Contacts of the strand formed by residues 1003 - 1016 (chain A) in PDB entry 6Q6Q
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 LYS1003 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A LYS* 4.2 0.4 - - - +
551A SER* 3.3 40.8 + - - +
552A ALA* 4.0 10.9 + - - +
554A GLU* 3.1 28.7 + - + -
556A LEU* 3.9 16.2 - - + -
996A PHE* 3.2 17.2 - - + -
1000A ASN* 3.3 13.0 - - - +
1001A TYR 3.5 0.2 - - - -
1002A TRP* 1.3 80.8 + - - +
1004A LYS* 1.3 68.8 - - - +
1172A GLU* 3.3 25.6 - - - +
1173A ILE 3.6 12.6 - - - +
1174A ASP* 2.4 38.4 + - - -
1175A CYS* 4.2 0.7 - - - -
1176A LEU* 5.8 0.4 - - - +
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Residues in contact with LYS1004 (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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996A PHE* 4.1 1.6 - - - -
997A ASN* 2.5 51.1 + - + +
1000A ASN 3.5 6.7 - - - +
1001A TYR 4.2 6.5 - - - -
1003A LYS* 1.3 79.5 - - - +
1005A LYS* 1.3 61.3 + - - +
1172A GLU* 3.4 3.3 - - - +
1173A ILE* 2.8 44.7 + - + +
1175A CYS* 3.8 8.8 - - - -
1286A ALA* 3.6 18.6 - - + +
1289A ALA 3.6 9.5 + - - -
1290A ALA* 3.7 37.2 - - + +
1293A GLU* 2.8 29.5 + - - +
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Residues in contact with LYS1005 (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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993A VAL* 3.4 25.0 - - + +
996A PHE* 3.5 44.3 - - + +
997A ASN* 2.9 25.5 + - - +
1004A LYS* 1.3 74.4 - - - +
1006A GLY* 1.3 59.5 + - - +
1170A GLU* 4.0 21.5 + - - +
1171A VAL 3.2 5.6 - - - +
1172A GLU* 3.9 28.0 + - + -
1183A ILE* 4.1 13.1 - - + +
1285A ASP* 4.3 1.0 - - - +
1286A ALA* 3.4 14.0 - - - +
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Residues in contact with GLY1006 (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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993A VAL* 4.2 3.4 - - - -
1005A LYS* 1.3 75.9 - - - +
1007A LEU* 1.3 62.6 + - - +
1170A GLU* 3.4 9.0 - - - +
1171A VAL 2.7 33.9 + - - -
1282A ALA* 3.3 24.7 - - - -
1285A ASP* 3.3 9.4 - - - -
1286A ALA* 3.6 3.7 - - - +
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Residues in contact with LEU1007 (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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948A GLU* 4.3 5.4 - - - +
986A TYR* 3.5 35.0 + - + +
989A ARG* 3.9 24.7 - - + +
990A LYS* 3.8 45.1 + - + +
993A VAL* 4.6 7.6 - - + -
1006A GLY* 1.3 74.5 - - - +
1008A ALA* 1.3 65.2 + - - +
1168A CYS* 3.9 9.0 - - - -
1169A SER 3.3 21.3 - - - +
1170A GLU* 3.7 21.3 - - + +
1282A ALA* 4.1 2.8 + - - -
1285A ASP* 3.0 21.9 + - - +
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Residues in contact with ALA1008 (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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948A GLU* 3.3 11.0 - - - +
951A ARG* 5.1 2.0 - - - +
986A TYR* 4.7 3.1 - - - -
1007A LEU* 1.3 78.1 - - - +
1009A MET* 1.3 63.0 + - - +
1167A ALA 4.1 0.2 - - - +
1168A CYS* 3.3 6.1 - - - -
1169A SER 3.1 30.6 + - - +
1278A SER* 3.5 13.8 - - - +
1281A PHE* 3.7 17.9 - - + +
1282A ALA 3.5 23.8 - - - +
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Residues in contact with MET1009 (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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948A GLU* 3.0 16.7 + - + +
951A ARG* 2.8 31.4 + - - -
977A TRP* 3.9 31.6 - - + +
980A CYS* 4.3 15.5 - - - +
981A MET* 3.6 41.5 - - + +
984A SER* 4.3 1.6 - - - +
986A TYR* 3.6 30.1 - - + -
1008A ALA* 1.3 77.4 - - - +
1010A VAL* 1.3 63.1 + - - +
1166A ALA* 4.8 0.4 - - + -
1167A ALA 3.2 22.2 - - - +
1168A CYS* 3.9 12.1 - - + -
1278A SER* 5.0 0.2 - - - -
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Residues in contact with VAL1010 (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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933A GLU* 4.2 7.6 - - - +
951A ARG* 3.9 20.4 - - - +
977A TRP* 4.1 3.6 - - - -
1009A MET* 1.3 81.3 - - - +
1011A PRO* 1.3 73.0 - - + +
1166A ALA* 3.3 4.5 - - - +
1167A ALA 3.0 36.3 + - - +
1274A PHE* 4.2 6.3 - - + -
1275A LEU* 4.3 15.0 - - + +
1277A CYS* 3.9 31.9 - - - -
1278A SER* 4.3 15.9 - - - +
1281A PHE* 3.9 9.6 - - + -
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Residues in contact with PRO1011 (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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896A ASN* 3.4 5.4 + - - +
897A ALA* 4.0 18.2 - - + -
898A TYR* 3.2 39.9 - - + +
933A GLU* 3.5 3.1 - - - +
951A ARG* 3.7 10.5 - - + -
955A MET* 4.8 7.0 - - - -
973A LEU* 4.7 6.5 - - + -
977A TRP* 3.9 20.2 - - + -
1010A VAL* 1.3 85.0 - - - +
1012A LEU* 1.3 62.0 + - - +
1165A GLY 3.5 6.7 - - - +
1166A ALA* 4.3 3.4 - - + -
1274A PHE* 3.1 24.6 - - - -
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Residues in contact with LEU1012 (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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896A ASN* 3.7 1.1 - - - -
897A ALA* 4.9 0.9 - - - -
925A PHE* 3.5 32.1 - - + -
973A LEU* 3.6 10.6 - - - +
1011A PRO* 1.3 78.8 - - - +
1013A LYS* 1.3 59.7 + - - +
1014A PHE* 4.3 6.3 - - + +
1163A VAL 4.2 10.1 - - - +
1164A TYR* 3.2 6.4 - - - -
1165A GLY 2.7 39.3 + - - +
1189A MET* 3.8 30.1 - - + -
1271A SER* 3.8 28.0 - - - +
1274A PHE* 3.6 12.3 - - + -
1275A LEU* 3.6 19.5 - - + -
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Residues in contact with LYS1013 (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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893A LYS 5.1 0.2 - - - +
895A ASP* 3.6 20.1 + - - -
896A ASN* 3.0 45.3 + - - +
897A ALA* 4.3 4.5 - - + +
925A PHE* 3.6 16.5 - - - -
956A TYR* 4.1 4.7 - - + -
962A THR* 4.6 2.0 - - - +
964A TYR* 3.8 4.9 + - - -
968A ILE* 4.1 25.6 - - + -
973A LEU* 5.1 1.3 - - + -
1012A LEU* 1.3 73.6 - - - +
1014A PHE* 1.3 58.3 + - - +
1015A PRO* 3.2 24.8 - - - +
1162A PHE* 3.3 36.4 - - + -
1163A VAL 3.5 3.6 - - - -
1164A TYR* 3.5 31.0 - - + +
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Residues in contact with PHE1014 (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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893A LYS* 3.5 27.8 - - + -
922A GLY* 3.7 15.3 - - - -
925A PHE* 3.6 27.4 - + + -
1012A LEU* 4.1 8.0 - - + -
1013A LYS* 1.3 73.1 - - - +
1015A PRO* 1.3 70.9 - - - +
1016A VAL* 3.5 22.3 + - + +
1089A SER* 4.0 7.0 - - - -
1162A PHE* 4.6 1.3 - - - -
1163A VAL* 2.9 35.7 + - + +
1267A GLY 5.4 0.2 - - - -
1270A GLU* 3.4 45.3 - - + -
1271A SER* 3.6 28.5 - - - +
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Residues in contact with PRO1015 (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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889A MET* 5.3 0.3 - - - +
893A LYS* 3.6 46.7 + - + -
925A PHE* 4.8 0.2 - - + -
964A TYR* 4.1 7.0 - - - +
1013A LYS* 3.2 34.1 - - - +
1014A PHE* 1.3 95.5 - - - +
1016A VAL* 1.3 60.9 + - - +
1017A GLY 4.3 0.7 + - - -
1159A PHE* 3.5 34.2 - - + -
1161A TYR 4.1 0.2 - - - +
1162A PHE* 3.5 14.8 - - + -
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Residues in contact with VAL1016 (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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1014A PHE* 3.7 29.6 - - + +
1015A PRO* 1.3 76.4 - - - +
1017A GLY* 1.3 60.7 + - - +
1089A SER* 4.4 10.1 - - - -
1090A VAL* 3.6 20.2 - - + -
1159A PHE* 3.3 6.5 - - - +
1160A GLU* 3.1 26.0 + - + +
1161A TYR* 3.2 57.8 + - + +
1163A VAL* 4.0 6.7 - - + -
1267A GLY 4.1 5.4 - - - +
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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