Contacts of the strand formed by residues 1085 - 1089 (chain A) in PDB entry 1HKN
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 PHE1085 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1053A GLU* 3.4 4.3 - - - -
1054A VAL* 2.8 39.6 + - + +
1056A ILE* 4.4 14.1 - - + -
1065A LEU* 3.2 34.3 - - + -
1066A ALA* 3.7 25.6 - - - -
1067A MET* 4.1 7.4 - - + -
1073A LEU* 4.7 0.7 - - + -
1082A GLU 4.0 4.3 - - - -
1083A CYS 3.2 23.6 - - - -
1084A LEU* 1.3 73.8 - - - +
1086A LEU* 1.3 65.8 + - - +
1087A GLU 3.5 0.7 + - - -
1097A TYR* 4.4 20.2 - - + -
1098A ILE 3.3 17.0 - - - +
1099A SER* 3.7 20.2 - - - -
1100A LYS 4.2 0.2 - - - +
1109A VAL* 3.4 32.3 - - + -
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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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1052A GLY 3.3 2.5 - - - +
1053A GLU* 4.0 32.3 - - + +
1085A PHE* 1.3 71.3 - - - +
1087A GLU* 1.3 64.5 + - - +
1088A ARG* 3.5 23.8 + - - +
1096A THR 3.4 5.2 - - - +
1097A TYR* 4.5 1.1 - - - -
1098A ILE* 2.7 55.2 + - + +
1100A LYS* 4.1 20.4 - - + -
1103A ALA* 3.9 22.7 - - + -
6092F ASN* 4.0 22.2 - - + +
6093F HIS* 4.3 5.8 - - + +
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Residues in contact with GLU1087 (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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1012A LYS* 5.6 1.4 + - - -
1046A LEU* 3.5 13.3 - - - +
1052A GLY* 2.7 23.1 + - - +
1054A VAL* 4.1 20.9 - - + +
1085A PHE 3.5 2.2 + - - -
1086A LEU* 1.3 70.4 - - - +
1088A ARG* 1.3 79.7 + - - +
1089A LEU 4.3 0.6 + - - +
1095A ASN* 3.4 21.8 - - - +
1096A THR 3.6 4.5 - - - -
1097A TYR* 2.7 42.1 + - + -
1134A PRO* 5.6 0.9 - - - +
6133F LEU* 4.9 2.4 - - - +
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Residues in contact with ARG1088 (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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1051A VAL 5.4 0.2 + - - -
1052A GLY* 3.0 27.9 + - - -
1053A GLU* 6.0 0.4 - - - +
1086A LEU* 3.9 28.7 - - + +
1087A GLU* 1.3 94.4 + - - +
1089A LEU* 1.3 66.0 + - - +
1090A GLU* 3.6 6.2 + - - +
1095A ASN* 3.4 4.1 - - - -
1096A THR* 2.8 49.0 + - - +
1098A ILE* 5.1 2.9 - - + -
6089F LEU* 6.0 0.7 - - + -
6092F ASN 3.1 23.2 + - - -
6093F HIS* 2.8 39.0 + - + +
6094F TYR* 4.2 14.1 + - - -
6095F ASN* 5.8 0.7 - - - -
6133F LEU* 3.3 26.6 - - - +
6134F PRO* 5.6 3.8 - - - -
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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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1087A GLU 4.3 0.6 - - - -
1088A ARG* 1.3 75.4 - - - +
1090A GLU* 1.3 72.1 + - - +
1091A GLU* 5.5 0.7 - - - +
1093A HIS* 3.5 52.9 - - + +
1094A TYR 3.6 2.5 - - - +
1095A ASN* 3.2 16.2 - - - +
6012F LYS* 4.1 17.1 + - - +
6134F PRO* 3.7 31.5 + - + +
6135F LEU* 3.7 33.7 - - - +
6136F PRO* 3.7 19.1 - - + -
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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