Contacts of the helix formed by residues 197 - 206 (chain G) in PDB entry 1KN0
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 GLU 197 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G LYS* 2.6 29.3 + - - +
194G GLN* 5.0 1.2 + - - -
195G ASP 3.8 2.2 - - - +
196G LEU* 1.3 84.7 - - - +
198G PRO* 1.3 60.5 - - - +
199G SER* 3.3 5.5 - - - -
200G VAL* 3.1 18.4 + - + +
201G GLU* 2.8 31.9 + - - +
42H ALA* 3.1 23.0 - - - +
45H GLN* 2.8 26.7 + - - +
77H GLU* 4.7 10.5 + - + +
78H MET* 4.3 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 198 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194G GLN* 5.6 2.7 - - - +
196G LEU* 3.9 22.8 - - + +
197G GLU* 1.3 86.2 - - - +
199G SER* 1.3 64.5 + - - +
201G GLU* 3.9 7.1 - - + +
202G GLU* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G GLU* 3.3 4.4 - - - -
198G PRO* 1.3 81.3 - - - +
200G VAL* 1.3 64.7 + - - +
202G GLU* 3.6 9.8 + - - +
203G ALA* 3.3 19.8 + - - +
38H ALA* 3.9 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G GLU* 3.1 24.5 + - + +
199G SER* 1.3 73.7 - - - +
201G GLU* 1.3 65.9 + - - +
202G GLU 2.7 6.1 + - - -
203G ALA* 3.0 3.5 + - - +
204G ARG* 3.0 50.8 + - - +
35H GLU* 4.9 3.1 - - + +
38H ALA* 3.5 37.0 - - + +
39H ILE* 3.3 26.2 - - + +
42H ALA* 4.0 9.2 - - + -
77H GLU 4.5 1.3 - - - +
78H MET* 3.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G LEU* 4.4 11.7 - - + -
197G GLU 2.8 23.5 + - - +
198G PRO* 3.9 6.5 - - + +
200G VAL* 1.3 73.3 - - - +
202G GLU* 1.3 61.0 + - - +
204G ARG* 3.5 15.8 + - - +
205G TYR* 3.2 21.9 + - + +
77H GLU* 4.5 5.1 + - - +
36I TYR* 3.5 33.1 + - - -
37I GLN* 4.6 11.1 - - - +
40I GLN* 3.7 18.3 + - - +
41I LYS* 5.3 7.7 + - - +
44I ARG* 4.5 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G PRO 3.0 17.8 + - - +
199G SER* 3.6 8.5 - - - +
200G VAL 2.7 4.6 + - - -
201G GLU* 1.3 71.3 - - - +
203G ALA* 1.3 67.2 + - - +
204G ARG 3.0 1.1 - - - -
205G TYR* 2.9 17.3 + - - +
206G ASN* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G SER 3.3 9.9 + - - +
200G VAL 3.0 6.5 + - - +
202G GLU* 1.3 80.0 + - - +
204G ARG* 1.3 62.2 + - - +
206G ASN* 3.4 12.2 + - - +
207G SER* 3.2 19.4 + - - -
32H THR* 4.4 4.3 + - - -
34H GLU* 3.4 22.5 - - + +
35H GLU* 3.3 33.0 - - - +
38H ALA* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200G VAL* 3.0 28.9 + - - +
201G GLU* 3.5 23.9 + - - +
203G ALA* 1.3 75.3 - - - +
205G TYR* 1.3 59.5 + - - +
207G SER* 2.7 29.6 + - - -
208G CYS* 3.6 10.3 + - - -
35H GLU* 3.1 33.6 + - - +
77H GLU 3.1 16.0 + - - -
78H MET 2.6 39.2 + - - -
79H PHE* 3.2 19.2 + - - +
80H GLY* 3.6 4.4 - - - +
82H ASN* 5.6 0.4 - - - -
116H LYS* 4.7 7.2 - - - +
36I TYR* 2.7 48.8 + - + +
40I GLN* 3.9 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G GLU* 3.2 18.2 + - - +
202G GLU* 2.9 11.0 + - - +
204G ARG* 1.3 79.9 - - - +
206G ASN* 1.3 69.2 + - - +
207G SER 3.2 3.3 + - - -
208G CYS* 3.3 16.7 + - - +
33I ALA* 3.3 47.8 + - + +
34I GLU* 4.7 6.6 + - - +
36I TYR* 4.5 9.4 - + + -
37I GLN* 3.3 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G GLU* 3.0 38.3 + - - +
203G ALA* 3.7 11.1 - - - +
204G ARG 3.1 0.2 - - - -
205G TYR* 1.3 88.9 - - - +
207G SER* 1.3 56.3 + - - +
208G CYS 3.3 8.0 + - - +
34H GLU* 4.7 13.2 - - + +
----------------------------------------------------------
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