Contacts of the helix formed by residues 1145 - 1149 (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 PRO1145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1104A ARG 4.0 14.8 - - - +
1105A ASP* 3.5 13.9 - - - +
1109A ARG* 3.4 28.9 - - - +
1126A MET* 3.9 15.9 - - + -
1144A LEU* 1.3 84.0 - - + +
1146A VAL* 1.3 63.9 + - - +
1147A ARG 3.3 2.7 - - - -
1148A TRP* 2.9 23.5 + - + -
1149A MET* 3.3 19.7 + - + +
7B GLU 3.2 13.5 - - - +
8B TYR* 3.8 12.7 - - + -
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Residues in contact with VAL1146 (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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1144A LEU* 2.8 19.8 + - + +
1145A PRO* 1.3 70.5 - - - +
1147A ARG* 1.3 61.9 + - + +
1148A TRP 3.2 4.0 + - - -
1149A MET* 3.3 22.4 + - - +
1154A LEU* 3.7 16.1 - - + +
1183A TYR* 5.6 0.2 - - - -
1188A ASN* 4.4 8.7 - - + +
1191A VAL* 3.8 22.6 - - + +
1192A LEU* 3.4 35.4 - - + -
1195A VAL* 5.8 0.7 - - - +
7B GLU 3.9 2.4 + - - -
9B VAL* 4.0 28.0 - - + +
11B ILE* 4.8 11.7 - - + -
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Residues in contact with ARG1147 (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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1145A PRO 3.2 1.6 + - - -
1146A VAL* 1.3 77.7 - - + +
1148A TRP* 1.3 80.1 + - + +
1149A MET 3.6 0.7 - - - -
1166A TRP* 5.6 0.2 + - - -
1170A VAL* 4.1 12.0 - - - +
1181A GLN* 3.4 26.2 + - - +
1182A PRO* 3.0 21.4 + - + +
1183A TYR* 2.8 64.2 + - + -
1184A GLN* 4.4 1.0 - - - +
1186A LEU 2.7 23.0 + - - -
1187A SER* 3.8 1.4 - - - +
1188A ASN* 3.2 32.0 + - - +
1191A VAL* 3.5 21.0 - - + +
6B GLY 5.1 5.9 + - - -
7B GLU* 5.1 2.4 + - - +
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Residues in contact with TRP1148 (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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1058A LYS* 6.2 1.8 - - + -
1105A ASP* 5.7 0.9 - - - +
1106A LEU 3.4 26.5 - - - +
1107A ALA* 3.4 7.3 - - + +
1109A ARG* 3.3 35.7 - - - +
1145A PRO* 2.9 19.1 + - + +
1147A ARG* 1.3 100.9 - - + +
1149A MET* 1.3 60.3 + - - +
1166A TRP* 3.5 10.8 - - - -
1167A SER* 2.6 32.2 + - - +
1170A VAL* 3.5 26.8 - - + +
1171A VAL* 4.9 0.2 - - + -
1174A GLU* 3.0 39.4 + - - -
1181A GLN* 4.3 7.4 - - - -
1182A PRO* 3.6 26.9 - - + -
7B GLU* 3.9 25.6 - - + -
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Residues in contact with MET1149 (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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1104A ARG 5.4 1.6 - - - +
1144A LEU* 3.6 35.4 - - + -
1145A PRO* 3.4 27.1 - - + +
1146A VAL* 3.3 16.2 + - - +
1147A ARG 5.3 0.5 - - - -
1148A TRP* 1.3 80.4 - - - +
1150A SER* 1.3 66.1 + - - +
1153A SER* 3.8 25.4 - - - +
1154A LEU* 3.8 27.2 - - + +
1159A PHE* 3.7 36.6 - - + -
1166A TRP* 3.4 11.5 + - - -
1167A SER* 4.7 1.3 - - - +
1195A VAL* 4.3 4.5 - - - +
11B ILE* 4.8 2.5 - - + -
13B PHE* 4.7 3.8 - - + -
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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