Contacts of the helix formed by residues 1134 - 1152 (chain v) in PDB entry 6FF7
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 SER1134 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132v PHE* 4.0 9.5 - - - +
1133v THR* 1.3 81.0 - - - +
1135v HIS* 1.3 65.3 + - - +
1136v GLU* 3.3 9.5 + - - -
1137v ASP* 3.7 8.6 + - - +
1138v HIS* 3.7 14.2 + - - +
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Residues in contact with HIS1135 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134v SER* 1.3 74.1 - - - +
1136v GLU* 1.3 60.8 + - - +
1138v HIS* 3.5 8.4 + - - +
1139v ASP* 2.9 29.7 + - - +
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Residues in contact with GLU1136 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134v SER* 3.3 6.2 - - - -
1135v HIS* 1.3 76.7 - - - +
1137v ASP* 1.3 58.8 + - - +
1139v ASP* 3.8 6.3 - - - +
1140v PHE* 2.9 30.8 + - - +
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Residues in contact with ASP1137 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132v PHE* 5.0 8.1 - - + -
1133v THR* 5.1 4.0 - - - +
1134v SER* 3.7 16.7 + - - +
1135v HIS 3.3 0.4 - - - -
1136v GLU* 1.3 76.0 - - - +
1138v HIS* 1.3 60.5 + - - +
1140v PHE* 3.9 4.5 - - - +
1141v PHE* 2.9 32.7 + - - +
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Residues in contact with HIS1138 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2v PHE* 5.0 11.0 - - + -
1132v PHE* 4.5 14.6 - - + +
1134v SER 3.7 10.5 + - - +
1135v HIS* 3.5 11.4 + - - +
1137v ASP* 1.3 78.4 - - - +
1139v ASP* 1.3 56.1 + - - +
1141v PHE* 3.9 3.1 - - - +
1142v GLN* 2.9 31.8 + - - +
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Residues in contact with ASP1139 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135v HIS 2.9 18.9 + - - +
1136v GLU* 3.8 7.6 - - - +
1138v HIS* 1.3 75.4 - - - +
1140v PHE* 1.3 57.2 + - - +
1142v GLN* 3.4 6.3 + - - +
1143v HIS* 3.0 28.4 + - - +
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Residues in contact with PHE1140 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136v GLU 2.9 17.5 + - - +
1137v ASP* 3.9 6.1 - - - +
1138v HIS 3.3 0.2 - - - -
1139v ASP* 1.3 77.0 - - - +
1141v PHE* 1.3 57.3 + - - +
1143v HIS* 3.2 7.8 + - - +
1144v VAL* 2.9 26.7 + - - +
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Residues in contact with PHE1141 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137v ASP 2.9 16.9 + - - +
1138v HIS* 4.3 2.7 - - - +
1140v PHE* 1.3 75.1 - - - +
1142v GLN* 1.3 60.5 + - - +
1144v VAL* 3.6 8.9 - - + +
1145v GLU* 3.0 30.0 + - - +
1174v ILE* 4.6 16.3 - - + +
1179v CYS* 5.8 1.2 - - - +
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Residues in contact with GLN1142 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138v HIS 2.9 20.5 + - - +
1139v ASP* 3.6 7.2 - - - +
1140v PHE 3.2 0.2 - - - -
1141v PHE* 1.3 77.2 - - - +
1143v HIS* 1.3 58.1 + - - +
1145v GLU* 3.5 3.7 + - - +
1146v MET* 2.9 30.2 + - - +
1174v ILE* 5.1 7.1 - - + +
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Residues in contact with HIS1143 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139v ASP 3.0 16.9 + - - +
1140v PHE* 3.7 7.0 - - - +
1142v GLN* 1.3 73.7 - - - +
1144v VAL* 1.3 59.9 + - - +
1146v MET* 3.8 5.7 - - - +
1147v HIS* 2.9 31.5 + - - +
1197v LEU* 6.3 3.4 - - + -
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Residues in contact with VAL1144 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140v PHE 2.9 13.2 + - - +
1141v PHE* 3.6 12.8 - - - +
1142v GLN 3.3 0.2 - - - -
1143v HIS* 1.3 75.8 - - - +
1145v GLU* 1.3 58.5 + - - +
1147v HIS* 3.3 6.0 + - - +
1148v LEU* 2.9 29.3 + - - +
1179v CYS* 5.1 14.1 - - + -
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Residues in contact with GLU1145 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141v PHE 3.0 16.0 + - - +
1142v GLN* 4.2 4.0 - - - +
1144v VAL* 1.3 76.1 - - - +
1146v MET* 1.3 57.6 + - - +
1148v LEU* 3.7 5.5 - - - +
1149v ARG* 2.9 29.3 + - - +
1174v ILE* 5.1 10.1 - - + -
1175v ASP* 4.7 16.8 - - + +
1178v LEU* 5.6 6.7 - - + +
1179v CYS* 5.5 8.2 - - + +
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Residues in contact with MET1146 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142v GLN 2.9 20.1 + - - +
1143v HIS* 3.8 7.9 - - - +
1145v GLU* 1.3 77.9 - - - +
1147v HIS* 1.3 60.0 + - - +
1149v ARG* 3.6 14.2 + - - +
1150v SER* 3.8 8.5 + - - -
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Residues in contact with HIS1147 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143v HIS 2.9 17.8 + - - +
1144v VAL* 3.8 5.4 - - - +
1146v MET* 1.3 77.2 - - - +
1148v LEU* 1.3 58.8 + - - +
1150v SER* 3.3 5.9 + - - -
1151v GLU* 2.9 31.6 + - + +
1193v VAL* 5.0 17.7 - - + -
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Residues in contact with LEU1148 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144v VAL 2.9 17.2 + - - +
1145v GLU* 3.3 6.9 + - - +
1147v HIS* 1.3 74.7 - - - +
1149v ARG* 1.3 62.6 + - - +
1150v SER 3.2 0.2 - - - -
1151v GLU* 4.0 4.7 - - - +
1152v HIS* 2.9 37.3 + - + +
1178v LEU* 4.5 20.9 - - + +
1179v CYS* 5.6 2.5 - - - -
1182v PHE* 6.4 2.2 - - + -
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Residues in contact with ARG1149 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145v GLU 2.9 16.5 + - - +
1146v MET* 3.8 9.9 - - - +
1147v HIS 3.3 0.4 - - - -
1148v LEU* 1.3 78.5 - - - +
1150v SER* 1.3 58.9 + - - +
1152v HIS 4.7 1.1 - - - -
1153v PRO* 4.6 13.7 - - - +
1160v HIS* 5.3 14.6 - - + -
1161v LEU* 6.0 4.3 - - + +
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Residues in contact with SER1150 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146v MET 3.8 7.5 + - - -
1147v HIS* 3.3 7.9 + - - -
1148v LEU 3.2 0.2 - - - -
1149v ARG* 1.3 80.4 - - - +
1151v GLU* 1.3 61.9 + - - +
1152v HIS 5.0 0.2 - - - -
1153v PRO* 4.9 3.5 - - - +
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Residues in contact with GLU1151 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147v HIS* 2.9 18.7 + - + +
1148v LEU* 4.7 1.6 - - - -
1150v SER* 1.3 80.3 - - - +
1152v HIS* 1.3 58.9 + - + +
1153v PRO 3.9 1.5 - - - -
1189v LYS* 5.2 16.1 - - + +
1193v VAL* 6.1 4.7 - - + -
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Residues in contact with HIS1152 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148v LEU* 2.9 28.6 + - + +
1149v ARG* 4.6 1.9 - - - +
1151v GLU* 1.3 78.8 - - + +
1153v PRO* 1.3 65.1 - - - +
1154v PRO 3.9 0.7 - - - -
1181v GLN* 5.7 10.3 - - + +
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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