Contacts of the helix formed by residues 187 - 196 (chain Y) 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 Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184Y TYR* 2.9 32.8 + - + +
186Y ASN* 1.3 81.9 - - - +
188Y LYS* 1.3 62.8 + - - +
189Y ALA* 3.1 14.6 + - - +
190Y SER* 2.5 40.5 + - - -
191Y TYR 3.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Y LEU 5.4 0.2 + - - -
134Y LEU* 3.3 44.6 + - + +
136Y ILE 4.3 11.5 + - - -
175Y MET* 4.0 16.5 - - + +
180Y TYR* 3.7 37.0 - - + +
186Y ASN 2.8 16.3 + - - +
187Y ASP* 1.3 71.3 - - - +
189Y ALA* 1.3 59.7 + - + +
190Y SER 3.3 0.2 - - - -
191Y TYR* 3.4 8.5 - - - +
192Y ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134Y LEU* 3.8 26.9 - - + +
187Y ASP* 3.1 11.3 + - - +
188Y LYS* 1.3 82.0 - - + +
190Y SER* 1.3 62.5 + - - +
192Y ALA* 3.3 4.0 + - - +
193Y LYS* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184Y TYR* 3.7 23.8 - - - -
187Y ASP* 2.5 30.3 + - - -
189Y ALA* 1.3 75.3 - - - +
191Y TYR* 1.3 60.8 + - - +
193Y LYS* 3.7 9.2 - - - +
194Y GLY* 2.9 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 191 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Y TYR 4.9 1.3 - - - -
32Y ILE* 4.5 12.3 - - + +
91Y PHE* 3.9 9.2 - - - -
173Y VAL* 4.1 5.0 - - + +
174Y ASP 2.9 29.2 + - - -
175Y MET* 3.7 21.5 - - + -
179Y ALA* 3.8 23.5 + - - +
180Y TYR* 3.5 30.7 - + + -
184Y TYR* 3.6 35.5 + + + -
187Y ASP 3.5 2.6 + - - -
188Y LYS* 3.2 13.9 + - - +
189Y ALA 3.2 0.4 - - - -
190Y SER* 1.3 80.6 - - - +
192Y ALA* 1.3 64.2 + - - +
194Y GLY* 3.3 0.5 + - - -
195Y ILE* 3.0 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130Y ASN* 3.9 20.9 - - + +
133Y LEU* 4.3 16.1 - - + +
134Y LEU* 4.2 16.4 - - + -
175Y MET* 5.3 1.1 - - + -
188Y LYS 2.9 13.4 + - - +
189Y ALA 3.3 8.7 + - - +
191Y TYR* 1.3 82.1 - - + +
193Y LYS* 1.3 61.7 - - - +
195Y ILE* 3.3 15.7 - - - +
196Y TRP* 3.1 22.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 193 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130Y ASN* 4.7 7.6 - - - +
189Y ALA 3.1 15.9 + - - +
190Y SER* 3.7 8.7 - - - +
192Y ALA* 1.3 78.7 - - - +
194Y GLY* 1.3 64.7 + - - +
195Y ILE 3.5 0.2 + - - -
196Y TRP* 3.5 22.2 + - - +
197Y ASN* 3.9 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Y TYR* 3.3 22.7 - - - -
184Y TYR* 4.5 6.7 - - - -
190Y SER 2.9 17.3 + - - -
191Y TYR 3.9 0.7 - - - -
193Y LYS* 1.3 80.5 - - - +
195Y ILE* 1.3 60.5 + - - +
197Y ASN* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Y TYR* 5.0 2.7 + - - -
32Y ILE* 4.2 8.5 - - + -
91Y PHE* 3.9 26.5 - - + -
95Y LEU* 4.0 9.6 - - + -
133Y LEU* 5.5 1.6 - - + -
173Y VAL* 4.2 27.1 - - + -
184Y TYR* 5.3 0.2 + - - -
191Y TYR* 3.0 45.9 + - + +
192Y ALA* 3.3 18.4 - - - +
194Y GLY* 1.3 71.3 - - - +
196Y TRP* 1.3 73.8 + - + +
197Y ASN 2.9 5.6 - - - -
198Y VAL* 2.9 29.7 + - + +
199Y ILE* 3.4 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 196 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Y GLY* 3.3 17.0 - - - -
122Y PHE* 4.5 2.7 - + + -
125Y PHE* 3.7 10.3 - + - -
126Y LYS* 4.0 41.5 - - + +
129Y PHE* 3.5 39.7 - + + -
130Y ASN* 2.7 29.5 + - - +
133Y LEU* 5.2 1.1 - - + +
171Y PHE* 3.5 35.4 - + - -
173Y VAL* 5.9 0.9 - - + -
192Y ALA 3.1 23.0 + - - -
193Y LYS* 3.5 15.0 - - + +
194Y GLY 3.2 1.2 - - - -
195Y ILE* 1.3 82.0 - - + +
197Y ASN* 1.3 60.9 + - - +
198Y VAL 3.3 0.7 + - - -
199Y ILE* 3.5 19.5 + - + +
201Y TRP* 3.6 31.2 + + - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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