Contacts of the strand formed by residues 1086 - 1092 (chain B) in PDB entry 5J67
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
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Residue Dist Surf HB Arom Phob DC
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1054B HIS* 5.6 1.8 - - - +
1071B LEU* 4.4 9.9 - - + -
1077B LEU* 3.4 32.4 - - + +
1082B GLY* 3.9 11.1 + - - +
1083B THR* 3.6 24.3 + - - +
1084B SER 5.3 0.9 - - - -
1085B CYS* 1.3 87.6 - - + +
1087B ALA* 1.3 65.0 + - - +
1103B VAL* 3.4 21.8 - - + -
1104B ILE 3.3 5.4 - - - +
1105B PHE* 3.8 29.2 - - + -
1106B LYS* 5.6 0.2 - - - -
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Residues in contact with ALA1087 (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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1077B LEU* 5.1 2.9 - - - -
1083B THR* 4.9 1.8 - - + -
1086B VAL* 1.3 76.0 - - - +
1088B ALA* 1.3 60.4 + - - +
1103B VAL* 3.3 4.8 - - - +
1104B ILE* 2.8 39.2 + - + +
1106B LYS* 4.8 4.7 - - - +
1244B TYR* 3.4 35.4 - - + +
1245B LEU 5.0 0.2 - - - -
1246B PHE* 3.7 21.3 - - + -
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Residues in contact with ALA1088 (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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1073B PHE* 3.6 28.7 - - + -
1077B LEU* 3.7 34.0 + - + +
1078B LEU* 4.6 5.2 - - + -
1087B ALA* 1.3 73.7 - - - +
1089B GLY* 1.3 59.9 + - - +
1102B SER* 3.3 6.7 - - - +
1103B VAL* 4.2 0.9 - - - +
1245B LEU 3.0 17.6 - - - +
1246B PHE* 3.5 2.7 - - - -
1247B CYS* 3.0 20.9 + - - +
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Residues in contact with GLY1089 (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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1073B PHE* 4.0 6.8 - - - -
1088B ALA* 1.3 77.3 - - - +
1090B ARG* 1.3 59.1 - - - +
1091B SER* 5.7 0.2 - - - -
1100B ILE 3.8 0.4 - - - +
1101B TYR* 3.5 2.6 - - - -
1102B SER* 2.8 50.3 + - - +
1245B LEU* 4.0 11.9 - - - -
1247B CYS* 3.8 15.0 - - - -
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Residues in contact with ARG1090 (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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1073B PHE* 5.3 2.5 - - + -
1078B LEU* 5.8 2.2 - - + +
1089B GLY* 1.3 74.5 - - - +
1091B SER* 1.3 65.1 + - - +
1099B SER* 4.0 22.5 + - - +
1100B ILE 3.7 3.4 - - - +
1101B TYR* 3.5 39.2 + - + +
1245B LEU* 3.2 15.7 - - - +
1247B CYS* 3.9 6.1 - - - +
1263B LEU* 2.9 32.3 + - - +
1264B LYS* 3.3 20.8 + - - +
1266B THR* 3.0 24.2 + - - -
1267B LYS* 5.2 0.2 - - - +
1268B ILE* 3.4 38.2 - - + +
1270B CYS* 4.2 8.5 - - - -
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Residues in contact with SER1091 (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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1089B GLY 5.7 0.2 - - - -
1090B ARG* 1.3 78.8 - - - +
1092B HIS* 1.3 71.3 + - - +
1099B SER* 3.4 5.2 - - - -
1100B ILE* 2.7 48.1 + - - -
1245B LEU* 4.4 11.1 - - - +
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Residues in contact with HIS1092 (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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1091B SER* 1.3 81.5 + - - +
1093B GLY* 1.3 64.6 + - - +
1096B PRO* 4.2 18.2 - - + +
1097B GLU* 3.1 38.3 + - - -
1098B VAL 4.3 2.5 - - - -
1099B SER* 5.3 0.9 - - - -
1100B ILE* 4.6 1.4 - - - +
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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