Contacts of the strand formed by residues 1094 - 1101 (chain A) in PDB entry 5Z58
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 ARG1094 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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979A SER 3.6 6.5 - - - +
980A ARG* 4.4 24.1 - - + +
1089A CYS 4.0 0.3 - - - +
1090A ARG* 3.3 7.6 - - - +
1091A TYR* 2.9 63.7 + - + +
1092A ILE* 3.3 6.5 - - - +
1093A ASP* 1.3 95.5 + - - +
1095A ILE* 1.3 64.2 + - - +
1096A HIS* 4.3 22.2 - - + +
1190A CYS* 5.9 7.4 - - - +
1235A GLU* 5.8 2.4 + - - -
1239A ARG* 6.2 0.4 - - - +
229P LYS* 6.2 0.2 - - - +
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Residues in contact with ILE1095 (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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977A LEU* 3.7 2.6 - - + +
978A GLU* 3.3 6.4 - - - -
979A SER* 2.9 51.2 + - - +
981A PHE* 3.4 47.3 - - + -
1049A ASP* 4.4 3.8 - - - +
1052A VAL* 5.9 1.8 - - + -
1088A PHE* 4.1 9.9 - - + -
1089A CYS 4.0 0.9 - - - +
1090A ARG* 3.7 23.3 - - + +
1093A ASP 4.5 1.1 - - - +
1094A ARG* 1.3 83.2 - - - +
1096A HIS* 1.3 65.8 + - - +
1097A ILE* 3.6 32.8 - - + -
1157A ILE* 6.1 1.6 - - + -
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Residues in contact with HIS1096 (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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955A TRP* 3.8 10.2 - - + +
976A MET* 5.4 1.1 - - - -
977A LEU 3.6 3.8 - - - -
978A GLU* 3.8 16.1 + - + +
979A SER 5.7 0.2 - - - -
1087A LEU 3.8 0.7 - - - +
1088A PHE* 3.6 1.0 - - - -
1089A CYS* 2.9 53.1 + - + +
1091A TYR* 4.4 10.5 - - + +
1094A ARG* 4.3 27.9 - - + +
1095A ILE* 1.3 81.5 + - - +
1097A ILE* 1.3 64.1 + - - +
1188A ASN 3.5 24.9 + - - -
1189A MET* 3.4 47.3 - - + +
1190A CYS 4.4 4.6 + - - -
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Residues in contact with ILE1097 (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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955A TRP* 4.7 0.4 - - - -
975A VAL 3.7 0.7 - - - +
976A MET* 3.1 9.6 - - - +
977A LEU* 2.9 48.8 + - + +
1052A VAL* 4.5 13.9 - - + -
1053A LEU* 5.8 0.7 - - + -
1085A ILE* 4.9 7.2 - - + -
1087A LEU 3.4 7.0 - - - +
1088A PHE* 3.4 28.0 - - + -
1095A ILE* 3.6 23.3 - - + -
1096A HIS* 1.3 76.6 - - - +
1098A PHE* 1.3 63.1 + - - +
1099A PHE* 3.3 37.2 - - + -
1157A ILE* 4.6 16.4 - - + -
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Residues in contact with PHE1098 (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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955A TRP* 4.3 3.6 - - + -
959A ILE* 4.0 14.8 - - + -
962A LEU* 3.4 31.9 - - + -
965A VAL* 4.0 23.3 - - + -
966A TRP* 5.8 0.2 - + - -
974A ASN* 4.0 24.5 - - + -
975A VAL 3.5 7.0 - - - -
976A MET* 3.6 25.4 - - + -
1086A ARG* 3.0 34.0 + - + +
1087A LEU* 2.8 30.3 + - + +
1097A ILE* 1.3 75.2 - - - +
1099A PHE* 1.3 72.2 + - - +
1100A ARG* 5.1 2.5 - - + -
1185A LEU* 3.8 24.2 - - + -
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Residues in contact with PHE1099 (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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974A ASN* 3.2 9.5 - - - +
975A VAL* 2.8 41.8 + - + +
977A LEU* 5.2 1.6 - - + -
1084A PRO* 3.7 3.8 - - + -
1085A ILE* 3.3 42.0 - - + -
1097A ILE* 3.3 24.0 - - + -
1098A PHE* 1.3 83.2 - - - +
1100A ARG* 1.3 59.7 + - - +
1101A PHE* 3.4 33.9 - + + -
1153A VAL* 3.3 37.5 - - + -
1156A ASP* 5.8 2.2 - - - -
1157A ILE* 3.6 25.6 - - + -
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Residues in contact with ARG1100 (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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963A GLN 4.7 3.6 + - - -
964A ASP* 2.7 26.6 + - - +
965A VAL* 2.5 33.7 + - - +
966A TRP 4.8 0.6 - - - -
967A GLU* 3.1 23.8 + - - +
972A GLU* 3.4 32.9 - - - +
973A CYS 4.7 1.2 - - - +
974A ASN* 2.7 32.9 + - - +
1083A HIS 4.7 0.5 - - - +
1084A PRO* 3.1 28.1 + - - +
1086A ARG* 3.5 47.9 + - + +
1098A PHE* 5.1 3.1 - - + -
1099A PHE* 1.3 73.6 - - - +
1101A PHE* 1.3 67.3 + - - +
1102A THR* 4.4 1.3 + - + +
1105A GLU* 4.2 2.3 - - - +
1178A TYR* 5.1 2.2 - - - -
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Residues in contact with PHE1101 (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 GLU* 3.3 8.8 - - - +
973A CYS* 2.9 45.5 + - + +
975A VAL* 4.1 9.2 - - + -
1084A PRO* 3.4 27.4 - - + -
1099A PHE* 3.4 45.1 - + + -
1100A ARG* 1.3 82.1 - - - +
1102A THR* 1.3 70.3 + - - +
1105A GLU* 4.0 17.9 - - + -
1106A ALA* 4.1 11.4 - - + -
1109A LEU* 3.4 28.9 - - + -
1149A LEU* 4.7 8.1 - - + -
1153A VAL* 4.1 13.2 - - + -
188P TRP* 5.0 2.7 - + - -
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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