Contacts of the helix formed by residues 1163 - 1177 (chain A) in PDB entry 5M64
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 GLU1163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1070A LEU* 5.5 1.6 - - - +
1144A LEU* 5.7 1.6 - - - +
1147A PHE* 6.0 1.0 - - - -
1148A LEU* 3.5 37.5 - - + +
1151A ASN* 4.4 10.8 + - - -
1162A ASN* 1.3 80.6 - - - +
1164A LYS* 1.3 61.8 + - - +
1165A LYS 3.6 0.9 - - - -
1166A PHE* 3.3 30.9 - - - -
1167A ARG* 2.9 46.4 + - - +
1170A MET* 5.0 6.6 - - - +
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Residues in contact with LYS1164 (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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1162A ASN* 3.7 10.3 + - - +
1163A GLU* 1.3 76.8 - - - +
1165A LYS* 1.3 61.5 + - - +
1167A ARG* 2.9 32.3 + - - +
1168A ALA* 3.1 11.8 + - - +
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Residues in contact with LYS1165 (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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1074A TYR* 4.9 19.0 + - - -
1077A LEU* 5.1 18.3 - - + +
1160A GLY 5.1 1.4 + - - -
1161A VAL* 3.4 27.6 - - + +
1162A ASN* 2.4 47.1 + - - +
1164A LYS* 1.3 80.3 - - - +
1166A PHE* 1.3 58.2 + - - +
1168A ALA* 3.8 9.4 - - - +
1169A LEU* 2.9 27.4 + - - +
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Residues in contact with PHE1166 (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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1066A PHE* 4.4 6.7 - + + -
1069A CYS* 3.6 33.7 - - - -
1070A LEU* 3.9 38.1 - - + -
1073A TYR* 5.2 7.4 - - + -
1144A LEU* 5.3 2.7 - - + -
1147A PHE* 5.1 7.0 - + - -
1161A VAL* 4.8 10.5 - - + -
1162A ASN 3.6 20.0 - - - +
1163A GLU* 3.3 31.5 + - - +
1164A LYS 3.1 0.8 - - - -
1165A LYS* 1.3 80.6 - - - +
1167A ARG* 1.3 59.2 + - - +
1169A LEU* 3.4 25.1 - - + +
1170A MET* 3.0 48.4 + - + +
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Residues in contact with ARG1167 (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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1095A LEU* 5.3 19.5 - - + -
1144A LEU* 5.9 2.0 - - - +
1148A LEU* 4.0 24.5 - - - +
1163A GLU* 2.9 29.7 + - - +
1164A LYS* 2.9 23.2 + - - +
1166A PHE* 1.3 74.1 - - - +
1168A ALA* 1.3 59.2 + - - +
1170A MET* 3.3 29.5 - - + +
1171A GLN* 2.9 33.5 + - + +
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Residues in contact with ALA1168 (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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1082A PRO* 5.3 8.5 - - + +
1091A VAL* 6.5 0.9 - - + -
1133A LEU* 5.0 9.0 - - + +
1164A LYS 3.1 10.3 + - - +
1165A LYS* 4.1 9.4 - - - +
1167A ARG* 1.3 73.6 - - - +
1169A LEU* 1.3 60.2 + - - +
1171A GLN* 3.8 6.7 - - - +
1172A LEU* 3.0 30.5 + - - +
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Residues in contact with LEU1169 (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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1069A CYS* 4.6 9.9 - - + +
1073A TYR* 4.0 11.9 - - + +
1076A LEU* 3.7 34.5 - - + -
1077A LEU* 3.7 36.3 - - + -
1080A TYR* 5.5 3.6 - - + +
1082A PRO* 5.2 8.1 - - + -
1165A LYS 2.9 19.0 + - - +
1166A PHE* 3.4 33.7 - - + +
1167A ARG 3.2 0.2 - - - -
1168A ALA* 1.3 78.3 - - - +
1170A MET* 1.3 64.1 + - + +
1172A LEU* 3.4 4.3 + - - +
1173A LYS* 2.9 29.2 + - + +
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Residues in contact with MET1170 (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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1066A PHE* 4.5 14.1 - - + -
1069A CYS* 5.4 3.4 - - - -
1140A PHE* 4.4 12.8 - - + -
1144A LEU* 3.5 48.7 - - + -
1148A LEU* 6.4 0.7 - - + -
1163A GLU* 5.0 4.5 - - - +
1166A PHE* 3.0 36.5 + - + +
1167A ARG* 3.3 43.3 - - + +
1169A LEU* 1.3 80.0 - - + +
1171A GLN* 1.3 61.3 + - - +
1173A LYS* 3.6 10.9 - - + +
1174A TYR* 2.9 29.3 + - - +
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Residues in contact with GLN1171 (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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1095A LEU* 4.9 9.6 - - + +
1133A LEU* 4.1 17.2 - - + -
1134A GLY* 2.9 42.0 + - - +
1135A SER 3.9 3.6 + - - +
1136A VAL* 3.4 31.8 - - - +
1140A PHE* 5.6 2.5 - - - -
1167A ARG* 2.9 23.4 + - + +
1168A ALA* 3.8 8.7 - - - +
1169A LEU 3.2 0.2 - - - -
1170A MET* 1.3 75.9 - - - +
1172A LEU* 1.3 60.4 + - - +
1174A TYR* 3.3 4.9 + - - +
1175A MET* 2.9 31.0 + - - +
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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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1080A TYR* 3.7 39.5 - - + +
1081A ASN 4.8 0.4 - - - +
1082A PRO* 3.8 33.2 - - + +
1085A LEU* 4.1 28.3 - - + +
1133A LEU* 4.7 19.0 - - + +
1168A ALA 3.0 18.2 + - - +
1169A LEU* 3.9 3.4 - - - +
1171A GLN* 1.3 77.1 - - - +
1173A LYS* 1.3 56.7 + - - +
1175A MET* 3.8 7.8 - - + +
1176A ARG* 2.9 44.8 + - - +
84F TYR* 5.7 2.0 - - - +
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Residues in contact with LYS1173 (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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799A GLU* 6.2 3.1 - - - -
1059A LYS 4.8 6.4 + - - -
1061A SER* 4.8 3.1 + - - -
1062A HIS* 3.4 40.7 + - - +
1063A MET* 4.0 10.1 - - - +
1069A CYS* 6.2 6.7 - - + -
1076A LEU* 5.5 4.9 - - + -
1080A TYR* 3.3 42.2 + - + +
1140A PHE* 6.1 4.2 - - + -
1169A LEU* 2.9 21.0 + - + +
1170A MET* 3.6 11.7 - - + +
1171A GLN 3.2 0.2 - - - -
1172A LEU* 1.3 78.3 - - - +
1174A TYR* 1.3 65.7 + - + +
1176A ARG* 3.4 9.2 + - - +
1177A SER* 3.4 28.4 + - - +
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Residues in contact with TYR1174 (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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1053A ASP* 2.6 42.9 + - - -
1055A ILE* 4.5 13.4 - - + +
1063A MET* 5.7 5.4 - - + -
1129A PRO* 4.9 11.1 - - + +
1135A SER 3.8 8.5 - - - -
1136A VAL* 3.6 32.8 - - + -
1137A SER* 3.4 16.9 + - - -
1140A PHE* 3.8 45.8 - + + -
1170A MET 2.9 17.8 + - - +
1171A GLN* 3.8 6.1 - - - +
1173A LYS* 1.3 79.8 - - - +
1175A MET* 1.3 65.4 + - - +
1177A SER* 3.4 17.3 + - - +
1178A LEU* 3.9 6.1 + - + +
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Residues in contact with MET1175 (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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1089A LEU* 4.2 13.7 - - + -
1129A PRO* 3.3 29.8 - - + +
1130A ALA* 4.0 20.4 - - - +
1132A TYR 3.4 25.1 - - - +
1133A LEU* 3.6 23.8 - - + -
1135A SER 6.0 0.9 - - - +
1171A GLN* 2.9 22.5 + - - +
1172A LEU* 3.9 7.4 - - + +
1174A TYR* 1.3 78.1 - - + +
1176A ARG* 1.3 64.8 + - - +
1178A LEU* 3.2 20.5 + - - +
83F PRO* 5.9 0.4 - - + -
84F TYR* 3.8 35.8 - - + +
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Residues in contact with ARG1176 (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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1059A LYS* 3.4 22.4 + - + +
1079A LYS 5.4 2.2 + - - -
1080A TYR* 3.9 48.7 + - + +
1085A LEU* 3.8 26.3 - - - +
1172A LEU* 2.9 25.0 + - - +
1173A LYS 3.7 5.4 - - - +
1174A TYR 3.3 0.4 - - - -
1175A MET* 1.3 77.9 - - - +
1177A SER* 1.3 58.0 + - - +
1178A LEU* 3.1 6.8 + - - +
84F TYR* 5.0 18.1 + - - -
152F ILE* 6.1 1.6 - - - +
154F ASP* 4.3 32.4 + - - +
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Residues in contact with SER1177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055A ILE* 3.4 32.8 - - - +
1056A ASP* 3.7 5.0 + - - +
1059A LYS* 3.7 40.6 + - - +
1080A TYR* 5.5 1.2 + - - -
1173A LYS* 3.4 22.2 + - - -
1174A TYR* 3.8 11.2 - - - -
1175A MET 3.2 1.2 - - - -
1176A ARG* 1.3 73.3 - - - +
1178A LEU* 1.3 65.0 + - - +
1179A ILE 3.5 0.2 + - - -
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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