Contacts of the helix formed by residues 1086 - 1094 (chain J) in PDB entry 3F5P
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 ASP1086 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10J 741 5.6 0.4 - - - -
1084J ARG 4.4 0.2 - - - +
1085J GLY* 1.3 74.9 - - - -
1087J LEU* 1.3 63.1 + - - +
1088J LYS* 2.7 19.5 + - - +
1089J SER* 2.7 47.8 + - - -
1090J TYR* 3.0 19.6 + - - +
1139J ARG* 3.8 18.4 - - - +
1141J CYS 3.2 13.2 - - - +
1142J MET* 4.1 8.9 - - - -
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Residues in contact with LEU1087 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085J GLY 3.8 1.6 + - - -
1086J ASP* 1.3 71.2 - - - +
1088J LYS* 1.3 57.5 + - - +
1090J TYR* 4.2 3.1 - - + -
1091J LEU* 2.9 47.2 + - + +
1115J MET* 4.1 19.3 - - + -
1119J ILE* 3.9 27.6 - - + -
1138J ALA* 3.4 26.0 + - + +
1141J CYS* 2.9 25.4 + - + -
1143J VAL* 3.8 16.1 - - + +
1149J VAL* 3.8 26.2 - - + -
1201J VAL* 5.2 0.7 - - + -
1205J ILE* 4.4 15.0 - - + -
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Residues in contact with LYS1088 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086J ASP* 2.7 16.4 + - - +
1087J LEU* 1.3 75.7 - - - +
1089J SER* 1.3 64.8 + - - +
1091J LEU* 3.4 0.4 + - - -
1092J ARG* 3.0 55.8 + - - +
1138J ALA* 3.4 8.6 + - - -
1139J ARG* 3.7 29.8 - - + +
1178J TRP* 5.3 10.1 - - - -
1204J GLU* 4.3 16.3 + - - +
1209J ALA* 3.5 22.1 + - + +
1210J GLU 5.6 2.6 + - - -
1211J GLN* 6.1 1.8 - - - +
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Residues in contact with SER1089 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J 741 6.0 6.7 - - - -
1084J ARG 6.0 1.1 - - - -
1086J ASP* 2.7 36.6 + - - -
1088J LYS* 1.3 76.0 - - - +
1090J TYR* 1.3 63.8 + - - +
1092J ARG* 2.9 19.8 + - - +
1093J SER* 3.0 13.9 + - - -
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Residues in contact with TYR1090 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084J ARG* 4.2 29.8 + - + +
1086J ASP 3.0 17.3 + - - +
1087J LEU* 3.7 11.9 - - + +
1089J SER* 1.3 78.1 - - - +
1091J LEU* 1.3 65.7 + - + +
1093J SER* 2.7 28.4 + - - -
1094J LEU* 3.5 37.9 + - + +
1115J MET* 3.7 24.0 - - + +
1143J VAL* 4.1 21.8 - - + -
1147J PHE* 3.3 41.3 - + - -
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Residues in contact with LEU1091 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087J LEU* 2.9 44.4 + - + +
1088J LYS 3.7 4.5 - - - +
1090J TYR* 1.3 81.2 - - + +
1092J ARG* 1.3 61.8 + - - +
1094J LEU* 3.4 18.7 + - + +
1107J PRO* 5.3 1.8 - - + -
1115J MET* 4.6 8.5 - - + -
1138J ALA* 4.5 9.4 - - + -
1204J GLU 3.5 25.4 - - - +
1205J ILE* 3.7 32.5 - - + -
1208J LEU* 3.4 48.4 - - + +
1209J ALA* 4.0 7.0 - - + +
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Residues in contact with ARG1092 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088J LYS* 3.0 49.7 + - - +
1089J SER* 2.9 15.3 + - - +
1091J LEU* 1.3 75.5 - - - +
1093J SER* 1.3 55.3 + - - +
1094J LEU 2.9 6.4 + - - -
1095J ARG* 2.7 65.4 + - - +
1208J LEU 3.7 6.5 - - - -
1209J ALA* 3.3 16.8 + - + +
1210J GLU* 5.7 0.4 - - - +
1211J GLN 6.0 0.6 - - - +
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Residues in contact with SER1093 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089J SER 3.0 9.0 + - - -
1090J TYR* 2.7 33.5 + - - -
1092J ARG* 1.3 75.7 - - - +
1094J LEU* 1.3 62.3 + - - +
1095J ARG 3.2 8.4 + - - +
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Residues in contact with LEU1094 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090J TYR* 3.6 47.1 - - + +
1091J LEU* 3.5 14.4 - - + +
1092J ARG 2.9 1.2 - - - -
1093J SER* 1.3 82.2 - - - +
1095J ARG* 1.3 63.0 + - - +
1096J PRO* 4.0 2.3 - - - +
1107J PRO* 3.6 33.9 - - + -
1115J MET* 5.9 0.9 - - + -
1208J LEU* 3.5 20.6 - - + +
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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