Contacts of the strand formed by residues 1099 - 1105 (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 SER1099 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037B VAL* 3.6 4.9 - - - +
1038B ASP* 2.9 27.4 + - - +
1090B ARG* 4.0 18.1 + - - +
1091B SER 3.4 6.6 + - - -
1092B HIS* 5.3 0.9 - - - -
1097B GLU* 3.2 12.9 + - - -
1098B VAL* 1.3 76.0 - - - +
1100B ILE* 1.3 63.1 + - - +
1101B TYR* 3.9 22.7 - - - -
1264B LYS* 3.0 30.9 + - - +
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Residues in contact with ILE1100 (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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1035B GLU* 4.3 26.5 - - + +
1036B TRP 3.6 4.0 - - - +
1037B VAL* 3.8 26.7 - - + +
1089B GLY 3.8 0.9 - - - +
1090B ARG* 3.7 2.1 - - - -
1091B SER* 2.7 41.2 + - - +
1092B HIS 4.6 0.9 - - - +
1093B GLY* 3.5 25.4 - - - -
1094B GLU* 4.1 15.0 - - - +
1099B SER* 1.3 79.2 - - - +
1101B TYR* 1.3 70.5 + - - +
1102B SER* 4.8 3.3 + - - -
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Residues in contact with TYR1101 (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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1035B GLU* 3.4 1.6 - - - -
1036B TRP* 2.9 62.5 + + + +
1038B ASP* 3.4 43.0 + - + -
1050B TYR* 3.7 15.4 - + - -
1073B PHE* 3.5 30.5 - + + -
1089B GLY 3.5 2.0 - - - -
1090B ARG* 3.5 33.0 - - + +
1099B SER* 4.0 7.2 - - - -
1100B ILE* 1.3 78.5 - - - +
1102B SER* 1.3 62.6 + - - +
1263B LEU* 3.5 38.9 - - + +
1264B LYS* 3.9 10.9 + - - +
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Residues in contact with SER1102 (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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1033B SER* 6.5 0.4 - - - -
1034B LEU 3.2 14.6 - - - -
1035B GLU* 4.3 11.9 - - - +
1036B TRP* 4.6 4.3 - - - -
1073B PHE* 3.9 3.3 - - - -
1088B ALA* 3.3 5.1 - - - +
1089B GLY* 2.8 47.7 + - - +
1100B ILE* 4.8 4.4 + - - -
1101B TYR* 1.3 77.0 - - - +
1103B VAL* 1.3 62.0 + - - +
1245B LEU* 5.3 5.4 + - - +
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Residues in contact with VAL1103 (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 VAL 4.4 0.3 - - - +
1033B SER* 3.5 1.9 - - - -
1034B LEU* 2.8 41.1 + - + +
1036B TRP* 3.8 12.1 - - + -
1052B LEU* 3.7 30.1 - - + -
1077B LEU* 4.0 20.0 - - + -
1086B VAL* 3.4 29.8 - - + -
1087B ALA 3.3 8.1 - - - +
1088B ALA* 4.2 0.4 - - - +
1102B SER* 1.3 75.6 - - - +
1104B ILE* 1.3 64.0 + - - +
1105B PHE* 4.2 16.6 - - + -
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Residues in contact with ILE1104 (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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1025B VAL* 5.6 0.9 - - + -
1031B VAL* 4.2 11.0 - - + -
1032B VAL 3.5 11.2 - - - +
1033B SER* 3.7 18.8 - - - +
1085B CYS 3.6 1.0 - - - +
1086B VAL* 3.3 6.9 - - - +
1087B ALA* 2.8 42.4 + - + +
1103B VAL* 1.3 74.9 - - - +
1105B PHE* 1.3 66.6 + - - +
1106B LYS* 3.9 13.5 + - + +
1242B VAL* 6.3 0.2 - - + -
1244B TYR* 3.6 39.0 - - + -
1275B VAL* 3.7 27.8 - - + -
1277B MET* 4.4 6.1 - - + -
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Residues in contact with PHE1105 (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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1030B THR 4.2 0.8 - - - -
1031B VAL* 3.3 6.9 - - - +
1032B VAL 2.7 41.8 + - - +
1034B LEU* 4.1 13.0 - - + -
1052B LEU* 3.5 31.2 - - + -
1054B HIS* 3.7 35.0 - + - -
1071B LEU* 4.4 4.5 - - + -
1085B CYS 3.5 2.7 - - - -
1086B VAL* 3.8 24.5 - - + -
1103B VAL* 4.2 14.4 - - + -
1104B ILE* 1.3 74.9 - - - +
1106B LYS* 1.3 60.9 + - - +
1107B CYS 3.8 0.4 - - - +
1108B LEU* 3.8 27.1 - - + -
1116B PHE* 3.5 32.3 - + - -
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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