Contacts of the strand formed by residues 2 - 11 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ILE* 5.0 6.5 - - + -
40B GLU 4.0 3.1 - - - +
41B ASP 4.1 4.5 - - - +
42B VAL 4.5 2.0 - - - +
43B VAL* 4.3 8.7 - - + -
96B GLN* 2.9 58.6 - - + +
3C ILE* 1.3 90.4 + - - +
4C ARG* 3.2 45.3 - - + +
96C GLN* 3.4 9.7 - - - +
97C THR 2.6 41.5 + - - +
98C ASP* 4.5 10.1 + - - +
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Residues in contact with ILE 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A MET* 4.2 9.6 - - - -
3A ILE* 3.7 41.5 - - + +
3B ILE* 4.5 10.9 - - + +
43B VAL* 3.3 24.0 - - + +
2C MET* 1.3 98.5 - - - +
4C ARG* 1.3 58.7 + - - +
43C VAL* 3.9 11.9 - - + -
94C THR* 3.5 30.5 - - + -
95C VAL 3.2 3.4 - - - +
96C GLN* 3.8 33.2 - - + +
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Residues in contact with ARG 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLU* 3.3 26.7 + - - +
42B VAL 3.9 4.7 + - - +
43B VAL* 3.9 10.1 - - - +
96B GLN* 5.2 1.6 + - - -
2C MET* 3.2 34.8 + - + +
3C ILE* 1.3 78.2 - - - +
5C GLY* 1.3 59.5 + - - +
6C ILE* 5.3 0.2 - - - -
94C THR* 3.6 1.4 - - - +
95C VAL* 2.7 35.7 + - - +
97C THR* 3.8 17.4 + - + +
99C VAL 3.4 24.0 + - - -
100C PRO* 4.6 4.4 - - - +
101C GLN* 3.2 51.3 + - - +
104C ILE* 3.9 17.9 - - + -
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Residues in contact with GLY 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL 3.0 19.9 + - - -
44B GLN* 3.7 8.3 - - - -
72B PRO* 3.1 18.0 - - - +
4C ARG* 1.3 75.0 - - - +
6C ILE* 1.3 62.0 + - - -
92C MET* 3.4 21.8 - - - -
93C MET 3.8 1.3 - - - -
104C ILE* 3.8 7.6 - - - +
106C HIS* 3.4 6.6 + - - -
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Residues in contact with ILE 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ARG 4.9 0.2 - - - +
5C GLY* 1.3 76.2 - - - -
7C ARG* 1.3 63.1 + - - +
31C ILE* 3.6 25.6 - - + -
35C ASN* 3.6 18.2 - - + +
37C THR* 4.0 12.8 - - - +
91C VAL* 3.6 0.8 - - - +
92C MET* 3.3 6.1 - - - +
93C MET* 2.8 41.4 + - + +
95C VAL* 3.6 38.4 - - + -
104C ILE* 3.7 21.8 - - + -
105C ARG 3.3 25.6 - - - +
106C HIS* 3.7 2.9 - - + -
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Residues in contact with ARG 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PRO* 3.9 25.6 - - + -
73B VAL* 2.7 36.1 + - - +
74B THR* 3.6 12.1 + - - -
6C ILE* 1.3 73.7 - - - +
8C GLY* 1.3 74.8 + - - +
31C ILE* 4.1 6.8 - - - +
90C ARG* 3.6 12.1 - - - +
91C VAL 3.2 21.6 + - - +
92C MET* 4.0 18.2 - - - +
106C HIS* 3.0 25.6 - - + +
107C VAL 3.0 22.0 + - - -
108C TYR* 3.4 23.1 + - - +
202C TSA 2.9 43.9 + - - +
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Residues in contact with GLY 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ARG* 1.3 90.4 + - - +
9C ALA* 1.3 59.8 + - - +
27C LEU* 4.0 4.3 - - - -
31C ILE* 3.9 14.8 - - - -
90C ARG* 3.3 0.3 - - - -
91C VAL* 2.9 32.2 + - - +
107C VAL 3.0 14.4 - - - -
108C TYR* 4.7 2.0 - - - -
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Residues in contact with ALA 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ARG* 4.1 0.2 - - - +
8C GLY* 1.3 74.9 - - - +
10C THR* 1.3 63.2 + - - +
27C LEU* 3.8 7.8 - - - +
88C CYS* 4.5 0.7 - - - -
89C ILE 3.1 13.9 - - - +
90C ARG* 3.9 9.4 - - + -
107C VAL 3.2 4.8 + - - -
108C TYR* 3.5 25.2 - - + +
109C LEU 2.9 24.8 + - - -
112C ALA* 3.5 11.9 - - + -
115C LEU* 3.7 12.3 - - + -
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Residues in contact with THR 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ALA* 1.3 75.5 - - - +
11C THR* 1.3 76.9 + - - +
23C LYS* 3.9 36.2 + - + +
24C THR 4.6 0.7 - - - +
27C LEU* 3.9 20.0 - - + -
88C CYS* 3.4 3.5 - - - -
89C ILE* 2.9 41.0 + - + +
109C LEU* 3.4 19.1 - - - +
110C GLU* 3.3 21.0 - - - +
112C ALA* 3.8 0.4 - - - -
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Residues in contact with THR 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C THR* 1.3 84.0 + - - +
12C VAL* 1.3 66.8 + - - +
23C LYS* 3.7 18.2 - - - +
85C LEU* 3.6 31.6 - - + -
86C LYS 3.8 14.8 - - - +
87C LYS 3.1 9.4 - - - +
88C CYS* 3.9 3.1 - - + +
89C ILE 4.7 0.4 - - - +
110C GLU* 3.3 8.8 - - - +
111C LYS* 3.0 36.7 + - + +
112C ALA* 3.7 6.5 - - + +
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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