Contacts of the strand formed by residues 1084 - 1089 (chain A) in PDB entry 1SIW
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 LYS1084 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1074A ILE* 5.8 2.0 - - - -
1082A GLN* 4.4 2.9 - - - +
1083A GLU* 1.3 77.9 - - - +
1085A ALA* 1.3 70.3 + - - +
1086A LEU* 3.7 14.1 + - + +
1122A ALA 5.5 0.2 - - - -
1123A ASP* 3.1 28.7 + - - +
1126A ASP* 2.7 35.1 + - + +
1127A LEU* 3.6 26.2 - - + -
1222A VAL 3.6 0.5 - - - +
1223A VAL* 3.5 4.4 - - - +
1224A VAL* 2.8 37.5 + - - +
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Residues in contact with ALA1085 (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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441A HIS* 5.0 13.0 - - + +
1070A VAL* 4.0 26.2 - - + -
1074A ILE* 5.7 2.7 - - + +
1084A LYS* 1.3 78.5 - - - +
1086A LEU* 1.3 69.2 + - - +
1221A PHE* 4.4 15.0 - - + -
1222A VAL 3.3 8.7 - - - +
1223A VAL* 4.4 1.1 - - - +
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Residues in contact with LEU1086 (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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1084A LYS* 4.2 18.2 - - + +
1085A ALA* 1.3 82.4 - - - +
1087A ASN* 1.3 67.0 + - - +
1088A PHE 3.4 0.2 + - - -
1119A LEU* 3.9 22.7 - - + -
1123A ASP* 3.5 39.0 - - + +
1127A LEU* 5.0 6.1 - - + -
1157A GLY* 3.8 18.8 - - - +
1158A MET 4.9 1.3 - - - +
1159A THR* 4.4 9.4 - - + -
1221A PHE* 3.3 9.6 - - - -
1222A VAL* 2.9 35.6 + - - +
1224A VAL* 3.9 24.9 - - + -
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Residues in contact with ASN1087 (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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299A GLN* 3.4 36.6 + - - +
442A PHE* 4.7 3.7 - - - -
547A TRP* 3.6 10.8 - - - -
1086A LEU* 1.3 69.1 - - - +
1088A PHE* 1.3 61.4 + - - +
1089A LEU* 3.6 7.4 + - - +
1157A GLY 3.0 18.3 + - - +
1158A MET* 3.6 1.8 - - + +
1159A THR* 2.9 30.9 + - - +
1218A ARG 3.0 18.1 + - - -
1219A ASP* 3.9 1.2 + - - +
1220A GLU 2.9 21.5 + - - -
1221A PHE* 3.5 31.9 - - + -
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Residues in contact with PHE1088 (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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1086A LEU 3.4 1.0 + - - -
1087A ASN* 1.3 69.7 - - - +
1089A LEU* 1.3 67.6 + - - +
1090A THR* 3.5 20.7 + - + +
1117A VAL* 5.1 5.6 - - + -
1137A VAL* 4.1 12.6 - - + -
1144A LEU* 4.0 19.1 - - + -
1159A THR* 3.5 20.9 - - + -
1161A MET* 3.8 34.5 - - + -
1184A HIS* 3.8 9.2 - - + -
1187A VAL* 3.5 24.9 - - + -
1188A THR* 5.1 7.6 - - + -
1217A ASN 4.2 10.6 - - - +
1218A ARG* 4.0 4.5 - - - +
1220A GLU* 2.9 26.3 + - + +
1222A VAL* 3.7 27.1 - - + -
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Residues in contact with LEU1089 (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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282A PRO* 5.4 3.4 - - + -
299A GLN* 4.4 11.2 - - + -
547A TRP* 3.9 7.2 - - + -
1087A ASN* 3.6 17.0 - - - +
1088A PHE* 1.3 73.1 - - - +
1090A THR* 1.3 65.4 + - - +
1091A PRO* 3.5 10.1 - - + -
1158A MET* 3.6 37.9 - - + -
1159A THR 2.9 15.2 + - - +
1160A MET* 3.1 11.9 - - + +
1161A MET 3.0 24.1 + - - -
1218A ARG* 3.5 49.1 - - + +
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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