Contacts of the helix formed by residues 93 - 100 (chain 4) 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 93 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1801 HIS* 3.7 34.8 - - + +
1811 LEU* 3.8 26.0 - - + -
11891 CLA 5.4 11.7 - - + +
884 SER* 4.8 2.5 - - - -
894 THR* 3.3 30.5 - - + +
904 LEU 5.9 0.4 - - - -
914 PHE 3.4 0.2 - - - -
924 VAL* 1.3 76.5 - - + +
944 GLU* 1.3 61.6 + - - +
964 ILE* 3.5 26.9 + - + +
974 LEU* 4.4 3.1 + - - +
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Residues in contact with GLU 94 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904 LEU 3.4 10.8 - - - +
914 PHE* 3.0 27.7 + - - +
934 ILE* 1.3 79.5 - - - +
954 PHE* 1.3 81.9 + - + +
964 ILE 3.4 1.2 + - - -
974 LEU* 3.4 22.1 - - - +
984 SER* 3.7 4.2 + - - -
12084 CLA 2.5 74.4 + - + +
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Residues in contact with PHE 95 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914 PHE* 2.6 42.3 + + + +
924 VAL* 3.5 5.5 + - - +
934 ILE 3.4 0.8 - - - -
944 GLU* 1.3 99.3 - - + +
964 ILE* 1.3 60.4 + - - +
974 LEU 3.3 0.4 - - - -
984 SER* 2.7 30.9 + - - -
994 HIS* 3.2 13.3 + - - +
1024 GLU* 5.8 0.2 - - - -
12054 CLA 3.7 21.8 - + + -
12074 CLA 3.9 20.6 - - + -
12084 CLA 2.4 54.1 - + + -
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Residues in contact with ILE 96 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924 VAL* 3.4 23.8 - - + +
934 ILE* 3.5 23.6 - - + +
944 GLU 3.3 0.6 - - - -
954 PHE* 1.3 74.6 - - - +
974 LEU* 1.3 66.0 - - - +
994 HIS* 3.3 18.9 - - + +
1004 TYR* 3.5 35.3 - - + +
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Residues in contact with LEU 97 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934 ILE 4.4 2.8 + - - +
944 GLU* 3.4 13.6 + - - +
964 ILE* 1.3 77.3 - - - +
984 SER* 1.3 72.0 + - - +
994 HIS 3.0 1.0 + - - -
1004 TYR* 3.6 16.1 + - + -
1014 VAL* 3.5 25.1 + - + +
12084 CLA 5.9 7.9 - - + -
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Residues in contact with SER 98 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944 GLU 3.7 4.1 + - - -
954 PHE* 2.7 42.4 + - - +
974 LEU* 1.3 81.4 - - - +
994 HIS* 1.3 62.9 + - - +
1014 VAL* 2.8 26.2 + - - +
1024 GLU* 2.9 40.3 + - - +
12074 CLA 5.8 0.3 - - - +
12084 CLA 5.1 15.3 - - - -
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Residues in contact with HIS 99 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954 PHE 3.2 10.9 + - - +
964 ILE* 3.3 15.7 - - + +
974 LEU 3.0 2.6 + - - -
984 SER* 1.3 77.5 + - - +
1004 TYR* 1.3 68.6 + + - +
1024 GLU* 2.8 28.3 + - - +
1034 ILE* 3.0 37.3 + - + +
11974 CLA 5.6 2.1 - + - -
11984 CLA 3.8 45.8 + + + -
12074 CLA 3.3 37.3 - - + +
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Residues in contact with TYR 100 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964 ILE* 3.5 39.0 + - + +
974 LEU* 3.6 13.2 + - + -
994 HIS* 1.3 86.1 - + - +
1014 VAL* 1.3 58.7 + - - +
1024 GLU 3.6 0.4 - - - -
1034 ILE* 3.6 11.9 - - + -
1044 ARG* 4.6 6.8 - - - +
1074 GLN* 5.0 1.2 + - - -
11974 CLA 3.5 36.3 - + + +
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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