Contacts of the strand formed by residues 1086 - 1090 (chain A) in PDB entry 7CN9
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 LYS1086 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1082A CYS* 3.9 0.7 - - - -
1084A ASP* 3.1 42.7 + - + +
1085A GLY* 1.3 76.8 - - - +
1087A ALA* 1.3 61.2 + - - +
1088A HIS* 2.7 38.2 - - - -
1117A THR* 5.6 2.2 + - - -
1122A VAL* 3.2 38.8 - - + +
1124A GLY 5.1 2.5 - - - -
1125A ASN* 5.3 0.9 - - - +
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Residues in contact with ALA1087 (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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1080A ALA* 5.2 1.3 - - + -
1081A ILE 3.3 7.4 - - - +
1082A CYS* 3.6 24.5 - - - -
1085A GLY 3.7 2.4 + - - -
1086A LYS* 1.3 71.4 - - - +
1088A HIS* 1.3 60.1 + - - +
1089A PHE* 3.2 39.2 + - + -
1122A VAL* 3.9 3.5 - - - -
1123A SER 3.9 10.9 + - - -
1124A GLY 3.9 11.5 + - - +
1126A CYS* 3.7 13.9 - - + +
1132A ILE* 5.4 0.2 - - + -
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Residues in contact with HIS1088 (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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1080A ALA* 4.2 0.7 - - - -
1081A ILE* 2.9 24.4 + - + +
1083A HIS* 3.8 11.8 - - + +
1084A ASP* 4.0 10.4 + - - -
1086A LYS* 2.7 48.8 + - - -
1087A ALA* 1.3 68.3 - - - +
1089A PHE* 1.3 60.7 + - - +
1095A PHE* 3.4 17.5 - - - -
1115A ILE* 5.1 2.0 - - + +
1117A THR* 5.6 5.0 + - - -
1120A THR* 3.3 24.7 - - + +
1121A PHE 3.7 2.9 - - - -
1122A VAL* 3.3 14.3 - - - +
1137A VAL* 3.3 48.1 - - + +
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Residues in contact with PHE1089 (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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1080A ALA* 3.1 24.2 - - + -
1087A ALA* 3.2 35.4 - - + -
1088A HIS* 1.3 73.5 - - - +
1090A PRO* 1.4 70.5 - - + +
1095A PHE* 3.6 2.0 - - - -
1120A THR* 2.1 36.6 + - - -
1121A PHE* 3.3 26.1 + + + +
1123A SER 2.7 34.5 - - - -
1124A GLY* 3.8 2.7 - - - -
1129A VAL* 3.8 25.4 - - + -
913B GLN* 5.7 2.5 - - + -
914B ASN* 4.7 17.3 - - + -
917B TYR* 3.3 39.0 - + + -
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Residues in contact with PRO1090 (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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1079A PRO 4.3 7.6 - - - +
1089A PHE* 1.4 92.0 - - + +
1091A ARG* 1.3 68.2 + - - +
1092A GLU* 3.3 2.9 + - - +
1093A GLY 3.6 32.7 + - - +
1094A VAL* 4.2 8.1 - - + +
1095A PHE* 3.4 34.5 - - + -
1104A VAL* 5.1 4.3 - - + -
1119A ASN 4.3 4.9 - - - +
1121A PHE* 3.9 7.3 - - - -
900B MET* 5.4 2.2 - - + -
913B GLN* 4.8 17.9 + - - +
917B TYR* 6.0 1.3 - - + -
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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