Contacts of the helix formed by residues 1208 - 1219 (chain A) in PDB entry 1K3A
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 PRO1208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1079A LEU* 3.8 25.4 - - + +
1082A MET* 3.4 35.2 - - + -
1083A ILE* 4.7 6.3 - - + -
1206A ASN 3.9 3.4 - - - +
1207A CYS* 1.3 94.4 - - - +
1209A ASP* 1.3 67.4 + - - +
1210A MET* 4.5 3.4 - - + +
1211A LEU* 3.0 32.3 + - + +
1212A LEU* 3.1 9.4 + - - +
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Residues in contact with ASP1209 (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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1207A CYS 3.4 3.1 + - - +
1208A PRO* 1.3 71.2 - - - +
1210A MET* 1.3 63.1 + - + +
1212A LEU* 3.2 20.5 + - - +
1213A GLU* 3.0 25.5 + - - +
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Residues in contact with MET1210 (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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1083A ILE* 4.2 19.3 - - + -
1208A PRO* 3.2 2.9 + - + +
1209A ASP* 1.3 78.4 - - + +
1211A LEU* 1.3 58.0 + - - +
1213A GLU* 3.5 6.0 + - - +
1214A LEU* 3.0 34.1 + - + +
1235A SER* 3.4 26.0 - - - +
1236A ILE* 3.8 20.4 - - + -
1239A GLU* 3.8 31.2 - - + +
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Residues in contact with LEU1211 (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 MET* 3.8 34.8 - - + +
1083A ILE* 3.3 28.0 - - + -
1086A ALA* 4.2 16.4 - - + -
1172A LEU* 4.2 16.3 - - + +
1175A ILE* 5.3 4.0 - - + -
1176A ALA* 5.1 3.6 - - + -
1207A CYS* 3.8 11.9 - - - -
1208A PRO* 3.0 25.5 + - + +
1210A MET* 1.3 74.3 - - - +
1212A LEU* 1.3 61.5 + - - +
1214A LEU* 3.7 20.1 - - + +
1215A MET* 2.9 38.8 + - + +
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Residues in contact with LEU1212 (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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1203A LYS* 3.8 40.2 - - + -
1204A PRO* 4.0 9.9 - - + +
1207A CYS* 3.8 37.9 - - + +
1208A PRO 3.1 12.8 + - - +
1209A ASP* 3.2 22.0 + - - +
1211A LEU* 1.3 75.2 - - - +
1213A GLU* 1.3 57.6 + - - +
1215A MET* 3.3 10.6 + - + +
1216A ARG* 2.9 27.4 + - - +
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Residues in contact with GLU1213 (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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1209A ASP 3.0 16.8 + - - +
1210A MET* 3.8 6.5 - - - +
1212A LEU* 1.3 74.9 - - - +
1214A LEU* 1.3 66.1 + - + +
1216A ARG* 2.7 50.3 + - - +
1217A MET* 2.9 43.9 + - - +
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Residues in contact with LEU1214 (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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1086A ALA* 5.1 2.2 - - + -
1168A PHE* 4.9 1.3 - - + -
1172A LEU* 3.6 24.7 - - + -
1210A MET 3.0 25.9 + - - +
1211A LEU* 3.7 14.4 - - + +
1212A LEU 3.4 0.2 - - - -
1213A GLU* 1.3 75.9 - - + +
1215A MET* 1.3 59.1 + - - +
1217A MET* 3.1 20.9 + - + +
1218A CYS* 2.8 37.1 + - - -
1232A ILE* 4.2 29.8 - - + -
1235A SER* 3.9 20.6 - - - +
1236A ILE* 4.0 26.9 - - + -
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Residues in contact with MET1215 (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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1169A GLY* 3.8 15.9 - - - +
1172A LEU* 4.0 13.2 - - + +
1173A TRP* 3.9 29.2 - - - +
1176A ALA* 4.6 0.2 - - + -
1202A ASP 5.1 0.2 - - - +
1204A PRO* 4.0 15.9 - - + -
1207A CYS* 3.7 28.0 - - - -
1211A LEU* 2.9 29.1 + - + +
1212A LEU* 3.4 12.3 - - + +
1213A GLU 3.2 0.2 - - - -
1214A LEU* 1.3 76.7 - - - +
1216A ARG* 1.3 63.7 + - - +
1218A CYS* 3.1 5.7 + - - -
1219A TRP* 2.9 64.2 + - + -
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Residues in contact with ARG1216 (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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1200A LEU* 6.0 4.8 - - + +
1212A LEU 2.9 14.4 + - - +
1213A GLU* 2.7 48.2 + - - +
1215A MET* 1.3 75.9 - - - +
1217A MET* 1.3 70.4 + - - +
1219A TRP* 3.5 13.1 + - - +
1220A GLN* 3.2 43.4 + - - +
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Residues in contact with MET1217 (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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1213A GLU* 2.9 45.7 + - - +
1214A LEU* 3.1 25.8 + - + +
1216A ARG* 1.3 80.6 - - - +
1218A CYS* 1.3 64.5 + - - +
1220A GLN* 3.3 26.3 + - - +
1225A MET 5.6 0.2 - - - -
1226A ARG* 3.6 2.4 - - - +
1227A PRO* 3.4 44.0 - - + +
1231A GLU* 5.8 3.1 - - + +
1232A ILE* 5.8 0.7 - - + -
1235A SER* 5.3 9.9 - - - +
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Residues in contact with CYS1218 (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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1165A VAL* 3.4 41.5 - - - +
1166A TRP* 3.6 11.6 - - - -
1168A PHE* 3.8 24.5 - - - -
1169A GLY* 3.8 17.9 - - - -
1172A LEU* 5.1 0.4 - - - -
1214A LEU* 2.8 26.7 + - - +
1215A MET 3.8 1.8 - - - +
1217A MET* 1.3 73.8 - - - +
1219A TRP* 1.3 58.8 + - + +
1220A GLN 3.4 0.7 - - - -
1226A ARG* 3.2 23.5 + - - -
1227A PRO* 4.3 3.1 - - - -
1232A ILE* 4.0 9.2 - - - -
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Residues in contact with TRP1219 (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 TRP* 3.4 49.0 + + + -
1169A GLY* 3.3 28.3 - - - -
1170A VAL* 3.6 8.8 - - + +
1173A TRP* 4.0 3.4 - + + -
1183A TYR* 5.9 1.1 - - - -
1200A LEU* 3.6 46.9 - - + +
1201A LEU* 3.8 53.4 - - + -
1202A ASP 4.9 1.3 - - - -
1215A MET* 2.9 50.8 + - + +
1216A ARG* 3.5 8.7 + - - +
1217A MET 3.1 0.4 - - - -
1218A CYS* 1.3 85.4 - - + +
1220A GLN* 1.3 63.5 + - - +
1221A TYR* 3.3 2.9 + - - +
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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