Contacts of the strand formed by residues 1234 - 1241 (chain A) in PDB entry 3AVR
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 CYS1234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A EDO 4.1 2.1 + - - -
1039A GLN* 4.1 0.9 - - - -
1137A LYS* 2.8 47.0 + - - +
1158A ASN* 3.6 7.2 - - - +
1160A GLY 3.2 13.5 - - - +
1161A PRO* 4.2 0.9 - - - -
1162A GLY 3.6 20.6 - - - +
1163A ASP 4.4 6.7 - - - -
1164A CYS* 3.5 31.9 - - - -
1230A ALA* 4.4 4.7 - - - -
1232A GLY 3.8 0.6 + - - -
1233A TRP* 1.3 77.1 - - - +
1235A ASN* 1.3 65.1 + - - +
1236A ASN* 3.6 9.2 - - - -
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Residues in contact with ASN1235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A EDO 4.9 0.6 + - - -
984A PHE 3.1 21.5 + - - +
985A SER* 3.9 1.2 - - - +
986A THR* 3.1 28.4 + - - +
989A LEU* 4.0 8.3 - - - +
1039A GLN* 3.1 25.3 + - - -
1134A LEU* 4.1 5.2 - - + -
1135A TYR 3.0 11.0 - - - +
1136A MET* 3.5 11.4 - - - +
1158A ASN* 3.2 7.6 - - - +
1159A ILE* 2.8 40.8 + - + +
1160A GLY 3.1 7.8 + - - -
1234A CYS* 1.3 73.3 - - - +
1236A ASN* 1.3 64.0 + - - +
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Residues in contact with ASN1236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134A LEU* 3.4 4.4 - - - +
1135A TYR* 2.8 44.4 + - + +
1137A LYS* 3.1 30.6 + - - +
1156A ASN* 3.0 33.9 + - - +
1157A ILE 3.3 5.6 - - - -
1158A ASN* 3.7 9.8 - - - +
1159A ILE* 4.2 2.0 - - - -
1164A CYS* 3.5 16.4 - - - -
1166A TRP* 5.1 0.4 - - - -
1212A GLN* 3.3 17.8 + - - -
1234A CYS* 3.6 2.3 - - - -
1235A ASN* 1.3 79.7 - - - +
1237A ILE* 1.3 64.7 + - - +
1501A OGA 4.3 0.4 + - - -
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Residues in contact with ILE1237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981A LEU* 6.1 0.7 - - + -
984A PHE* 3.7 39.0 - - + -
1090A LEU* 4.6 0.4 - - + -
1103A LEU* 3.7 31.4 - - + -
1132A VAL* 4.1 10.8 - - + -
1133A GLN 3.3 9.6 - - - +
1134A LEU* 4.0 13.9 - - + -
1135A TYR* 5.1 0.2 - - - -
1156A ASN* 3.3 1.4 - - - -
1157A ILE* 2.8 51.0 + - + +
1159A ILE* 4.0 14.4 - - + -
1236A ASN* 1.3 79.8 - - - +
1238A ALA* 1.3 64.9 + - - +
1239A TRP* 4.1 10.7 - - + -
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Residues in contact with ALA1238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133A GLN 2.9 31.9 + - - +
1135A TYR* 4.1 7.4 - - + -
1155A VAL 3.0 18.2 - - - +
1156A ASN* 3.8 7.9 - - - +
1237A ILE* 1.3 78.6 - - - +
1239A TRP* 1.3 70.0 - - - +
1501A OGA 3.6 21.1 - - - +
27B M3L 3.5 19.5 - - - -
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Residues in contact with TRP1239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103A LEU* 4.0 22.4 - - + -
1106A LEU* 3.6 26.9 - - + -
1110A VAL 2.8 29.5 + - - -
1111A ARG 3.8 0.4 - - - -
1112A VAL* 3.6 30.0 - - + +
1128A GLY 3.5 10.1 - - - -
1129A MET 3.7 8.3 - - - +
1131A THR 3.8 15.7 - - - +
1132A VAL* 3.9 13.0 - - + -
1154A SER* 3.4 3.6 - - - -
1155A VAL* 2.9 46.4 + - + +
1157A ILE* 4.2 14.4 - - + -
1237A ILE* 4.1 13.9 - - + -
1238A ALA* 1.3 107.2 - - - +
1240A ASN* 1.3 80.2 + - - +
1241A VAL* 3.8 7.5 - - + +
27B M3L 3.6 8.9 - - - -
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Residues in contact with ASN1240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112A VAL 4.9 0.5 - - - +
1117A ASN* 4.1 4.7 + - - -
1119A LEU* 3.5 23.5 - - + +
1128A GLY 3.8 0.2 + - - -
1129A MET* 2.9 53.6 + - + +
1148A GLU* 3.1 34.9 + - - +
1149A ASN* 5.3 1.2 + - - +
1152A PHE* 3.6 4.3 + - + -
1153A CYS 2.9 19.1 + - - +
1154A SER* 3.5 5.2 - - - -
1239A TRP* 1.3 79.0 - - - +
1241A VAL* 1.3 69.7 + - - +
27B M3L 3.1 18.4 - - - +
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Residues in contact with VAL1241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109A PHE 4.1 7.2 - - - +
1110A VAL 4.0 5.4 - - - +
1111A ARG 3.6 24.2 - - - +
1117A ASN* 3.6 13.7 - - + +
1119A LEU* 4.0 5.8 - - - -
1152A PHE* 3.8 2.1 - - - -
1153A CYS* 3.0 36.9 + - + +
1155A VAL* 3.9 12.8 - - + -
1219A TRP* 3.4 38.6 - - + -
1239A TRP* 3.8 13.5 - - + +
1240A ASN* 1.3 81.2 - - - +
1242A GLY* 1.3 59.5 + - - +
1243A PRO* 4.4 2.2 - - + -
1248A GLN* 3.6 0.2 - - - +
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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