Contacts of the helix formed by residues 1165 - 1178 (chain A) in PDB entry 5LUQ
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 LEU1165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1108A MSE 3.5 27.8 - - + -
1109A GLU* 3.5 24.5 - - - +
1112A ALA* 3.4 29.3 - - + +
1113A LEU 4.5 2.9 - - - +
1116A ALA* 4.8 0.6 - - - +
1157A PHE* 4.8 7.2 - - + -
1160A SER 3.7 9.4 - - - +
1162A SER* 3.1 43.7 + - - +
1163A LEU 3.7 0.6 - - - -
1164A CYS* 1.3 77.0 - - - +
1166A LEU* 1.3 49.8 + - - +
1168A LEU* 2.5 35.6 + - + -
1169A VAL* 2.6 32.4 + - + -
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Residues in contact with LEU1166 (chain A).
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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1161A ALA* 4.2 13.2 - - + -
1162A SER 5.3 1.0 - - - +
1163A LEU 3.8 6.3 - - - +
1164A CYS* 2.9 3.7 - - - +
1165A LEU* 1.3 79.0 - - - +
1167A ASP* 1.3 61.6 + - - +
1168A LEU 2.8 3.3 + - - -
1169A VAL* 4.1 4.9 - - + +
1170A LYS* 3.1 52.9 + - - +
1256A TRP* 3.7 28.5 - - + -
1259A LEU* 4.9 1.3 - - + +
1260A LEU* 3.5 31.6 - - + -
1263A ALA* 3.8 26.5 - - + -
1264A LEU* 4.3 9.0 - - + -
1340A ARG* 6.1 0.9 - - - +
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Residues in contact with ASP1167 (chain A).
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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1129A ASP* 6.1 0.2 - - - +
1164A CYS* 3.9 6.3 + - - +
1165A LEU 3.4 0.6 - - - -
1166A LEU* 1.3 79.3 - - - +
1168A LEU* 1.3 67.9 + - + +
1170A LYS* 3.8 15.9 + - - +
1171A TRP* 3.3 22.6 + - - +
1267A TYR* 4.6 7.4 + - - -
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Residues in contact with LEU1168 (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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1108A MSE 4.4 14.6 - - + -
1112A ALA* 3.8 25.4 - - + -
1115A HIS* 5.3 4.0 - - + +
1129A ASP* 3.4 35.2 - - + +
1132A ASP* 3.7 21.8 - - + +
1136A ARG* 6.2 0.4 - - - +
1164A CYS* 3.8 22.7 - - - +
1165A LEU* 2.5 18.4 + - + +
1167A ASP* 1.3 80.1 - - + +
1169A VAL* 1.3 63.0 + - - +
1171A TRP* 3.1 9.0 - - + +
1172A LEU* 2.9 29.1 + - - +
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Residues in contact with VAL1169 (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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1154A PRO* 5.1 0.7 - - - +
1157A PHE* 3.7 55.4 - - + +
1158A PRO* 3.8 17.7 - - + -
1161A ALA* 4.5 4.9 - - + -
1165A LEU* 2.6 46.4 + - + +
1166A LEU* 3.5 7.2 - - - +
1168A LEU* 1.3 69.4 - - - +
1170A LYS* 1.3 71.0 + - + +
1172A LEU* 2.9 11.1 + - - +
1173A LEU* 2.9 23.7 + - + +
1264A LEU* 4.7 5.6 - - + -
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Residues in contact with LYS1170 (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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1166A LEU* 3.1 59.0 + - - +
1167A ASP* 3.5 15.8 + - - +
1169A VAL* 1.3 79.3 - - + +
1171A TRP* 1.3 65.6 + - - +
1173A LEU* 2.9 27.8 + - + +
1174A ALA* 3.0 15.6 + - - +
1263A ALA* 4.3 6.9 - - - +
1264A LEU* 5.1 6.7 - - + -
1267A TYR* 3.4 64.0 + - + -
1340A ARG* 5.5 1.0 - - - +
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Residues in contact with TRP1171 (chain A).
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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1132A ASP* 5.5 5.6 - - + -
1135A CYS* 5.2 4.7 - - + -
1136A ARG* 3.1 65.8 - - + +
1139A GLU* 5.8 0.4 - - - -
1167A ASP 3.3 18.8 + - - +
1168A LEU* 3.1 14.5 - - + +
1170A LYS* 1.3 78.2 - - - +
1172A LEU* 1.3 109.6 + - + +
1174A ALA* 3.5 3.5 + - - +
1175A HIS* 2.9 68.9 + + + +
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Residues in contact with LEU1172 (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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1108A MSE 3.4 42.6 - - + -
1135A CYS* 5.5 7.9 - - + +
1139A GLU* 5.5 2.2 - - - +
1153A LEU* 4.7 2.9 - - + -
1154A PRO* 3.8 19.1 - - + -
1157A PHE* 3.8 20.9 - - + -
1168A LEU 2.9 18.4 + - - +
1169A VAL 3.3 6.7 - - - +
1171A TRP* 1.3 100.1 - - + +
1173A LEU* 1.3 64.6 + - - +
1175A HIS* 4.2 0.2 - - - -
1176A CYS* 2.8 42.8 + - - +
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Residues in contact with LEU1173 (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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1154A PRO* 3.3 34.3 - - + +
1155A ARG* 4.0 15.0 - - + +
1158A PRO* 3.7 25.6 - - + -
1169A VAL* 2.9 11.9 + - + +
1170A LYS* 2.9 28.6 + - + +
1172A LEU* 1.3 78.8 - - - +
1174A ALA* 1.3 65.9 + - - +
1177A GLY* 3.0 20.3 + - - -
1219A PHE* 5.9 3.8 - - + -
1264A LEU* 5.9 1.3 - - + -
1268A ASN* 5.0 10.5 - - - +
1271A ILE* 6.0 6.7 - - + -
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Residues in contact with ALA1174 (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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1170A LYS 3.0 10.1 + - - +
1171A TRP* 4.2 2.7 - - - +
1173A LEU* 1.3 80.0 - - - +
1175A HIS* 1.3 57.3 + - - +
1178A ARG* 3.0 23.5 + - - +
1215A GLU* 2.9 37.4 - - + +
1271A ILE* 6.4 2.2 - - + -
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Residues in contact with HIS1175 (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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1136A ARG* 4.7 5.6 + - + +
1139A GLU* 3.1 42.5 - - + +
1171A TRP* 2.9 64.2 + + + +
1172A LEU* 3.7 2.7 - - - +
1174A ALA* 1.3 79.1 - - - +
1176A CYS* 1.3 59.8 + - - +
1178A ARG* 3.0 37.9 + - - +
1179A PRO* 3.0 10.2 - - + +
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Residues in contact with CYS1176 (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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1139A GLU* 3.8 28.3 - - - +
1150A LYS* 5.2 6.5 - - - +
1151A ARG* 4.3 17.2 - - + -
1154A PRO* 4.2 21.8 - - + -
1172A LEU* 2.8 35.5 + - - +
1173A LEU 4.4 0.2 - - - +
1175A HIS* 1.3 79.2 - - - +
1177A GLY* 1.3 63.1 + - - +
1178A ARG 2.9 1.1 - - - -
1179A PRO* 3.1 13.6 - - - +
1180A GLN* 3.5 21.7 + - - +
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Residues in contact with GLY1177 (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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1151A ARG* 4.7 13.8 - - - +
1173A LEU 3.0 15.5 + - - -
1174A ALA 3.9 0.9 - - - -
1176A CYS* 1.3 76.3 - - - +
1178A ARG* 1.3 63.1 - - - +
1180A GLN 3.6 15.6 + - - -
1213A LYS 4.0 12.8 + - - +
1215A GLU* 4.2 10.0 - - - -
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Residues in contact with ARG1178 (chain A).
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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1174A ALA* 3.0 17.2 + - - +
1175A HIS* 3.0 41.5 + - - +
1176A CYS 2.9 1.2 - - - -
1177A GLY* 1.3 79.6 - - - +
1179A PRO* 1.3 62.5 - - + +
1180A GLN 3.2 2.6 + - - -
1213A LYS* 4.0 25.7 + - - +
1215A GLU* 3.5 32.5 + - - +
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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