Contacts of the strand formed by residues 1087 - 1094 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1086F GLY* 1.3 74.0 - - - +
1088F TRP* 1.3 61.4 + - - +
1153F ILE* 3.3 18.2 - - - +
1154F ASP* 4.4 8.3 - - + -
1156F THR* 6.2 0.2 - - - +
1221F GLU 5.5 2.5 - - - +
1222F GLY 4.8 3.1 - - - +
1223F PHE* 3.7 24.7 - - + +
1224F GLU* 3.1 20.5 + - - +
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Residues in contact with TRP1088 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083F VAL* 5.9 3.8 - - + -
1087F ARG* 1.3 76.9 - - - +
1089F TYR* 1.3 62.1 + - - +
1104F TRP* 3.5 22.9 - - + -
1152F MET* 3.3 25.1 - - - +
1153F ILE* 3.6 10.6 + - + +
1223F PHE* 3.7 5.9 - - - +
1224F GLU 3.2 10.5 - - - +
1226F PHE* 3.9 27.8 - - + -
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Residues in contact with TYR1089 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088F TRP* 1.3 76.4 - - - +
1090F PHE* 1.3 60.0 + - - +
1091F GLU* 3.8 18.0 + - + +
1104F TRP* 4.2 2.0 - - - -
1150F GLY* 4.4 14.1 - - - -
1151F CYS 3.3 13.7 - - - -
1152F MET* 4.3 11.0 - - + -
1163F THR* 4.3 22.9 - - + +
1166F GLY* 6.0 0.2 - - - -
1203F ASN* 5.2 2.1 - - - +
1204F LEU 5.3 5.2 - - - +
1205F GLY* 5.5 1.6 + - - -
1211F LEU* 3.6 31.9 - - + +
1212F ARG 5.8 1.3 - - - -
1213F PHE* 3.7 22.9 + - - +
1214F PHE* 3.6 42.4 - + + -
1218F GLY* 5.9 2.0 - - - -
1223F PHE* 4.3 5.8 - - + +
1224F GLU 3.7 3.6 + - - -
1225F PRO* 4.4 9.2 - - + +
1226F PHE* 4.6 10.7 + - - +
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Residues in contact with PHE1090 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089F TYR* 1.3 75.1 - - - +
1091F GLU* 1.3 65.4 + - - +
1092F PHE* 3.7 13.5 - + + -
1102F VAL* 3.5 33.0 - - + -
1103F GLY 5.1 4.3 - - - -
1104F TRP* 3.6 25.4 - + + -
1150F GLY* 3.3 3.1 - - - -
1151F CYS* 2.5 50.2 + - + +
1190F PRO* 3.6 33.0 - - + -
1191F VAL 4.0 7.9 - - - -
1192F CYS* 3.5 30.1 - - - -
1202F LEU* 5.0 3.4 - - + -
1203F ASN 3.8 21.3 - - - -
1204F LEU* 5.5 3.1 - - - -
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Residues in contact with GLU1091 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089F TYR* 3.8 21.7 + - + +
1090F PHE* 1.3 79.1 - - - +
1092F PHE* 1.3 60.9 + - - +
1093F GLU 4.4 0.2 - - - -
1148F VAL* 6.4 1.3 - - + -
1149F VAL 3.8 2.9 - - - -
1150F GLY* 4.5 1.8 - - - -
1203F ASN* 3.1 55.1 + - + +
1210F SER 5.3 1.8 - - - +
1211F LEU* 5.2 2.7 - - + -
1212F ARG* 6.1 3.8 - - + +
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Residues in contact with PHE1092 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839F LEU* 5.4 2.9 - - + -
1090F PHE* 3.7 13.9 - + + -
1091F GLU* 1.3 75.3 - - - +
1093F GLU* 1.3 57.8 + - - +
1094F ALA* 4.0 10.0 + - + -
1100F MET* 3.7 34.5 - - + -
1101F ARG 5.8 2.2 - - - -
1102F VAL* 4.0 12.6 - - + -
1143F TRP* 4.0 27.4 - + - -
1148F VAL* 3.3 2.4 - - - +
1149F VAL* 2.6 48.3 + - + +
1192F CYS* 3.9 35.0 - - + -
1193F SER 4.6 8.5 - - - -
1200F GLY* 4.3 12.1 - - - -
1201F HIS 3.2 28.5 - - - -
1202F LEU* 4.2 2.2 - - + -
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Residues in contact with GLU1093 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835F ARG* 4.8 15.9 - - - +
1092F PHE* 1.3 73.0 - - - +
1094F ALA* 1.3 62.8 + - - +
1095F VAL* 3.6 1.6 + - - +
1146F GLY 5.7 1.3 - - - +
1147F ASP 3.6 8.5 - - - +
1148F VAL* 3.8 19.7 - - + -
1201F HIS* 2.9 45.5 + - + +
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Residues in contact with ALA1094 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092F PHE* 4.0 9.8 + - + -
1093F GLU* 1.3 73.4 - - - +
1095F VAL* 1.3 63.4 + - - +
1096F THR 3.9 13.0 - - - +
1097F THR* 5.3 2.9 - - - -
1100F MET* 3.7 28.5 - - - -
1143F TRP* 4.7 12.3 - - + -
1144F GLN 5.7 2.7 - - - +
1145F SER 3.1 15.8 - - - +
1146F GLY* 4.5 3.3 - - - -
1147F ASP 3.6 11.3 + - - +
1200F GLY* 3.9 7.4 - - - -
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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