Contacts of the strand formed by residues 974 - 980 (chain A) in PDB entry 1WXR
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 974 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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937A THR* 3.9 29.2 - - + +
941A LYS* 3.9 18.2 - - - +
942A ALA* 3.5 32.5 - - + +
964A LYS* 5.2 2.9 - - - +
972A LEU* 5.0 6.3 - - + -
973A ASP* 1.3 83.0 - - - +
975A PRO* 1.3 70.9 - - + +
976A LEU* 3.3 9.6 + - + +
1016A VAL* 3.5 6.9 - - - +
1017A LEU* 3.0 39.4 + - + +
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Residues in contact with PRO 975 (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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942A ALA* 5.1 0.2 - - - +
943A ASP 4.4 1.2 - - - +
944A LYS* 3.4 37.3 - - - +
973A ASP* 3.7 10.3 - - - +
974A ILE* 1.3 85.9 - - + +
976A LEU* 1.3 63.9 + - - +
977A VAL 3.5 5.4 - - - +
1009A GLU* 5.8 1.3 - - - +
1014A GLU* 3.4 32.1 - - + +
1015A TRP 3.9 1.1 - - - +
1016A VAL* 3.8 16.1 - - + -
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Residues in contact with LEU 976 (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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935A MET* 2.7 42.3 - - + +
937A THR* 5.0 1.8 - - - +
942A ALA* 3.6 31.2 - - + -
943A ASP 4.2 2.0 - - - +
944A LYS* 3.6 3.0 - - - -
945A LEU 3.1 11.4 + - - -
958A ILE* 4.1 10.8 - - + -
960A VAL* 3.5 33.0 - - + -
974A ILE* 3.3 16.8 + - + +
975A PRO* 1.3 77.4 - - - +
977A VAL* 1.3 65.0 + - + +
1004A LEU* 4.0 13.0 - - + -
1015A TRP* 3.0 13.4 + - + +
1017A LEU* 3.9 19.7 - - + -
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Residues in contact with VAL 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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935A MET* 4.6 3.1 - - + -
944A LYS* 4.5 2.0 - - - -
945A LEU* 3.3 25.8 - - + +
947A ILE* 4.1 13.2 - - + -
958A ILE* 4.3 27.8 - - + -
975A PRO* 3.5 2.3 - - - +
976A LEU* 1.3 88.6 + - + +
978A SER* 1.3 66.9 + - - +
979A ALA* 5.0 0.2 - - + -
988A PHE* 3.8 28.5 - - + -
1014A GLU* 3.5 6.2 - - - +
1015A TRP* 3.2 46.4 + - + +
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Residues in contact with SER 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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944A LYS* 3.3 23.6 - - - -
945A LEU 3.0 7.3 + - - -
946A VAL* 3.7 10.8 - - - +
947A ILE* 2.8 31.2 + - - +
977A VAL* 1.3 76.4 - - - +
979A ALA* 1.3 63.8 + - - +
1012A LYS* 3.4 26.7 - - - +
1013A LYS 3.6 6.3 - - - -
1014A GLU* 3.9 15.0 - - - +
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Residues in contact with ALA 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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947A ILE* 3.3 13.2 - - + -
951A ALA* 4.2 12.3 - - + -
977A VAL* 5.0 0.9 - - + -
978A SER* 1.3 77.3 + - - +
980A PRO* 1.3 80.4 - - + +
981A GLU 3.4 0.2 + - - -
983A THR* 3.6 13.0 - - + +
988A PHE* 5.6 0.7 - - + -
1012A LYS* 3.6 10.1 - - - +
1013A LYS 2.9 23.1 + - - -
1015A TRP* 4.0 18.8 - - + -
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Residues in contact with PRO 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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947A ILE* 3.6 19.5 - - + +
948A ASN* 4.5 0.7 - - - -
949A LYS 3.5 41.5 - - - +
950A SER* 3.6 4.7 - - - +
951A ALA* 4.5 1.6 - - + -
979A ALA* 1.3 91.2 - - + +
981A GLU* 1.3 66.5 + - - +
982A ALA* 3.2 6.5 - - + +
983A THR* 2.9 29.7 + - - +
1011A GLY 5.1 2.2 - - - +
1012A LYS* 5.8 0.7 - - + -
1013A LYS* 3.6 3.3 - - - +
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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