Contacts of the helix formed by residues 1139 - 1150 (chain O) in PDB entry 6IY3
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 SER1139 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56I C 5.1 8.7 - - - -
1137O THR 3.2 4.4 - - - -
1138O LYS* 1.3 75.6 - - - +
1140O ASP* 1.3 56.9 + - - +
1141O GLU 3.6 0.7 - - - -
1142O ARG* 3.5 33.1 - - - +
1143O SER* 3.0 28.1 + - - -
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Residues in contact with ASP1140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137O THR 5.1 0.7 - - - +
1138O LYS* 2.9 12.0 + - + +
1139O SER* 1.3 75.0 - - - +
1141O GLU* 1.3 60.8 + - - +
1143O SER* 2.8 24.5 + - - -
1144O GLU* 2.9 16.6 + - - +
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Residues in contact with GLU1141 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132O ARG 5.6 1.3 - - - +
1137O THR* 3.7 30.1 + - + +
1140O ASP* 1.3 75.4 - - - +
1142O ARG* 1.3 60.3 + - - +
1144O GLU* 3.7 20.0 - - - +
1145O LEU* 2.8 52.1 + - + +
1148O LEU* 5.9 0.7 - - - +
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Residues in contact with ARG1142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I A 2.3 48.9 + - - -
56I C 4.7 9.9 + - - -
826O SER* 5.6 3.4 + - - -
1133O LEU* 4.1 24.6 - - + +
1134O ASP 2.9 26.8 + - - -
1135O GLY* 3.3 12.1 + - - -
1137O THR* 3.7 25.1 - - + +
1138O LYS* 5.2 1.1 - - - +
1139O SER* 3.5 30.1 + - - +
1140O ASP 3.1 0.6 - - - -
1141O GLU* 1.3 79.6 - - - +
1143O SER* 1.3 62.0 + - - +
1145O LEU* 3.5 11.4 + - - +
1146O LEU* 3.9 15.4 - - - +
1166O GLY* 4.5 15.2 + - - -
1169O GLY 5.8 0.7 - - - +
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Residues in contact with SER1143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139O SER* 3.0 14.6 + - - -
1140O ASP* 2.8 24.3 + - - -
1142O ARG* 1.3 77.1 - - - +
1144O GLU* 1.3 60.0 + - - +
1146O LEU* 4.1 19.6 + - - +
1147O ARG* 5.3 3.1 + - - +
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Residues in contact with GLU1144 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1140O ASP* 2.9 19.4 + - - +
1141O GLU* 3.8 19.3 - - - +
1142O ARG 3.2 0.4 - - - -
1143O SER* 1.3 76.6 + - - +
1145O LEU* 1.3 59.6 + - - +
1146O LEU 3.1 9.9 + - - -
1147O ARG* 3.2 48.3 + - - +
1148O LEU* 3.3 38.6 + - - +
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Residues in contact with LEU1145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131O LEU* 3.8 31.0 - - + -
1132O ARG 3.6 24.0 - - - +
1133O LEU* 4.4 18.8 - - + -
1137O THR* 5.5 2.7 - - + -
1141O GLU* 2.8 37.8 + - + +
1142O ARG* 3.5 5.1 + - - +
1143O SER 3.5 0.8 - - - -
1144O GLU* 1.3 74.4 - - - +
1146O LEU* 1.3 59.8 + - + +
1147O ARG 3.2 0.7 - - - -
1148O LEU* 3.2 25.6 + - + +
1149O PHE* 3.0 28.6 + - - +
1159O PHE* 4.5 13.9 - - + -
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Residues in contact with LEU1146 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1133O LEU* 6.3 0.7 - - + -
1142O ARG 3.9 14.6 - - - +
1143O SER* 4.1 15.9 - - - +
1144O GLU 3.1 0.8 + - - -
1145O LEU* 1.3 79.6 - - + +
1147O ARG* 1.3 59.4 + - + +
1149O PHE* 4.9 2.5 - - + -
1150O ASN* 2.9 48.2 + - - +
1169O GLY 4.9 6.3 - - - +
1170O LEU* 3.3 46.4 - - + +
1171O ASN* 5.1 8.7 - - + +
1172O LEU* 5.1 5.8 - - + -
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Residues in contact with ARG1147 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1143O SER 5.3 1.4 + - - -
1144O GLU* 3.2 43.0 + - - +
1146O LEU* 1.3 79.2 - - + +
1148O LEU* 1.3 66.0 + - + +
1150O ASN* 3.5 4.3 - - - -
1151O ALA* 3.2 25.3 + - - +
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Residues in contact with LEU1148 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1131O LEU* 4.1 10.8 - - + -
1141O GLU* 5.9 0.7 - - - +
1144O GLU* 3.3 38.6 + - - +
1145O LEU* 3.2 26.9 + - + +
1147O ARG* 1.3 79.2 - - + +
1149O PHE* 1.3 59.7 + - - +
1151O ALA* 4.4 3.1 + - - +
1154O SER* 3.4 13.7 + - - -
1156O TYR* 3.7 19.4 - - + +
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Residues in contact with PHE1149 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1105O ARG* 2.4 54.4 + - + -
1106O VAL 5.1 0.4 - - - -
1107O LEU* 4.7 1.6 - - + -
1131O LEU* 3.9 14.8 - - + +
1145O LEU 3.0 15.4 + - - +
1146O LEU* 4.2 3.6 - - + +
1148O LEU* 1.3 78.8 - - - +
1150O ASN* 1.3 62.9 + - - +
1151O ALA 3.3 1.6 - - - -
1154O SER* 3.1 16.9 + - - -
1156O TYR* 4.1 18.1 - - + +
1157O LEU 4.0 16.2 - - - -
1158O CYS 4.3 2.5 - - - -
1159O PHE* 3.6 44.0 - + + -
1172O LEU* 3.7 34.5 - - + -
1174O THR* 4.0 4.3 - - - -
1175O ALA* 4.3 13.0 - - + -
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Residues in contact with ASN1150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105O ARG* 3.0 9.2 + - - +
1146O LEU* 2.9 34.9 + - - +
1147O ARG* 3.4 7.2 + - - -
1149O PHE* 1.3 82.4 - - - +
1151O ALA* 1.3 63.7 + - - +
1152O PRO* 3.7 4.7 - - - +
1171O ASN 5.7 0.2 + - - -
1172O LEU* 4.3 19.4 - - - +
1173O GLN* 5.3 4.2 + - - +
1174O THR* 2.3 43.2 + - + +
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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