAL 3.3 17.8 + - - -
108J TYR* 3.3 24.3 + - - +
212J TSA 2.7 46.4 + - - +
72L PRO* 3.9 20.4 - - + +
73L VAL 3.2 28.6 + - - +
74L THR* 4.1 13.7 + - - -
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Residues in contact with GLY 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ARG* 1.3 95.3 + - - +
9J ALA* 1.3 58.2 + - - +
27J LEU* 4.0 5.2 - - - -
31J ILE* 4.2 2.2 - - - -
90J ARG* 3.4 0.3 - - - -
91J VAL* 3.0 36.9 + - - +
107J VAL 3.0 15.3 - - - -
108J TYR* 4.7 3.3 - - - -
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Residues in contact with ALA 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J GLY* 1.3 74.0 - - - +
10J THR* 1.3 63.7 + - - +
27J LEU* 3.6 7.3 - - - +
88J CYS* 4.4 0.9 - - - -
89J ILE 3.3 9.0 - - - +
90J ARG* 3.8 12.8 - - + -
107J VAL 2.9 7.3 + - - +
108J TYR* 3.6 23.6 - - + -
109J LEU 2.9 25.6 + - - -
112J ALA* 3.6 12.3 - - + -
115J LEU* 3.7 13.5 - - + -
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Residues in contact with THR 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ALA* 1.3 76.2 - - - +
11J THR* 1.3 71.1 + - - +
23J LYS* 3.7 28.8 + - + +
24J THR* 4.9 0.7 - - - +
27J LEU* 3.9 22.9 - - + -
88J CYS* 3.3 7.1 - - - -
89J ILE* 2.9 48.4 + - + +
109J LEU* 3.8 12.1 - - - +
110J GLU* 3.5 19.9 - - - +
112J ALA* 3.7 7.8 - - - +
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Residues in contact with THR 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J THR* 1.3 87.4 + - - +
12J VAL* 1.3 68.1 + - - +
23J LYS* 4.0 12.6 + - - +
85J LEU* 3.7 40.8 - - + -
86J LYS 3.8 6.7 - - - +
87J LYS* 3.0 13.7 - - - +
88J CYS* 4.0 1.1 - - - -
89J ILE* 4.9 1.1 - - - +
110J GLU* 3.2 11.3 - - - +
111J LYS* 2.9 45.0 + - + +
112J ALA 4.3 0.9 - - - +
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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