Contacts of the strand formed by residues 1001 - 1007 (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 THR1001 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962A PHE* 4.0 3.4 - - - -
991A SER 3.7 17.9 - - - +
992A THR* 3.9 18.9 + - - +
993A ARG 3.9 13.7 - - - -
994A VAL* 4.2 2.1 + - - +
1000A VAL* 1.3 77.4 + - - +
1002A PRO* 1.3 79.5 - - + +
1020A TYR* 3.1 24.8 - - - -
1021A GLN* 3.0 29.9 + - + +
1022A VAL 4.8 5.8 + - - -
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Residues in contact with PRO1002 (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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958A ILE 3.6 23.1 - - - +
959A TRP* 4.6 0.7 - - - -
960A VAL* 3.7 28.0 - - + +
962A PHE* 3.9 11.0 - - + -
990A ALA* 3.4 19.4 - - + +
991A SER* 4.1 11.9 - - - +
993A ARG 4.8 7.4 - - - +
994A VAL* 6.1 0.2 - - - -
1000A VAL 4.6 1.1 - - - +
1001A THR* 1.3 100.8 - - + +
1003A ILE* 1.3 62.4 + - - +
1004A LEU* 4.8 5.2 - - + -
1017A LEU* 3.7 21.8 - - + -
1019A GLY 3.8 1.3 - - - +
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Residues in contact with ILE1003 (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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990A ALA* 4.6 2.2 - - - -
1001A THR 4.2 0.2 - - - +
1002A PRO* 1.3 79.5 - - - +
1004A LEU* 1.3 67.8 + - - +
1017A LEU* 3.4 7.0 - - - +
1018A ASP* 3.0 32.7 + - - +
1019A GLY* 2.8 20.8 + - - +
1020A TYR 2.9 36.3 - - - +
1021A GLN* 4.1 17.5 - - + +
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Residues in contact with LEU1004 (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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958A ILE* 4.0 26.7 - - + -
976A LEU* 4.0 19.7 - - + -
989A ARG* 4.3 1.8 - - - -
990A ALA* 4.1 27.5 - - + +
1002A PRO* 4.8 4.7 - - + -
1003A ILE* 1.3 83.7 - - - +
1005A SER* 1.3 62.2 + - - +
1006A VAL* 4.3 1.1 + - + +
1015A TRP* 4.0 33.2 - - + +
1016A VAL 3.3 3.8 - - - +
1017A LEU* 3.8 29.2 - - + +
1018A ASP* 3.3 6.3 - - - +
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Residues in contact with SER1005 (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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1004A LEU* 1.3 74.9 - - - +
1006A VAL* 1.3 62.3 + - - +
1007A ARG* 3.4 31.0 + - - -
1015A TRP* 3.3 3.6 - - - -
1016A VAL* 2.8 32.0 + - - +
1018A ASP* 2.6 38.1 + - - +
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Residues in contact with VAL1006 (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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985A ASP* 3.3 39.8 - - + +
988A PHE 5.4 0.4 - - - +
1004A LEU* 4.3 1.8 + - + +
1005A SER* 1.3 71.4 - - - +
1007A ARG* 1.3 57.7 + - - +
1008A LYS* 3.9 2.5 + - - +
1013A LYS* 3.6 34.1 - - + -
1014A GLU 3.3 6.5 - - - +
1015A TRP* 3.5 32.3 - - + +
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Residues in contact with ARG1007 (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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972A LEU 4.6 2.0 + - - -
973A ASP* 2.5 36.7 + - - +
1005A SER* 3.4 21.2 + - - -
1006A VAL* 1.3 72.5 - - - +
1008A LYS* 1.3 58.3 + - - +
1009A GLU* 2.9 20.3 + - + +
1013A LYS* 4.8 0.2 - - - -
1014A GLU* 3.0 30.7 + - + +
1016A VAL* 3.6 28.1 - - + +
1018A ASP* 3.3 34.1 + - - +
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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