Contacts of the strand formed by residues 973 - 981 (chain A) in PDB entry 1QWN
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 GLN 973 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A SER* 4.1 10.8 + - - +
964A ARG* 2.9 42.6 + - - +
966A THR* 2.8 19.2 + - - +
967A LYS 2.9 24.5 + - - +
968A SER* 3.8 8.7 + - - +
970A ALA* 2.9 26.6 + - - +
971A LYS 3.8 2.2 + - - +
972A THR* 1.3 73.8 - - - +
974A ARG* 1.3 60.3 + - - +
1041A SER 3.7 0.3 - - - +
1042A SER* 3.2 5.4 - - - -
1043A HIS* 2.8 48.8 + - + +
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Residues in contact with ARG 974 (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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964A ARG* 3.7 1.0 - - - +
965A LEU* 2.8 52.7 + - + +
966A THR* 2.9 29.0 + - + +
972A THR* 4.1 8.7 - - + +
973A GLN* 1.3 79.2 - - - +
975A VAL* 1.3 62.4 + - - +
1010A GLU* 5.1 4.8 + - - -
1016A PHE 4.4 12.7 + - - -
1019A ASN* 4.4 13.5 + - - +
1040A VAL* 3.8 33.8 - - + +
1041A SER 3.2 4.3 - - - -
1042A SER* 3.9 16.3 + - - +
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Residues in contact with VAL 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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444A ALA* 4.6 2.0 - - + +
962A MET* 4.2 11.9 - - + -
963A ARG 3.6 15.3 - - - +
964A ARG* 4.1 25.4 - - + +
965A LEU* 4.4 0.2 - - - -
974A ARG* 1.3 79.9 - - - +
976A GLY* 1.3 65.6 + - - +
977A TYR* 3.7 28.2 - - + +
1003A LEU* 3.3 28.0 - - + -
1040A VAL* 3.2 5.4 - - - +
1041A SER* 2.9 42.2 + - - +
1043A HIS* 4.5 6.7 - - + -
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Residues in contact with GLY 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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961A VAL 3.8 0.2 - - - +
962A MET* 3.4 4.5 - - - -
963A ARG 2.8 40.6 + - - -
965A LEU* 3.9 11.7 - - - +
975A VAL* 1.3 73.5 - - - +
977A TYR* 1.3 64.0 + - - -
1016A PHE* 3.5 21.8 - - - -
1039A TYR 3.4 7.0 - - - -
1040A VAL* 4.2 0.4 - - - -
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Residues in contact with TYR 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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627A MET* 4.9 0.2 - - + -
959A VAL* 4.1 10.8 - - + -
961A VAL 3.2 5.2 - - - +
962A MET* 3.5 42.9 - - + +
975A VAL* 3.7 21.9 - - + +
976A GLY* 1.3 75.9 - - - -
978A VAL* 1.3 63.0 + - - +
979A LEU* 4.0 6.0 + - + -
999A VAL* 3.4 61.0 + - + -
1000A CYS* 5.6 0.2 - - - -
1002A LEU* 3.7 26.7 - - + +
1003A LEU* 4.0 8.8 + - - +
1016A PHE* 3.4 1.5 - - - -
1038A ALA* 3.1 7.1 - - - +
1039A TYR* 2.8 40.7 + - + +
1041A SER* 3.7 19.3 + - - -
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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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175A TRP* 4.2 5.6 - - + -
179A LEU* 4.1 13.9 - - + -
959A VAL* 3.5 4.9 - - - -
960A SER* 2.8 39.6 + - - +
961A VAL* 2.9 36.2 + - + +
977A TYR* 1.3 76.8 - - - +
979A LEU* 1.3 61.4 + - - +
1014A LEU* 4.0 17.9 - - + +
1016A PHE* 3.9 15.5 - - + -
1036A THR* 3.5 28.3 - - + -
1037A ALA 3.5 5.2 - - - +
1038A ALA* 4.4 4.0 - - + -
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Residues in contact with LEU 979 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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957A LEU* 4.4 22.9 - - + -
958A ASP 3.4 5.2 - - - +
959A VAL* 3.7 22.2 - - + -
977A TYR* 4.6 3.1 - - + -
978A VAL* 1.3 76.2 - - - +
980A HIS* 1.3 59.9 + - - +
997A LEU* 4.7 9.0 - - + +
999A VAL* 3.6 33.7 - - + +
1028A ALA* 5.7 1.1 - - + +
1029A PRO 4.6 7.9 - - - +
1030A GLU* 4.6 6.7 - - - -
1031A VAL* 4.0 13.6 - - + +
1036A THR* 3.2 6.2 - - - +
1037A ALA 2.8 34.5 + - - +
1039A TYR* 4.2 25.4 - - + -
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Residues in contact with HIS 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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175A TRP* 3.9 20.6 + + + -
214A TYR* 4.0 4.3 - - - -
811A LEU* 3.6 33.5 + - + +
956A ASP 3.7 1.8 - - - +
957A LEU* 3.6 3.7 - - - -
958A ASP* 2.8 41.0 + - + +
960A SER* 3.4 20.7 + - - +
979A LEU* 1.3 73.9 - - - +
981A ARG* 1.3 82.8 + - - +
982A THR* 3.8 15.5 + - - -
1034A MET* 4.3 7.6 - - + -
1035A GLU 3.3 5.7 + - - -
1036A THR* 2.8 21.7 + - - +
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Residues in contact with ARG 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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954A ARG* 4.1 14.6 - - - +
956A ASP* 3.3 41.1 + - - +
957A LEU* 3.0 25.8 - - + +
980A HIS* 1.3 78.3 - - - +
982A THR* 1.3 60.2 + - - +
1030A GLU* 2.9 34.8 + - - +
1031A VAL* 2.4 37.3 + - + +
1032A CYS 3.5 11.2 - - - +
1033A PRO* 3.7 24.2 - - - +
1034A MET* 2.7 32.6 + - - -
1035A GLU 3.1 8.4 + - - -
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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