Contacts of the helix formed by residues 187 - 196 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184X TYR* 3.0 28.1 + - + +
185X LEU 3.2 0.4 - - - -
186X ASN* 1.3 82.6 - - - +
188X LYS* 1.3 60.3 + - - +
189X ALA* 3.1 11.1 + - - +
190X SER* 2.6 41.2 + - - -
191X TYR 3.4 6.2 + - - -
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Residues in contact with LYS 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X LEU 5.3 0.2 + - - -
134X LEU* 3.3 41.1 + - + +
136X ILE 4.1 11.9 + - - -
175X MET* 3.9 21.2 - - + +
180X TYR* 3.7 37.6 - - + +
186X ASN 2.8 15.6 + - - +
187X ASP* 1.3 71.6 - - - +
189X ALA* 1.3 59.3 + - + +
191X TYR* 3.2 8.9 + - - +
192X ALA* 2.9 28.4 + - - +
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Residues in contact with ALA 189 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X LEU* 3.7 31.6 - - + -
187X ASP* 3.0 9.9 - - - +
188X LYS* 1.3 82.6 - - + +
190X SER* 1.3 58.9 + - - +
192X ALA* 3.4 2.6 + - - +
193X LYS* 3.0 51.0 + - - +
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Residues in contact with SER 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X TYR* 3.6 22.0 - - - -
187X ASP* 2.6 35.6 + - - -
189X ALA* 1.3 74.4 - - - +
191X TYR* 1.3 61.3 + - - +
193X LYS* 3.8 8.2 - - - +
194X GLY* 2.9 23.9 + - - -
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Residues in contact with TYR 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X TYR 4.9 2.2 - - - -
32X ILE* 4.6 12.5 - - + +
91X PHE* 3.8 19.6 - - - -
173X VAL* 4.0 6.0 - - + +
174X ASP 3.0 28.9 + - - -
175X MET* 3.7 18.8 - - - -
179X ALA* 3.8 24.2 + - + +
180X TYR* 3.5 33.4 - + + -
184X TYR* 3.6 35.2 + + + -
187X ASP 3.4 2.6 + - - -
188X LYS* 3.2 13.2 + - - +
190X SER* 1.3 76.9 - - - +
192X ALA* 1.3 67.4 + - - +
194X GLY* 3.1 1.6 + - - -
195X ILE* 3.0 43.1 + - + +
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Residues in contact with ALA 192 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X ASN* 3.5 20.9 - - + +
133X LEU* 3.9 21.3 - - + +
134X LEU* 4.2 14.4 - - + -
175X MET* 5.4 0.9 - - - -
188X LYS 2.9 16.1 + - - +
189X ALA* 3.7 4.7 - - - +
190X SER 3.3 0.2 - - - -
191X TYR* 1.3 83.6 - - + +
193X LYS* 1.3 62.1 + - - +
194X GLY 3.3 0.3 + - - -
195X ILE* 3.3 16.7 - - - +
196X TRP* 3.2 18.2 + - - -
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Residues in contact with LYS 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X ASP* 6.1 0.9 - - - -
130X ASN* 4.1 24.9 - - - +
134X LEU* 5.8 2.5 - - - +
189X ALA* 3.0 36.9 + - - +
190X SER* 4.0 7.4 - - - +
191X TYR 3.3 0.2 - - - -
192X ALA* 1.3 77.0 - - - +
194X GLY* 1.3 61.0 + - - +
196X TRP* 3.6 19.1 + - - +
197X ASN* 4.1 6.4 + - - -
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Residues in contact with GLY 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X TYR* 3.4 25.5 - - - -
184X TYR* 4.6 7.0 - - - -
190X SER 2.9 15.4 + - - -
191X TYR 3.1 2.4 + - - -
193X LYS* 1.3 74.3 - - - +
195X ILE* 1.3 65.1 + - - +
196X TRP 3.2 2.7 - - - -
197X ASN* 3.1 26.6 + - - +
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Residues in contact with ILE 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X TYR* 5.0 2.9 + - - -
32X ILE* 4.4 7.9 - - + -
91X PHE* 4.0 13.7 - - + -
95X LEU* 3.9 19.3 - - + -
133X LEU* 5.6 1.1 - - + -
173X VAL* 4.0 30.7 - - + -
184X TYR* 5.3 0.2 + - - -
191X TYR* 3.0 42.8 + - + +
192X ALA* 3.3 20.6 - - - +
194X GLY* 1.3 74.0 - - - +
196X TRP* 1.3 72.1 + - + +
197X ASN 3.0 0.4 - - - -
198X VAL* 3.0 31.4 + - + +
199X ILE* 3.3 13.9 - - + +
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Residues in contact with TRP 196 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X GLY* 3.4 16.6 - - - -
122X PHE* 4.9 1.1 - + + -
125X PHE* 3.7 19.7 - + - -
126X LYS* 3.7 43.9 - - + +
129X PHE* 3.6 38.8 - + + -
130X ASN* 2.8 31.7 + - - +
133X LEU* 5.3 1.1 - - + -
171X PHE* 3.6 22.7 - + - -
173X VAL* 5.8 0.4 - - + -
192X ALA 3.2 20.3 + - - -
193X LYS* 3.6 17.5 - - + +
194X GLY 3.2 0.8 - - - -
195X ILE* 1.3 82.3 - - + +
197X ASN* 1.3 62.6 + - - +
198X VAL 3.3 0.9 + - - -
199X ILE* 3.5 15.1 + - + +
201X TRP* 3.8 26.3 + + - -
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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