Contacts of the strand formed by residues 1086 - 1093 (chain B) in PDB entry 1CJY
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 VAL1086 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049B PHE 3.5 9.2 - - - +
1050B ILE* 3.7 16.7 - - - +
1051B SER* 4.6 9.0 + - - +
1052B THR* 4.8 0.6 + - + -
1084B GLU* 3.6 14.7 + - + +
1085B ASN* 1.3 77.2 - - - +
1087B LEU* 1.3 62.4 + - - +
1088B GLU* 3.5 16.6 + - + +
1106B THR* 4.1 14.1 - - - +
1107B PHE 3.6 3.8 - - - +
1108B THR* 4.0 23.1 - - + +
1109B VAL* 5.4 0.2 - - - -
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Residues in contact with LEU1087 (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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1020B PHE* 4.0 13.5 - - + -
1022B VAL* 3.9 29.4 - - + -
1048B LEU* 4.0 26.9 - - + -
1049B PHE 3.6 5.6 - - - +
1050B ILE* 3.6 26.7 - - + -
1077B PHE* 4.3 6.3 - - + -
1085B ASN 4.2 0.6 + - - -
1086B VAL* 1.3 72.0 - - - +
1088B GLU* 1.3 59.7 + - - +
1089B ILE* 3.7 21.8 + - + +
1106B THR* 3.3 8.4 + - - -
1107B PHE* 2.7 38.9 + - + +
1109B VAL* 5.0 1.0 - - - +
1134B MET* 4.0 20.6 - - + -
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Residues in contact with GLU1088 (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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1047B GLU 3.6 1.3 - - - +
1048B LEU* 3.4 5.9 - - - -
1049B PHE* 2.7 75.2 + - + +
1051B SER* 4.6 8.3 + - - -
1086B VAL* 4.3 15.5 - - + +
1087B LEU* 1.3 76.1 - - - +
1089B ILE* 1.3 60.9 + - - +
1090B THR* 4.9 4.9 - - - +
1104B THR* 5.5 9.0 - - + +
1105B ALA 3.7 6.1 - - - +
1106B THR* 4.8 3.4 - - - +
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Residues in contact with ILE1089 (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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1046B VAL* 3.8 22.7 - - + -
1047B GLU 3.6 2.0 - - - -
1048B LEU* 4.0 6.7 - - + -
1087B LEU* 3.8 25.8 - - + +
1088B GLU* 1.3 75.0 - - - +
1090B THR* 1.3 66.9 + - - +
1103B GLY 3.9 0.3 - - - +
1104B THR* 3.4 4.7 - - - +
1105B ALA* 2.8 40.4 + - + +
1106B THR 4.3 4.5 - - - +
1107B PHE* 4.2 7.4 - - + -
1122B PHE* 3.6 39.5 - - + -
1124B PHE* 4.3 5.5 - - + -
1130B MET* 4.0 18.8 - - - -
1132B LEU* 3.8 15.0 - - + -
1134B MET* 4.6 0.2 - - + -
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Residues in contact with THR1090 (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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1046B VAL* 3.3 9.2 - - - +
1047B GLU* 2.9 53.0 + - - +
1088B GLU* 4.9 3.8 - - - +
1089B ILE* 1.3 80.8 + - - +
1091B LEU* 1.3 63.3 + - - +
1092B MET* 3.3 32.7 + - - +
1101B THR* 3.7 12.1 - - - +
1103B GLY 3.4 12.3 - - - +
1104B THR* 4.4 11.6 + - - +
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Residues in contact with LEU1091 (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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1027B ALA* 5.6 0.7 - - + -
1030B VAL* 4.2 20.6 - - + -
1044B PRO* 3.9 27.1 - - + -
1045B TYR 3.8 5.8 - - - +
1071B TRP* 4.5 6.5 - - + -
1089B ILE 4.3 0.2 - - - -
1090B THR* 1.3 70.5 - - - +
1092B MET* 1.3 65.4 + - - +
1101B THR* 3.7 3.6 - - - -
1102B LEU* 2.9 38.6 + - + -
1103B GLY 3.0 17.4 + - - +
1124B PHE* 4.3 27.2 - - + -
1128B THR* 4.2 21.1 - - + +
1130B MET* 3.5 27.4 - - + -
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Residues in contact with MET1092 (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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1044B PRO* 3.2 27.2 - - - +
1045B TYR* 2.9 60.9 + - + +
1047B GLU* 4.4 13.2 - - + +
1090B THR* 3.3 35.7 - - + +
1091B LEU* 1.3 75.5 - - - +
1093B ASP* 1.3 61.6 + - - +
1094B ALA 4.0 0.4 - - - -
1099B ASP* 3.9 20.4 - - + +
1100B GLU 3.3 11.7 - - - +
1101B THR* 3.6 17.5 - - + +
1102B LEU* 4.5 4.2 - - - +
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Residues in contact with ASP1093 (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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1032B LYS* 2.7 33.5 + - - +
1042B PRO* 4.2 2.0 - - - -
1043B ASP 2.8 26.7 + - - +
1045B TYR* 4.5 0.2 - - - -
1092B MET* 1.3 72.6 - - - +
1094B ALA* 1.3 64.1 + - - +
1095B ASN* 3.2 12.0 + - - +
1099B ASP* 3.2 3.2 - - - -
1100B GLU* 2.7 43.2 + - + +
1102B LEU* 4.1 21.5 - - + -
1951B CA 2.5 24.6 - - - -
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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