Contacts of the helix formed by residues 193 - 204 (chain A) in PDB entry 4OMD
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 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A MET 5.5 2.3 + - - -
190A ASN* 3.4 28.9 + - - +
191A ASP 3.2 2.6 + - - +
192A ASN* 1.3 77.8 - - - +
194A HIS* 1.3 70.1 + - + +
195A GLY 3.4 1.6 - - - -
196A THR* 3.2 7.5 + - - -
197A ARG* 3.1 71.5 + - - +
355A ASP* 3.6 16.7 + - - +
356A LEU* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP* 2.6 28.7 + - - -
154A ASP* 3.2 15.0 + - - +
191A ASP 4.7 1.1 - - - +
193A ARG* 1.3 83.6 - - + +
195A GLY* 1.3 63.1 + - - +
197A ARG* 3.2 9.5 + - - +
198A CYS* 3.2 29.0 + - - -
253A SER* 3.2 32.8 - - - -
364A HIS* 4.5 9.0 - + - -
368A SER* 2.7 30.7 + - - -
4H ARG* 3.5 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.9 5.3 - - - +
153A ASP* 3.1 22.8 + - - -
154A ASP* 2.7 18.2 + - - -
155A GLY 3.3 20.2 - - - -
156A ILE* 5.2 0.3 - - - +
194A HIS* 1.3 74.7 - - - +
196A THR* 1.3 56.2 + - - +
198A CYS* 3.3 3.6 + - - +
199A ALA* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASP* 4.5 0.4 + - - -
155A GLY 3.6 2.3 + - - -
156A ILE* 3.7 4.6 - - - +
157A GLU* 3.1 40.0 + - + +
160A HIS* 4.4 1.6 - - + -
163A LEU* 4.2 8.5 - - + +
184A PRO* 4.0 8.3 - - - +
192A ASN 4.7 0.7 + - - -
193A ARG* 3.2 11.9 + - - -
195A GLY* 1.3 72.9 - - - +
197A ARG* 1.3 66.1 + - - +
199A ALA* 3.4 6.7 + - - +
200A GLY 3.2 8.8 + - - -
354A THR* 2.8 38.8 + - - +
355A ASP 4.0 17.7 - - - +
356A LEU* 4.1 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ARG* 3.1 60.6 + - - +
194A HIS* 3.2 8.9 + - - +
196A THR* 1.3 77.8 - - - +
198A CYS* 1.3 63.2 + - - +
200A GLY 3.4 1.0 + - - -
201A GLU* 3.4 5.0 + - - +
353A THR* 2.7 32.8 + - + +
354A THR 3.2 18.6 - - - +
355A ASP* 2.6 38.2 + - - +
361A THR* 3.6 20.3 + - + +
363A SER* 3.4 25.9 + - - -
364A HIS* 3.7 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.1 16.6 - - + -
153A ASP* 4.3 3.4 - - - -
194A HIS* 3.2 25.7 + - - +
195A GLY 3.7 6.7 - - - +
196A THR 3.3 0.2 - - - -
197A ARG* 1.3 79.8 - - - +
199A ALA* 1.3 62.8 + - - +
201A GLU* 3.2 26.4 + - - +
202A VAL* 3.5 5.0 + - - +
251A SER* 5.9 0.2 - - - +
253A SER* 3.8 18.4 - - - +
364A HIS* 3.7 10.3 - - - -
368A SER 3.7 22.2 - - - -
372A PRO* 3.5 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.8 20.3 - - + +
156A ILE* 3.8 31.6 - - + -
163A LEU* 4.2 8.6 - - + +
195A GLY 3.0 17.4 + - - +
196A THR 3.7 4.9 - - - +
198A CYS* 1.3 76.9 - - - +
200A GLY* 1.3 63.0 + - - +
202A VAL* 3.1 5.5 + - - +
203A ALA* 3.0 21.0 + - - -
221A ILE* 4.1 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.9 11.8 - - - +
196A THR 3.2 8.1 + - - -
197A ARG 3.4 0.2 + - - -
198A CYS 3.3 0.4 - - - -
199A ALA* 1.3 79.4 - - - +
201A GLU* 1.3 61.6 + - - +
204A ALA* 3.1 32.0 + - - +
213A VAL 4.4 1.0 - - - +
214A GLY* 3.5 3.5 - - - -
353A THR* 3.2 16.9 - - - -
354A THR* 3.3 13.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
121A GLN* 6.3 0.4 - - - +
123A TYR* 5.8 0.7 - - - +
197A ARG 3.5 9.2 - - - +
198A CYS* 3.2 8.8 + - - +
200A GLY* 1.3 75.7 - - - +
202A VAL* 1.3 58.4 + - - +
213A VAL 4.6 1.7 - - - +
214A GLY* 3.3 2.5 - - - -
215A VAL* 3.0 31.2 + - - +
351A ILE* 3.6 19.6 - - + +
352A VAL 5.2 2.0 - - - +
353A THR* 3.2 9.2 + - - +
364A HIS* 2.9 33.0 + - - -
369A ALA* 2.5 37.6 - - - +
372A PRO* 3.4 21.4 - - + +
373A LEU* 3.5 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL* 3.9 33.0 - - + -
151A ILE* 4.0 15.3 - - + -
198A CYS 3.7 13.2 - - - +
199A ALA 3.1 5.8 + - - +
201A GLU* 1.3 77.9 - - - +
203A ALA* 1.3 61.9 + - + +
214A GLY* 3.8 0.9 - - - -
215A VAL 3.2 1.4 + - - +
216A ALA* 2.9 34.6 + - + +
219A ALA* 5.5 0.2 - - + -
221A ILE* 4.1 7.6 - - + -
372A PRO* 3.2 31.9 - - + +
375A ALA* 4.3 5.4 - - + -
376A GLY* 4.1 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP 4.1 2.6 - - - +
163A LEU* 4.3 6.0 - - - +
166A ASN* 3.0 18.7 + - - +
199A ALA 3.0 8.3 + - - -
202A VAL* 1.3 85.6 - - + +
204A ALA* 1.3 65.4 + - - +
205A VAL 3.3 0.7 + - - -
214A GLY* 4.1 1.3 - - - -
216A ALA 3.5 18.4 - - - +
217A TYR* 4.6 0.2 - - - -
219A ALA* 3.8 20.4 - - + +
221A ILE* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 3.3 29.2 - - - +
163A LEU* 4.3 3.1 - - - -
200A GLY* 3.1 28.0 + - - +
203A ALA* 1.3 77.0 - - - +
205A VAL* 1.3 65.4 + - - +
211A CYS* 6.5 0.2 - - - -
212A GLY 4.2 0.9 - - - +
213A VAL* 3.8 7.2 - - - +
214A GLY* 3.0 25.2 + - - +
217A TYR* 3.4 9.7 - - - +
353A THR* 6.2 1.3 - - - -
354A THR* 4.4 5.4 - - + +
----------------------------------------------------------
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