Contacts of the helix formed by residues 195 - 206 (chain A) in PDB entry 3GNI
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 HIS 195 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE 3.6 10.6 + - - -
152A ARG 3.1 33.4 + - - -
154A GLU* 3.5 52.3 + - + +
157A ALA* 4.0 7.5 - - - +
190A ASP 4.7 0.4 + - - -
191A LEU 4.9 4.9 + - - +
194A ARG* 1.3 92.1 - - + +
196A LYS* 1.3 53.7 + - - +
197A LEU 3.3 2.7 - - - -
198A LEU* 3.2 14.1 + - + +
199A SER* 2.8 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU 5.6 0.7 - - - +
193A THR* 3.1 38.4 + - - +
194A ARG 3.4 5.7 + - - +
195A HIS* 1.3 70.2 - - - +
197A LEU* 1.3 61.5 + - - +
199A SER* 3.9 6.5 - - - -
200A ALA* 3.0 28.4 + - - +
239A ASP* 3.3 29.0 + - - +
240A ARG* 3.9 13.9 - - - +
241A HIS* 3.7 35.5 - - + +
242A ASN* 4.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 5.9 2.5 - - - +
195A HIS 3.3 0.4 - - - -
196A LYS* 1.3 76.3 - - - +
198A LEU* 1.3 59.1 + - - +
200A ALA* 3.2 7.6 + - + +
201A GLU* 3.0 48.4 + - + +
241A HIS* 4.2 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 3.9 29.1 + - + +
157A ALA* 3.8 15.5 - - + -
158A LYS* 3.7 47.1 - - + +
161A LEU* 4.0 10.8 - - + -
162A TRP* 3.5 31.0 - - + -
191A LEU 5.7 0.2 - - - +
195A HIS* 3.2 19.6 + - + +
197A LEU* 1.3 78.3 - - - +
199A SER* 1.3 57.2 + - - +
201A GLU* 3.4 11.7 + - - +
202A PHE* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.9 3.3 - - - +
191A LEU 4.1 8.3 - - - -
192A LEU* 2.6 42.1 + - - +
195A HIS 2.8 16.9 + - - -
196A LYS* 3.9 7.6 - - - -
198A LEU* 1.3 74.9 - - - +
200A ALA* 1.3 59.3 + - - +
202A PHE* 3.4 8.0 + - - +
203A LEU* 2.9 42.5 + - - +
236A LEU* 4.9 0.2 - - - +
242A ASN* 4.8 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS 3.0 20.3 + - - +
197A LEU* 3.2 8.7 + - + +
199A SER* 1.3 77.4 + - - +
201A GLU* 1.3 56.7 + - + +
203A LEU* 3.4 1.4 + - - -
204A GLU* 3.1 25.6 + - - +
241A HIS* 3.2 29.4 - - + +
242A ASN* 3.5 14.1 + - - +
245A ILE* 3.5 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 5.4 4.7 + - - -
162A TRP* 4.0 10.7 - - + -
197A LEU* 3.0 34.3 + - + +
198A LEU* 3.7 20.4 - - - +
199A SER 3.3 0.2 - - - -
200A ALA* 1.3 74.8 - - + +
202A PHE* 1.3 65.8 + - - +
204A GLU* 3.3 5.1 + - - +
205A GLN* 3.0 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.1 44.2 - - + -
162A TRP* 3.5 17.1 - + + -
166A PHE* 3.3 28.7 - + - -
167A TYR* 3.9 11.2 - - - -
192A LEU* 4.0 12.8 - - + -
198A LEU 3.0 18.0 + - - +
199A SER* 3.4 5.8 + - - +
201A GLU* 1.3 76.4 - - - +
203A LEU* 1.3 74.8 + - + +
206A HIS* 2.7 65.5 + + + +
210A PHE* 3.6 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 4.2 4.5 - - + -
199A SER* 2.9 29.2 + - - +
200A ALA 3.8 1.3 - - - +
202A PHE* 1.3 90.4 - - + +
204A GLU* 1.3 60.7 + - - +
206A HIS 5.1 0.9 - - - -
207A TYR* 2.9 36.4 + - - +
210A PHE* 3.6 39.5 - - + -
211A PHE* 4.5 6.5 - - + -
236A LEU* 4.9 12.6 - - + -
242A ASN* 3.7 33.2 - - - +
245A ILE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA 3.1 14.6 + - - +
201A GLU* 3.3 6.3 + - - +
203A LEU* 1.3 76.7 - - - +
205A GLN* 1.3 63.7 + - + +
206A HIS 3.6 0.2 + - - -
207A TYR* 3.8 10.3 + - - +
244A THR* 3.4 28.4 - - + +
245A ILE* 3.7 23.0 - - + +
248A LYS* 4.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TRP* 3.1 33.7 + - - -
201A GLU* 3.0 33.8 + - - +
204A GLU* 1.3 79.3 - - + +
206A HIS* 1.3 73.3 + - + +
207A TYR 3.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU 4.9 0.7 - - - -
162A TRP* 3.4 50.0 + + - -
167A TYR* 3.5 28.5 - + - +
202A PHE* 2.7 55.1 + + + +
203A LEU 3.8 1.6 - - - -
205A GLN* 1.3 86.7 - - + +
207A TYR* 1.3 65.8 + - - +
208A ASP 3.1 3.3 + - - -
209A ARG* 3.3 6.0 + - + -
210A PHE* 3.0 21.8 + - + +
----------------------------------------------------------
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