Contacts of the strand formed by residues 1153 - 1161 (chain A) in PDB entry 3AVS
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 CYS1153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1152A PHE* 1.3 72.8 - - - +
1154A SER* 1.3 59.9 + - - +
1219A TRP* 3.6 32.1 - - + -
1220A ILE 3.2 10.8 - - - +
1221A ASN* 3.7 9.0 - - - -
1222A ALA* 3.5 25.8 - - - -
1240A ASN* 3.0 15.1 + - - -
1241A VAL* 3.1 36.1 + - + +
1243A PRO* 3.8 10.1 - - - -
1248A GLN* 3.2 14.5 + - - -
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Residues in contact with SER1154 (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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1148A GLU* 3.7 21.4 + - - +
1152A PHE 3.7 0.4 + - - -
1153A CYS* 1.3 75.0 - - - +
1155A VAL* 1.3 67.4 + - - +
1156A ASN* 5.2 0.6 - - - +
1218A VAL 3.6 0.8 - - - +
1219A TRP* 3.5 7.1 - - - -
1220A ILE* 2.9 42.9 + - - +
1238A ALA* 4.8 1.6 - - - +
1239A TRP 3.5 11.3 + - - -
1240A ASN* 3.9 1.6 + - - -
1501A OGA 2.8 35.0 + - - -
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Residues in contact with VAL1155 (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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1110A VAL* 4.1 17.7 - - + +
1154A SER* 1.3 79.2 + - - +
1156A ASN* 1.3 65.4 + - - +
1157A ILE* 4.9 0.2 - - + -
1217A LEU* 3.8 27.4 - - + -
1218A VAL 3.5 3.1 - - - -
1219A TRP* 3.9 28.3 - - + -
1238A ALA* 3.0 26.0 - - - +
1239A TRP* 2.9 46.9 + - + +
1241A VAL* 4.1 14.4 - - + -
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Residues in contact with ASN1156 (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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1135A TYR* 4.6 0.2 - - - -
1154A SER* 5.2 0.2 - - - +
1155A VAL* 1.3 77.2 - - - +
1157A ILE* 1.3 66.5 + - - +
1166A TRP* 3.6 22.7 - - + -
1212A GLN* 3.1 17.7 + - - -
1217A LEU* 3.3 2.4 - - - -
1218A VAL* 2.8 37.9 + - + +
1220A ILE* 6.3 0.4 - - + -
1236A ASN* 3.1 19.6 + - - +
1237A ILE 3.3 7.4 - - - -
1238A ALA* 3.8 7.5 - - - +
1501A OGA 3.0 50.4 + - - +
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Residues in contact with ILE1157 (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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973A LEU* 4.2 12.8 - - + -
974A ALA* 5.3 1.6 - - + -
979A LEU* 4.5 9.0 - - + -
981A LEU* 4.2 18.8 - - + -
1103A LEU* 4.8 1.6 - - + -
1106A LEU* 4.3 10.5 - - + -
1155A VAL* 4.9 0.2 - - + -
1156A ASN* 1.3 81.3 - - - +
1158A ASN* 1.3 73.9 + - - +
1159A ILE* 3.5 3.7 + - + -
1215A GLY 4.7 9.4 - - - +
1216A ASP 3.7 7.0 - - - +
1217A LEU* 3.9 29.2 - - + -
1236A ASN* 3.4 1.9 - - - -
1237A ILE* 2.9 47.8 + - + +
1239A TRP* 4.0 25.5 - - + -
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Residues in contact with ASN1158 (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* 4.2 1.4 - - - +
1157A ILE* 1.3 75.7 - - - +
1159A ILE* 1.3 60.1 + - - +
1160A GLY 2.9 21.1 + - - -
1162A GLY 2.9 21.7 + - - -
1163A ASP* 3.7 3.8 - - - +
1164A CYS* 3.8 5.8 - - - +
1212A GLN* 3.0 44.0 + - - +
1213A ARG 3.4 19.5 - - - +
1214A PRO* 4.0 0.9 - - - -
1215A GLY* 2.8 29.5 + - - -
1216A ASP 3.4 2.2 + - - -
1234A CYS* 3.5 9.8 - - - +
1235A ASN 3.1 7.4 - - - +
1236A ASN* 3.6 12.6 - - - +
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Residues in contact with ILE1159 (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* 3.4 57.0 - - + +
984A PHE* 3.6 43.3 - - + +
985A SER* 4.6 0.7 - - - -
1134A LEU* 5.4 0.2 - - + -
1157A ILE* 4.2 4.0 - - + +
1158A ASN* 1.3 73.1 - - - +
1160A GLY* 1.3 60.7 + - - +
1214A PRO* 4.1 4.3 - - - +
1235A ASN* 2.8 33.8 + - + +
1236A ASN* 4.3 5.4 - - - +
1237A ILE* 4.1 19.7 - - + +
1513A EDO 3.5 23.4 - - - -
1514A EDO 5.3 0.2 - - - +
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Residues in contact with GLY1160 (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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1158A ASN* 2.9 13.0 + - - -
1159A ILE* 1.3 82.0 - - - +
1161A PRO* 1.3 74.5 - - - +
1162A GLY 3.4 5.2 - - - -
1214A PRO* 3.6 13.0 - - - -
1234A CYS* 3.2 9.0 - - - -
1235A ASN 3.2 2.6 + - - -
1513A EDO 4.0 4.3 - - - -
1514A EDO 3.1 19.8 - - - -
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Residues in contact with PRO1161 (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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1160A GLY* 1.3 82.5 - - - +
1162A GLY* 1.3 57.0 + - - +
1163A ASP* 4.9 0.3 - - - +
1214A PRO* 3.3 16.9 - - + +
1233A TRP* 3.1 20.6 - - + +
1513A EDO 4.1 11.6 - - - +
1514A EDO 3.5 21.5 - - - +
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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