Contacts of the strand formed by residues 976 - 981 (chain A) in PDB entry 2W18
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 ARG 976 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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925A VAL* 3.5 10.8 - - - +
971A GLY* 3.6 0.7 - - - -
972A LEU* 2.8 43.1 + - + +
973A THR* 2.9 35.2 + - - +
974A LYS* 3.5 23.6 - - - +
975A ARG* 1.3 78.3 - - - +
977A LEU* 1.3 58.4 + - - +
991A VAL* 3.9 19.7 - - + +
992A MET 3.2 7.0 - - - +
993A THR* 3.7 21.8 - - + +
994A PHE* 4.7 0.7 - - - -
1004A GLN* 5.6 2.5 - - - +
1018A GLU* 4.1 4.9 + - - -
1024A GLU* 2.9 42.6 + - - -
1040A LEU* 4.1 23.1 + - - +
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Residues in contact with LEU 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923A VAL* 3.5 32.5 - - + -
925A VAL* 4.3 9.6 - - + -
933A CYS* 4.0 16.2 - - - -
944A ILE* 4.6 5.6 - - + -
962A LYS* 5.5 2.0 + - + -
969A VAL* 3.6 14.6 - - + -
970A LEU 3.5 7.0 - - - +
976A ARG* 1.3 76.2 - - - +
978A VAL* 1.3 74.6 + - - +
979A SER* 4.2 9.8 + - - +
990A GLU 3.6 1.2 - - - +
991A VAL* 3.5 2.6 - - - -
992A MET* 2.8 64.6 + - + +
994A PHE* 4.0 7.9 - - + -
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Residues in contact with VAL 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969A VAL* 3.2 2.8 - - - -
970A LEU* 2.9 43.7 + - + +
972A LEU* 3.9 25.9 - - + +
976A ARG 4.3 0.2 - - - -
977A LEU* 1.3 78.0 - - - +
979A SER* 1.3 64.2 + - - +
989A VAL* 4.1 9.2 - - + -
990A GLU 3.1 11.9 - - - +
991A VAL* 3.8 21.3 - - + +
1016A PHE* 3.7 39.5 - - + -
1026A LEU* 3.8 13.7 - - + -
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Residues in contact with SER 979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944A ILE* 4.4 8.3 - - - -
962A LYS* 3.9 27.5 + - - +
966A ILE* 4.3 14.1 - - - -
968A ALA 3.2 13.0 - - - -
969A VAL* 4.5 0.4 - - - -
977A LEU* 4.1 10.5 + - - +
978A VAL* 1.3 76.1 - - - +
980A SER* 1.3 61.3 + - - +
988A GLN 4.1 0.2 - - - +
989A VAL* 3.5 3.3 - - - +
990A GLU* 2.8 37.4 + - - +
1016A PHE* 4.0 5.4 - - - -
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Residues in contact with SER 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966A ILE* 3.6 4.2 - - - +
967A LYS* 2.7 29.0 + - - +
968A ALA* 3.0 9.7 + - - -
979A SER* 1.3 76.7 - - - +
981A SER* 1.3 61.7 + - - +
982A GLY 5.0 0.9 + - - -
987A GLN* 3.7 10.6 + - - +
988A GLN 3.1 16.4 + - - -
989A VAL* 3.6 11.2 - - - +
990A GLU* 6.1 0.2 - - - -
1013A ILE* 3.6 22.1 + - - +
1016A PHE* 3.8 19.1 - - - -
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Residues in contact with SER 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A ASN* 3.1 26.5 - - - -
966A ILE* 4.3 7.4 - - - -
967A LYS* 4.3 1.3 - - - +
980A SER* 1.3 74.4 - - - +
982A GLY* 1.3 69.7 + - - +
986A ASP 5.0 0.4 - - - -
987A GLN* 3.2 4.9 - - - +
988A GLN* 2.9 44.0 + - - +
990A GLU* 4.3 8.6 + - - -
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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