Contacts of the strand formed by residues 1087 - 1094 (chain B) in PDB entry 6X34
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 ARG1087 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086B GLY* 1.3 74.3 - - - +
1088B TRP* 1.3 61.4 + - - +
1153B ILE* 3.3 18.2 - - - +
1154B ASP* 4.4 8.5 - - + -
1156B THR* 6.2 0.2 - - - +
1221B GLU 5.5 2.5 - - - +
1222B GLY 4.8 2.9 - - - +
1223B PHE* 3.7 25.4 - - + +
1224B GLU* 3.1 20.4 + - - +
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Residues in contact with TRP1088 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083B VAL* 5.9 4.5 - - + -
1087B ARG* 1.3 75.6 - - - +
1089B TYR* 1.3 61.5 + - - +
1104B TRP* 3.5 23.3 - - + -
1152B MET* 3.3 26.2 - - - +
1153B ILE* 3.6 10.1 + - + +
1223B PHE* 3.7 6.4 - - - +
1224B GLU 3.2 11.0 - - - +
1226B PHE* 3.9 27.6 - - + -
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Residues in contact with TYR1089 (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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1088B TRP* 1.3 76.6 - - - +
1090B PHE* 1.3 60.1 + - - +
1091B GLU* 3.8 18.2 + - + +
1104B TRP* 4.2 1.6 - - - -
1150B GLY* 4.4 13.7 - - - -
1151B CYS 3.3 13.9 - - - -
1152B MET* 4.3 10.5 - - + -
1163B THR* 4.3 22.8 - - + +
1203B ASN* 5.2 1.9 - - - +
1204B LEU 5.3 5.0 - - - +
1205B GLY* 5.5 1.9 + - - -
1211B LEU* 3.6 33.6 - - + +
1212B ARG 5.8 1.1 - - - -
1213B PHE* 3.7 22.6 + - - +
1214B PHE* 3.6 42.0 - + + -
1218B GLY* 5.9 1.6 - - - -
1223B PHE* 4.3 6.1 - - + +
1224B GLU 3.7 3.8 + - - -
1225B PRO* 4.4 9.5 - - + +
1226B PHE* 4.7 11.4 + - - +
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Residues in contact with PHE1090 (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 TYR* 1.3 74.3 - - - +
1091B GLU* 1.3 67.0 + - - +
1092B PHE* 3.7 13.5 - + + -
1102B VAL* 3.5 32.5 - - + -
1103B GLY* 5.1 4.3 - - - -
1104B TRP* 3.6 26.7 - + + -
1150B GLY* 3.3 2.8 - - - -
1151B CYS* 2.5 50.1 + - + +
1190B PRO* 3.6 32.3 - - + -
1191B VAL 4.0 8.1 - - - -
1192B CYS* 3.5 30.1 - - - -
1202B LEU* 5.0 3.6 - - + -
1203B ASN 3.8 20.9 - - - -
1204B LEU* 5.5 3.4 - - - -
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Residues in contact with GLU1091 (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 TYR* 3.8 20.9 + - + +
1090B PHE* 1.3 80.1 - - - +
1092B PHE* 1.3 61.3 + - - +
1148B VAL* 6.4 1.3 - - + -
1149B VAL 3.8 3.6 - - - +
1150B GLY* 4.5 1.6 - - - -
1203B ASN* 3.1 55.9 + - + +
1210B SER 5.3 1.6 - - - +
1211B LEU* 5.2 2.5 - - + -
1212B ARG* 6.1 4.3 - - + +
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Residues in contact with PHE1092 (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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839B LEU* 5.4 2.5 - - + -
1090B PHE* 3.7 14.1 - + + -
1091B GLU* 1.3 75.3 - - - +
1093B GLU* 1.3 56.9 + - - +
1094B ALA* 4.0 10.5 + - + -
1100B MET* 3.7 35.0 - - + -
1101B ARG 5.8 2.9 - - - -
1102B VAL* 4.0 12.1 - - + -
1143B TRP* 4.0 27.1 - + - -
1148B VAL* 3.3 2.5 - - - +
1149B VAL* 2.6 49.4 + - + +
1192B CYS* 3.9 35.2 - - + -
1193B SER 4.6 8.5 - - - -
1200B GLY* 4.3 12.6 - - - -
1201B HIS 3.2 28.3 - - - -
1202B LEU* 4.2 2.9 - - + -
1203B ASN 5.0 0.2 - - - +
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Residues in contact with GLU1093 (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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835B ARG* 4.8 15.7 - - - +
1092B PHE* 1.3 72.6 - - - +
1094B ALA* 1.3 64.1 + - - +
1095B VAL* 3.6 1.0 + - - +
1146B GLY 5.7 1.3 - - - +
1147B ASP 3.6 9.4 - - - +
1148B VAL* 3.8 19.5 - - + -
1201B HIS* 2.9 45.3 + - + +
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Residues in contact with ALA1094 (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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1092B PHE* 4.0 9.6 + - + -
1093B GLU* 1.3 73.3 - - - +
1095B VAL* 1.3 63.6 + - - +
1096B THR 3.9 12.3 - - - +
1097B THR* 5.3 2.5 - - - -
1100B MET* 3.7 28.0 - - - -
1143B TRP* 4.7 13.4 - - + -
1144B GLN 5.7 2.7 - - - +
1145B SER 3.1 16.4 - - - +
1146B GLY* 4.5 3.1 - - - -
1147B ASP 3.6 12.0 + - - +
1199B VAL 4.1 0.4 - - - +
1200B GLY* 3.9 7.6 - - - -
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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