Contacts of the strand formed by residues 1086 - 1089 (chain B) in PDB entry 5JHN
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 LEU1086 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1067B TYR* 4.3 1.1 + - - -
1072B ILE* 4.0 15.3 - - + -
1077B ALA* 4.0 14.4 - - + +
1080B ARG* 4.9 3.8 - - + -
1082B ASP 4.6 2.2 - - - +
1083B ASP* 3.8 25.5 + - + -
1084B SER 3.8 1.4 - - - -
1085B TYR* 1.3 80.1 - - - +
1087B PHE* 1.3 61.6 + - - +
1098B CYS* 4.9 1.6 - - + -
1099B ILE 3.4 3.4 - - - +
1100B ASP* 3.5 38.6 - - + +
1158B PHE* 5.6 0.7 - - - -
6G THR* 3.8 15.5 - - + +
7G ALA 3.3 24.7 + - - +
8G ARG* 3.6 12.9 - - + +
9G ALA* 2.8 29.1 + - - +
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Residues in contact with PHE1087 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067B TYR* 3.6 42.2 - + + -
1086B LEU* 1.3 74.6 - - - +
1088B ASP* 1.3 83.5 + - - +
1089B LEU* 3.5 1.9 + - + +
1098B CYS* 3.2 4.6 - - - -
1099B ILE* 2.8 38.1 + - + +
1121B PRO* 4.0 10.3 - - + -
1136B ILE* 3.8 43.3 - - + -
1138B PHE* 4.4 4.7 - + - -
1152B PHE* 3.7 24.9 - + - -
9G ALA* 3.4 17.5 - - + -
10G SER* 3.9 22.2 - - - -
11G THR* 3.9 5.8 - - + -
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Residues in contact with ASP1088 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087B PHE* 1.3 89.3 - - - +
1089B LEU* 1.3 60.0 + - - +
1090B ASP 3.3 18.1 + - - +
1096B VAL* 4.5 4.9 - - + -
1097B TYR 4.1 2.0 - - - -
1098B CYS* 3.1 11.7 - - - -
1123B ARG* 4.4 4.0 + - - -
1157B ARG* 3.9 14.7 + - - +
4G LYS* 3.6 24.3 + - - -
8G ARG* 3.0 43.1 + - - +
9G ALA 2.8 15.1 + - - +
10G SER* 4.3 13.8 - - - -
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Residues in contact with LEU1089 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071B LEU* 4.2 16.6 - - + -
1087B PHE* 4.3 2.9 - - + +
1088B ASP* 1.3 72.8 - - - +
1090B ASP* 1.3 71.9 + - - +
1096B VAL* 3.6 7.6 - - - +
1097B TYR* 2.9 34.7 + - + +
1098B CYS* 4.2 5.2 - - - +
1099B ILE* 3.8 16.4 - - + -
1123B ARG* 4.8 1.1 - - - +
1132B ARG 3.9 18.4 - - - +
1133B PHE* 4.2 17.3 - - + -
1134B PRO* 3.7 37.9 - - + +
1136B ILE* 3.7 26.5 - - + -
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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