Contacts of the helix formed by residues 187 - 196 (chain A) in PDB entry 1KKC
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 ASP 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A TYR* 2.9 28.6 + - + +
185A LEU 4.6 0.4 - - - -
186A ASN* 1.3 80.5 - - - +
188A LYS* 1.3 59.7 + - - +
189A ALA* 3.6 10.9 + - - +
190A SER* 2.7 41.7 + - - -
191A TYR 3.5 6.4 + - - -
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Residues in contact with LYS 188 (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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133A LEU 5.1 0.6 + - - +
134A LEU* 3.5 42.4 + - + +
136A ILE 4.3 10.9 + - - -
175A MET* 3.7 21.1 - - + +
180A TYR* 3.7 32.5 - - + +
186A ASN 2.8 16.0 + - - +
187A ASP* 1.3 70.2 - - - +
189A ALA* 1.3 62.0 + - + +
191A TYR* 3.6 7.7 - - - +
192A ALA* 3.0 29.5 + - - +
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Residues in contact with ALA 189 (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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134A LEU* 3.5 28.7 - - + -
187A ASP* 3.1 10.8 + - - +
188A LYS* 1.3 84.0 - - + +
190A SER* 1.3 56.9 + - - +
192A ALA* 3.5 2.2 + - - +
193A LYS* 3.1 50.7 + - - +
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Residues in contact with SER 190 (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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184A TYR* 3.5 23.0 - - - -
187A ASP* 2.7 33.2 + - - -
189A ALA* 1.3 77.5 - - - +
191A TYR* 1.3 61.1 + - - +
193A LYS* 3.9 7.2 - - - +
194A GLY* 2.9 22.5 + - - -
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Residues in contact with TYR 191 (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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31A TYR 5.0 2.0 - - - -
32A ILE* 4.6 10.5 - - + -
91A PHE* 3.8 18.0 - - - -
173A VAL* 4.1 5.5 - - + +
174A ASP 2.8 29.3 + - - -
175A MET* 3.6 22.0 - - + -
179A ALA* 3.7 26.5 + - - +
180A TYR* 3.4 34.1 - + + -
184A TYR* 3.6 35.0 + + + -
187A ASP 3.5 3.7 + - - +
188A LYS 3.3 9.3 + - - +
190A SER* 1.3 76.2 - - - +
192A ALA* 1.3 61.4 + - - +
194A GLY* 3.1 1.0 + - - -
195A ILE* 2.9 50.5 + - + +
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Residues in contact with ALA 192 (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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130A ASN* 3.7 22.7 - - + +
133A LEU* 3.9 24.0 - - + +
134A LEU* 4.8 4.3 - - + -
175A MET* 5.2 0.9 - - - -
188A LYS 3.0 16.6 + - - +
189A ALA* 3.7 7.2 - - - +
191A TYR* 1.3 82.9 - - + +
193A LYS* 1.3 62.5 + - - +
195A ILE* 3.2 20.2 - - - +
196A TRP* 3.1 17.5 + - - -
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Residues in contact with LYS 193 (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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130A ASN* 3.9 26.0 - - - +
134A LEU* 5.5 4.6 - - - +
189A ALA* 3.1 35.3 + - - +
190A SER* 4.2 6.3 - - - +
191A TYR 3.3 0.2 - - - -
192A ALA* 1.3 75.9 - - - +
194A GLY* 1.3 60.8 + - - +
196A TRP* 3.5 21.1 - - + +
197A ASN* 4.1 5.9 + - - -
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Residues in contact with GLY 194 (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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31A TYR* 3.4 23.3 - - - -
184A TYR* 4.6 6.1 - - - -
190A SER 2.9 18.0 + - - -
191A TYR 3.1 1.1 + - - -
193A LYS* 1.3 75.3 - - - +
195A ILE* 1.3 63.8 + - - +
196A TRP 3.1 2.5 - - - -
197A ASN* 3.1 28.0 + - - +
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Residues in contact with ILE 195 (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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31A TYR* 5.0 2.4 + - - -
32A ILE* 4.2 8.3 - - + -
91A PHE* 4.0 15.5 - - + -
95A LEU* 3.9 21.1 - - + -
133A LEU* 5.5 1.3 - - + -
173A VAL* 4.0 26.7 - - + -
184A TYR* 5.3 0.2 + - - -
191A TYR* 2.9 44.1 + - + +
192A ALA* 3.2 22.4 - - - +
194A GLY* 1.3 77.5 - - - +
196A TRP* 1.3 67.3 + - + +
198A VAL* 2.9 32.9 + - + +
199A ILE* 3.4 12.9 + - + +
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Residues in contact with TRP 196 (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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103A GLY* 3.4 16.5 - - - -
122A PHE* 4.8 0.9 - + - -
125A PHE* 3.7 16.2 - + - -
126A LYS* 3.5 53.5 - - + +
129A PHE* 3.7 30.1 - + - -
130A ASN* 2.8 30.8 + - - +
133A LEU* 5.7 0.7 - - + -
171A PHE* 3.8 13.5 - + - -
173A VAL* 5.9 1.1 - - + -
192A ALA 3.1 19.3 + - - -
193A LYS* 3.5 20.0 - - + +
194A GLY 3.1 1.0 + - - -
195A ILE* 1.3 80.7 - - + +
197A ASN* 1.3 62.8 + - - +
198A VAL 3.3 1.0 + - - -
199A ILE* 3.5 21.8 + - + +
201A TRP* 3.7 29.3 + + - -
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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