Contacts of the helix formed by residues 105 - 113 (chain 1) in PDB entry 2WSC
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 105 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461 HIS* 6.3 2.7 - - + -
1011 GLU* 3.3 33.0 + - + +
1021 PHE 5.8 0.2 - - - -
1041 ALA* 1.3 78.4 - - + +
1061 ALA* 1.3 55.0 + - - +
1071 PHE* 2.9 10.8 + - + +
1081 VAL* 3.2 30.8 - - + +
1091 GLU* 4.2 7.1 - - - +
11951 CLA 5.5 9.2 - - + -
11961 CLA 5.8 2.0 - - - -
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Residues in contact with ALA 106 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021 PHE 5.1 2.9 - - - +
1031 LEU* 3.6 27.5 + - + +
1041 ALA 3.1 1.2 - - - -
1051 ILE* 1.3 75.3 - - - +
1071 PHE* 1.3 64.1 + - - +
1081 VAL 3.5 0.4 - - - -
1091 GLU* 4.7 6.5 - - - +
1101 HIS* 3.4 22.5 + - - +
11961 CLA 5.0 17.9 - - + -
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Residues in contact with PHE 107 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041 ALA 3.4 18.8 + - - +
1051 ILE* 2.9 2.7 - - - -
1061 ALA* 1.3 80.0 - - - +
1081 VAL* 1.3 64.3 + - + +
1101 HIS* 3.7 6.6 - + - -
1111 GLN* 3.3 34.0 + - + +
11951 CLA 3.4 36.3 - + + -
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Residues in contact with VAL 108 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051 ILE* 3.2 31.6 - - + +
1071 PHE* 1.3 79.3 - - + +
1091 GLU* 1.3 75.1 + - + +
1111 GLN* 3.0 11.4 + - - +
1121 ARG* 3.0 34.1 + - - +
11951 CLA 3.2 70.0 - - + +
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Residues in contact with GLU 109 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051 ILE* 4.2 12.9 + - - +
1061 ALA* 4.6 3.5 + - - +
1081 VAL* 1.3 82.1 - - + +
1101 HIS* 1.3 57.3 + - - +
1121 ARG* 3.3 40.0 + - + +
1131 SER* 2.7 37.6 + - - -
11961 CLA 2.2 95.6 + - + +
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Residues in contact with HIS 110 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061 ALA* 3.4 21.1 + - - +
1071 PHE* 3.7 8.3 + + - +
1091 GLU* 1.3 76.9 - - - +
1111 GLN* 1.3 102.3 + - + +
1131 SER* 3.5 10.4 + - - -
1141 MET* 3.3 41.7 - - + +
11961 CLA 5.9 0.2 - - - -
62G ASP* 5.7 5.4 + - - +
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Residues in contact with GLN 111 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071 PHE* 3.3 25.9 - - + +
1081 VAL 3.0 9.0 + - - +
1101 HIS* 1.3 109.2 + - + +
1121 ARG* 1.3 60.6 + - - +
1141 MET* 3.8 23.7 + - - +
1151 GLU* 4.8 2.8 + - - +
11951 CLA 3.6 42.2 - - + +
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Residues in contact with ARG 112 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381 ARG* 5.4 3.4 - - - +
391 TYR* 3.5 40.1 + - + +
421 SER* 4.6 18.2 - - - -
1081 VAL* 3.0 19.5 + - - +
1091 GLU* 2.9 50.1 + - + +
1111 GLN* 1.3 79.8 - - - +
1131 SER* 1.3 55.4 + - - +
1141 MET 3.4 3.1 + - - -
1151 GLU* 3.7 22.2 - - - +
11951 CLA 4.5 39.9 - - + +
11961 CLA 3.2 41.3 + - + +
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Residues in contact with SER 113 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091 GLU 2.7 13.4 + - - -
1101 HIS* 3.5 4.7 + - - -
1111 GLN 3.3 0.6 - - - -
1121 ARG* 1.3 77.2 - - - +
1141 MET* 1.3 68.1 + - - +
1151 GLU* 3.9 2.9 - - - +
11961 CLA 4.6 14.5 - - - +
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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