Contacts of the helix formed by residues 1173 - 1189 (chain A) in PDB entry 4K6J
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 GLY1173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1171A ALA 4.5 0.2 + - - -
1172A VAL* 1.3 76.9 - - - +
1174A THR* 1.3 67.0 + - - -
1175A THR* 3.4 3.1 - - - -
1176A GLY 3.2 3.8 + - - +
1177A GLN* 2.9 29.0 + - - +
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Residues in contact with THR1174 (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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1173A GLY* 1.3 70.9 - - - -
1175A THR* 1.3 56.7 + - + +
1177A GLN* 3.2 13.2 + - + +
1178A LYS* 2.7 68.1 + - + +
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Residues in contact with THR1175 (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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1173A GLY* 5.0 1.4 - - - -
1174A THR* 1.3 78.6 - - + +
1176A GLY* 1.3 64.5 + - - +
1178A LYS* 3.2 8.8 + - + +
1179A SER* 2.8 33.3 + - - -
1182A ARG* 4.7 2.3 + - - +
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Residues in contact with GLY1176 (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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1172A VAL* 3.6 21.1 - - - -
1173A GLY 3.2 4.2 + - - +
1175A THR* 1.3 84.2 + - - +
1177A GLN* 1.3 61.3 + - - +
1179A SER* 3.3 7.0 + - - -
1180A ILE* 3.1 30.9 + - - +
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Residues in contact with GLN1177 (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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1163A LEU* 4.0 20.5 - - + +
1167A ASN* 2.9 38.8 + - - +
1172A VAL* 3.1 29.1 + - + +
1173A GLY* 2.9 22.4 + - - +
1174A THR* 3.5 10.7 + - + +
1176A GLY* 1.3 73.7 - - - +
1178A LYS* 1.3 59.2 + - + +
1180A ILE* 3.3 4.7 + - - +
1181A SER* 3.0 31.7 + - - +
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Residues in contact with LYS1178 (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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1174A THR* 2.7 46.3 + - + +
1175A THR* 3.7 8.5 - - + +
1177A GLN* 1.3 75.4 - - + +
1179A SER* 1.3 57.4 + - - +
1181A SER* 3.2 9.7 + - - -
1182A ARG* 2.9 48.4 + - - +
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Residues in contact with SER1179 (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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1134A GLN* 5.4 0.3 + - - -
1175A THR 2.8 15.0 + - - -
1176A GLY* 3.3 12.0 + - - -
1178A LYS* 1.3 73.8 - - - +
1180A ILE* 1.3 64.5 + - - +
1182A ARG* 3.3 27.8 + - - +
1183A VAL* 3.0 31.9 + - - +
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Residues in contact with ILE1180 (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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1127A LEU* 4.2 28.3 - - + -
1159A LEU* 4.7 7.0 - - + +
1162A PHE* 4.2 26.0 - - + -
1163A LEU* 4.2 33.9 - - + -
1166A MET* 5.0 6.1 - - + -
1172A VAL* 5.3 7.0 - - + -
1176A GLY 3.1 22.1 + - - +
1177A GLN* 3.6 7.2 - - - +
1179A SER* 1.3 77.4 - - - +
1181A SER* 1.3 65.7 + - - +
1183A VAL* 3.1 8.6 + - - +
1184A ILE* 3.0 30.7 + - + +
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Residues in contact with SER1181 (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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1163A LEU* 3.4 15.6 - - - +
1177A GLN* 3.0 16.0 + - - +
1178A LYS* 3.2 12.9 + - - -
1180A ILE* 1.3 77.5 - - - +
1182A ARG* 1.3 58.1 + - - +
1184A ILE* 3.1 16.0 + - - +
1185A GLU* 2.9 27.2 + - - +
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Residues in contact with ARG1182 (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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1134A GLN* 4.5 6.0 - - - +
1175A THR* 4.7 3.2 + - - +
1178A LYS* 2.9 35.1 + - - +
1179A SER* 3.6 34.0 - - - +
1180A ILE 3.2 0.4 - - - -
1181A SER* 1.3 75.1 - - - +
1183A VAL* 1.3 57.2 - - - +
1185A GLU* 3.3 10.5 + - + +
1186A TYR* 2.9 29.6 + - - +
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Residues in contact with VAL1183 (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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1126A ALA 5.1 0.4 - - - +
1127A LEU* 4.3 20.2 - - + +
1130A GLY* 4.1 27.6 - - - +
1131A CYS* 4.8 2.2 - - + +
1134A GLN* 3.5 33.7 - - - +
1159A LEU* 4.0 21.5 - - + -
1179A SER 3.0 17.6 + - - +
1180A ILE* 3.1 9.8 + - - +
1182A ARG* 1.3 76.1 - - - +
1184A ILE* 1.3 63.0 + - - +
1186A TYR* 3.5 2.9 + - - +
1187A LEU* 3.1 25.3 + - + +
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Residues in contact with ILE1184 (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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1156A THR* 3.9 16.0 - - - +
1159A LEU* 3.7 28.3 - - + +
1160A LYS* 3.8 46.2 - - + +
1163A LEU* 4.5 7.6 - - + -
1180A ILE* 3.0 21.4 + - + +
1181A SER* 3.1 15.2 + - - +
1183A VAL* 1.3 75.0 - - - +
1185A GLU* 1.3 60.8 + - - +
1187A LEU* 3.8 0.9 - - - -
1188A GLU* 2.8 50.1 + - - +
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Residues in contact with GLU1185 (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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1181A SER 2.9 13.1 + - - +
1182A ARG* 3.4 13.2 - - - +
1184A ILE* 1.3 76.2 - - - +
1186A TYR* 1.3 67.9 + - - +
1188A GLU* 3.0 31.4 + - - +
1189A HIS* 3.0 43.1 + - + +
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Residues in contact with TYR1186 (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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1130A GLY 5.0 0.9 - - - -
1133A CYS* 3.3 18.2 + - + -
1134A GLN* 3.4 49.9 + - + +
1137A PRO* 4.3 12.3 - - - +
1140A VAL* 3.9 10.4 - - + +
1182A ARG 2.9 17.2 + - - +
1183A VAL 3.7 4.9 - - - +
1185A GLU* 1.3 78.9 - - - +
1187A LEU* 1.3 71.6 + - + +
1189A HIS* 3.0 19.9 + - + +
1190A CYS* 3.5 28.1 - - - -
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Residues in contact with LEU1187 (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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1130A GLY* 4.0 17.3 - - - -
1133A CYS* 4.1 28.0 - - + -
1152A PHE* 3.8 31.3 - - + +
1155A MET* 3.7 28.5 - - + -
1156A THR* 3.4 20.6 - - + -
1159A LEU* 4.1 20.9 - - + -
1183A VAL* 3.1 17.1 + - + +
1186A TYR* 1.3 86.3 - - + +
1188A GLU* 1.3 58.5 + - - +
1189A HIS 3.0 0.2 - - - -
1190A CYS* 2.9 30.6 + - - +
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Residues in contact with GLU1188 (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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1156A THR* 4.1 18.7 + - + +
1160A LYS* 3.1 35.9 + - - -
1184A ILE* 2.8 21.9 + - - +
1185A GLU* 3.0 29.4 + - - +
1187A LEU* 1.3 76.1 - - - +
1189A HIS* 1.3 66.8 + - + +
1190A CYS* 3.3 5.1 + - - +
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Residues in contact with HIS1189 (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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1185A GLU* 3.0 42.9 + - - +
1186A TYR* 3.0 14.8 + - + +
1188A GLU* 1.3 88.9 + - + +
1190A CYS* 1.3 60.7 + - - +
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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