Contacts of the helix formed by residues 1255 - 1264 (chain A) in PDB entry 1RQQ
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 THR1255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1188A THR* 5.9 7.2 - - + -
1192A MET* 3.5 4.0 - - - -
1253A ARG 5.1 2.2 - - - +
1254A PRO* 1.3 77.0 - - + +
1256A PHE* 1.3 65.2 + - - +
1257A LEU* 3.6 9.8 + - - +
1258A GLU* 2.9 43.2 + - - +
1259A ILE* 2.9 22.0 + - - +
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Residues in contact with PHE1256 (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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1117A ALA* 3.5 26.6 - - + +
1120A MET* 3.5 43.7 - - + -
1121A ALA* 3.8 15.0 - - + +
1124A ASN* 5.1 3.4 - - + -
1133A LEU* 4.5 0.2 - - + -
1188A THR* 3.7 34.3 - - - -
1191A ASP* 3.8 16.4 - - + -
1192A MET* 3.4 38.3 - - + +
1195A PHE* 3.8 22.4 - + + -
1255A THR* 1.3 73.1 - - - +
1257A LEU* 1.3 63.2 - - - +
1259A ILE* 3.1 5.7 + - + +
1260A VAL* 3.0 25.8 + - - +
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Residues in contact with LEU1257 (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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1121A ALA* 3.9 22.9 - - + +
1124A ASN* 6.0 2.0 - - - +
1125A ALA* 6.5 0.4 - - + -
1255A THR* 3.2 8.4 + - - +
1256A PHE* 1.3 76.7 - - - +
1258A GLU* 1.3 59.1 + - - +
1260A VAL* 3.1 4.5 + - + +
1261A ASN* 2.8 29.6 + - - +
1276A PHE* 4.1 10.5 - - + -
1277A PHE* 3.7 30.1 - - + -
1282A ASN* 3.8 27.4 - - - +
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Residues in contact with GLU1258 (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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1254A PRO* 3.5 16.5 - - + +
1255A THR* 2.9 48.0 + - - +
1257A LEU* 1.3 78.2 - - + +
1259A ILE* 1.3 62.2 + - - +
1261A ASN* 3.3 10.8 + - + +
1262A LEU* 3.0 23.9 + - - +
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Residues in contact with ILE1259 (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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1117A ALA* 3.7 18.2 - - + -
1192A MET* 3.4 28.7 - - + -
1195A PHE* 3.2 35.4 - - + -
1241A LEU* 4.6 16.8 - - + -
1245A CYS* 4.5 3.6 - - - -
1254A PRO* 4.4 13.7 - - + -
1255A THR 2.9 17.4 + - - +
1256A PHE* 3.1 8.5 + - + +
1258A GLU* 1.3 77.8 - - - +
1260A VAL* 1.3 64.0 + - - +
1262A LEU* 3.1 16.0 + - - +
1263A LEU* 3.2 31.1 - - + +
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Residues in contact with VAL1260 (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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1114A ALA* 4.1 7.9 - - + +
1117A ALA* 3.8 6.5 - - + +
1118A ASP* 3.7 33.2 - - - +
1121A ALA* 5.2 2.2 - - + -
1256A PHE 3.0 15.5 + - - +
1257A LEU* 3.6 6.5 - - - +
1259A ILE* 1.3 75.1 - - - +
1261A ASN* 1.3 53.4 + - - +
1263A LEU* 2.7 10.2 + - - -
1264A LYS* 2.7 34.5 + - + +
1271A PHE* 3.8 24.7 - - + -
1277A PHE* 3.6 35.7 - - + -
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Residues in contact with ASN1261 (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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1257A LEU 2.8 16.7 + - - +
1258A GLU* 3.6 11.0 + - - +
1260A VAL* 1.3 76.5 - - - +
1262A LEU* 1.3 61.0 + - - +
1264A LYS* 3.3 46.4 + - - +
1265A ASP* 5.1 1.0 - - - +
1277A PHE* 3.7 22.3 - - + -
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Residues in contact with LEU1262 (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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1237A ARG* 3.3 22.2 + - + +
1241A LEU* 3.6 32.1 - - + -
1258A GLU 3.0 13.1 + - - +
1259A ILE* 3.4 11.4 - - - +
1260A VAL 3.1 0.2 - - - -
1261A ASN* 1.3 76.9 - - - +
1263A LEU* 1.3 70.6 + - + +
1265A ASP* 5.6 2.4 - - - +
1266A ASP* 4.7 0.2 - - - +
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Residues in contact with LEU1263 (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 ILE* 3.8 31.9 - - + +
1113A ALA* 4.2 9.9 - - + -
1114A ALA* 4.1 29.8 - - + +
1237A ARG* 3.9 17.9 - - + +
1241A LEU* 4.6 13.0 - - + -
1259A ILE* 3.2 26.9 - - + +
1260A VAL 2.7 13.3 + - - +
1262A LEU* 1.3 98.6 - - + +
1264A LYS* 1.3 63.9 + - - +
1265A ASP 3.0 4.7 + - - -
1266A ASP* 3.2 14.3 + - - +
1267A LEU* 3.2 13.3 - - + +
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Residues in contact with LYS1264 (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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1260A VAL* 2.7 17.2 + - + +
1261A ASN* 3.3 39.7 + - - +
1262A LEU 3.8 0.2 - - - -
1263A LEU* 1.3 71.8 - - - +
1265A ASP* 1.3 91.9 + - - +
1267A LEU* 3.9 21.4 + - - +
1271A PHE* 5.4 0.7 - - - -
1272A PRO* 5.9 2.4 - - - +
1277A PHE* 4.4 13.5 - - + -
1278A HIS* 4.4 25.4 + - + +
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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