Contacts of the strand formed by residues 4 - 13 (chain C) in PDB entry 3CJS
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 VAL 4 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C LYS* 1.3 71.9 - - - +
5C VAL* 1.3 63.0 + - - +
6C ALA 3.8 13.7 - - - +
7C VAL* 4.2 11.4 - - + -
58C THR* 3.7 24.0 - - + -
59C ILE 3.7 4.7 - - - +
60C TYR* 3.7 22.9 - - + -
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Residues in contact with VAL 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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3C LYS 3.9 1.1 - - - +
4C VAL* 1.3 78.6 - - - +
6C ALA* 1.3 65.8 + - + +
30C HIS* 5.0 12.6 + - + +
59C ILE* 2.9 28.0 + - + +
60C TYR 3.8 13.2 - - - +
61C ALA* 3.7 29.4 - - + +
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Residues in contact with ALA 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 VAL* 3.8 3.4 - - - +
5C VAL* 1.3 84.1 - - + +
7C VAL* 1.3 67.2 + - - +
8C VAL* 4.1 2.0 - - + -
30C HIS* 3.4 44.4 - - + +
57C ILE 4.3 0.2 - - - -
58C THR* 3.5 2.8 - - - -
59C ILE* 2.8 34.4 + - + +
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Residues in contact with VAL 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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4C VAL* 4.2 13.7 - - + -
6C ALA* 1.3 80.6 - - - +
8C VAL* 1.3 60.8 + - - +
9C LYS* 3.8 16.5 + - - +
56C GLU* 3.5 41.3 - - + +
57C ILE 3.2 5.6 - - - +
58C THR* 4.0 13.2 - - + +
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Residues in contact with VAL 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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6C ALA* 4.8 0.4 - - + -
7C VAL* 1.3 74.5 - - - +
9C LYS* 1.3 63.8 + - - +
10C LEU* 3.9 17.0 - - + -
26C ALA* 3.7 43.7 - - + +
27C LEU* 5.1 0.9 - - + -
29C GLN* 4.4 3.1 - - - +
30C HIS* 3.9 15.5 - - + -
55C VAL 3.6 1.6 - - - +
56C GLU* 3.5 1.2 - - - -
57C ILE* 2.7 54.1 + - + +
59C ILE* 3.8 19.5 - - + -
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Residues in contact with LYS 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 VAL* 3.8 17.0 + - - +
8C VAL* 1.3 77.9 - - - +
10C LEU* 1.3 68.9 + - - +
55C VAL 3.4 4.7 - - - +
56C GLU* 4.3 28.7 + - + -
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Residues in contact with LEU 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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8C VAL* 3.9 9.8 + - + -
9C LYS* 1.3 82.8 - - - +
11C GLN* 1.3 62.4 + - - +
12C LEU* 4.1 26.0 - - + -
22C PRO* 4.0 20.2 - - + -
23C VAL* 4.3 11.2 - - + +
26C ALA* 3.9 22.2 - - + -
27C LEU* 4.3 14.1 - - + -
37C PHE* 4.7 0.4 - - + -
54C PRO* 3.4 3.5 - - - +
55C VAL* 2.7 48.7 + - + -
57C ILE* 3.8 21.5 - - + -
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Residues in contact with GLN 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 LEU* 1.3 79.2 - - - +
12C LEU* 1.3 68.1 + - - +
13C PRO* 4.6 1.7 - - - +
22C PRO* 5.4 3.0 - - - +
52C ILE* 3.9 23.2 - - + +
53C VAL 3.5 4.0 - - - -
54C PRO* 4.2 20.6 - - + +
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Residues in contact with LEU 12 (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 LEU* 4.1 13.2 - - + -
11C GLN* 1.3 84.0 - - - +
13C PRO* 1.4 73.3 - - + +
14C ALA 3.3 0.5 + - - -
17C ALA* 4.2 12.3 - - + -
22C PRO* 4.2 21.1 - - + -
23C VAL* 3.8 27.1 - - + -
37C PHE* 3.8 33.4 - - + -
41C PHE* 3.6 19.2 - - + -
52C ILE* 4.3 4.0 - - - -
53C VAL* 2.7 40.6 + - - +
55C VAL* 4.1 11.7 - - + -
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Residues in contact with PRO 13 (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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11C GLN 4.6 1.8 - - - +
12C LEU* 1.4 89.2 - - + +
14C ALA* 1.3 68.0 + - - +
15C GLY 3.3 0.9 + - - -
16C LYS* 3.0 44.5 + - + +
17C ALA* 3.8 2.5 + - - +
41C PHE* 3.6 7.8 - - - -
50C ASP 5.5 1.6 - - - +
51C ALA 3.8 4.9 - - - +
52C ILE* 4.1 17.0 - - + -
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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