Contacts of the helix formed by residues 190 - 197 (chain C) in PDB entry 1KQG
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 ARG 190 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER* 3.5 31.3 - - - +
3C LYS 4.1 6.1 - - - +
4C SER* 2.3 50.3 + - - +
5C LYS 3.5 4.1 + - - +
7C ILE* 3.6 21.9 - - + +
188C VAL 3.5 1.4 + - - -
189C SER* 1.3 71.3 - - - +
191C ARG* 1.3 51.5 + - - +
193C ALA* 3.0 11.8 - - - +
194C LYS* 2.8 44.6 + - - +
201C TYR* 2.4 56.5 + - + +
208C GLU* 3.1 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU* 2.9 38.8 + - + +
285B VAL* 3.0 37.7 - - - +
288B ASP* 5.3 1.4 + - - -
189C SER* 3.0 7.3 + - - +
190C ARG* 1.3 75.1 - - - +
192C TRP* 1.4 56.4 + - - +
194C LYS* 3.1 18.5 + - + +
195C LYS* 2.8 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU* 3.5 28.9 - - + +
9C ARG* 3.3 33.0 - - - -
176C VAL* 4.1 6.6 + - + +
177C LYS 2.9 29.3 + - - -
178C GLY* 4.2 4.9 - - - -
179C SER* 3.6 35.0 + - - +
188C VAL* 3.3 33.9 - - + -
189C SER* 2.8 20.0 + - - +
191C ARG* 1.4 70.9 - - - +
193C ALA* 1.4 66.7 + - - +
195C LYS* 4.8 0.7 - - - -
196C HIS* 2.8 60.8 + + - +
197C HIS* 3.8 24.7 - + - -
200C TRP* 5.0 0.4 - + - -
810C HEM 4.3 7.6 - - - -
811C HQO 5.9 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.5 31.6 - - + -
189C SER 3.1 4.9 + - - +
190C ARG 3.0 14.1 - - - +
192C TRP* 1.4 86.9 - - + +
194C LYS* 1.3 54.1 + - - -
197C HIS* 2.7 44.3 + - - +
200C TRP* 4.1 7.4 - - + -
201C TYR* 3.5 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER* 4.4 12.6 + - - -
101C HIS* 5.5 0.9 - - - +
190C ARG* 2.8 30.7 + - - +
191C ARG* 3.1 18.3 + - + +
193C ALA* 1.3 73.6 - - - +
195C LYS* 1.4 61.2 - - + +
198C PRO* 3.1 31.2 - - - +
201C TYR* 4.0 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASN* 3.1 18.6 + - - +
283B LYS 2.7 24.0 + - - +
284B GLU* 3.3 25.0 + - - +
286B ASP* 4.8 16.4 + - - +
98C GLY 4.6 8.0 + - - -
100C GLU* 4.5 2.9 - - - +
101C HIS* 3.5 54.8 + - + +
191C ARG* 2.8 20.6 + - + +
192C TRP* 4.0 2.2 - - - +
194C LYS* 1.4 78.8 - - + +
196C HIS* 1.3 79.3 + - + +
198C PRO* 3.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASN* 3.1 47.4 + - - -
283B LYS 4.6 4.8 + - - -
284B GLU* 4.8 0.6 + - - -
100C GLU* 3.4 24.1 + - - +
106C VAL* 3.0 24.8 - - - +
176C VAL* 3.7 23.7 - - + +
177C LYS 4.8 0.2 + - - -
192C TRP* 2.8 54.7 + + + +
195C LYS* 1.3 96.3 + - + +
197C HIS* 1.4 75.5 + - + +
198C PRO* 3.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG* 3.1 24.3 + - - -
106C VAL* 3.1 26.6 - - + +
107C GLY 2.6 23.6 + - - +
108C LYS 2.9 17.6 + - - -
109C TYR* 3.7 2.0 - - - -
110C ASN* 3.7 6.4 + - - -
113C GLN* 3.4 21.5 + - - -
192C TRP* 3.8 16.4 - + - -
193C ALA* 2.7 20.8 + - - +
196C HIS* 1.4 90.4 + - + +
198C PRO* 1.4 68.3 - - - +
200C TRP* 3.0 24.2 + - + -
201C TYR 3.1 8.1 + - - -
810C HEM 4.2 1.8 + - - -
811C HQO 5.9 2.4 + - - -
----------------------------------------------------------
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