Contacts of the strand formed by residues 194 - 200 (chain A) in PDB entry 2O7R
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 ILE 194 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 4.9 4.5 - - + -
163A CYS* 3.4 16.6 - - + +
165A ILE* 3.7 24.0 - - + -
182A ALA* 3.7 31.0 - - + -
186A ALA* 6.4 0.7 - - + -
189A LEU* 4.2 14.4 - - + -
192A LEU* 4.1 7.1 + - + +
193A LYS* 1.3 76.6 - - - +
195A LYS* 1.3 68.3 + - - +
196A GLY 3.7 22.2 - - - +
197A LEU* 4.6 0.2 - - + -
264A LEU 5.3 0.5 - - - +
266A TRP* 3.1 53.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A SER* 3.0 22.5 + - - +
162A ASN* 2.9 46.5 + - - +
163A CYS 2.7 7.8 + - - +
164A PHE* 3.9 21.3 - - + -
193A LYS* 4.3 15.5 - - - -
194A ILE* 1.3 79.0 - - - +
196A GLY* 1.3 58.1 + - - +
265A GLY 4.2 2.8 - - - +
266A TRP* 3.5 10.1 - - - -
267A ARG* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A CYS 3.7 2.4 + - - -
164A PHE* 3.3 20.5 - - - -
165A ILE 3.1 21.8 + - - -
194A ILE* 3.7 8.0 - - - +
195A LYS* 1.3 83.2 - - - +
197A LEU* 1.3 69.5 + - - +
266A TRP* 4.5 3.6 - - - -
267A ARG 3.0 14.4 - - - -
326A PHE* 4.8 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
----------------------------------------------------------
165A ILE* 3.3 26.9 - - + +
175A ALA 4.5 6.5 - - - +
176A TYR* 4.8 16.2 - - + +
179A GLY* 3.9 28.3 - - - -
194A ILE* 4.6 0.7 - - + -
196A GLY* 1.3 83.2 - - - +
198A VAL* 1.3 64.9 + - - +
199A LEU* 4.1 10.8 - - + -
261A ILE* 4.6 11.0 - - + -
266A TRP* 4.0 24.7 - - + -
267A ARG 3.0 5.6 + - - +
268A VAL* 3.4 27.6 - - + -
269A MET 2.8 25.7 + - - +
326A PHE* 3.9 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 6.3 0.9 - - + -
164A PHE* 4.7 12.3 - - + -
165A ILE 2.8 10.8 + - - +
166A MET* 3.1 38.8 - - + +
167A GLY 3.0 25.8 + - - +
197A LEU* 1.3 79.0 - - - +
199A LEU* 1.3 66.4 + - - +
200A ASP* 4.9 1.1 - - + +
269A MET* 3.6 24.2 - - + -
271A VAL* 6.2 0.4 - - + -
319A PHE* 4.3 4.9 - - + -
323A LEU* 4.0 17.5 - - + -
326A PHE* 3.8 22.4 - - + -
327A VAL* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLY 4.1 2.2 - - - -
172A GLY 3.6 19.1 - - - +
175A ALA* 4.1 7.6 - - + -
176A TYR* 3.8 31.0 - - + +
197A LEU* 4.4 12.8 - - + -
198A VAL* 1.3 78.4 - - - +
200A ASP* 1.3 61.7 + - - +
201A GLU 3.5 1.6 + - - -
202A PRO* 3.6 21.8 - - + +
268A VAL* 4.2 20.4 - - + -
269A MET* 2.8 16.0 + - - +
270A VAL* 3.5 8.6 - - + -
271A VAL* 3.1 23.8 + - - +
285A LEU* 3.8 28.5 - - + -
289A LEU* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 4.6 12.1 - - - -
166A MET* 4.5 17.0 - - + +
167A GLY 2.9 18.6 + - - +
168A GLU* 3.3 24.3 - - + +
169A SER 2.9 19.2 + - - -
198A VAL* 3.7 1.3 + - + +
199A LEU* 1.3 69.5 - - - +
201A GLU* 1.3 76.8 + - - +
202A PRO* 3.1 1.3 - - - +
271A VAL* 3.4 11.9 - - + +
309A LYS* 2.7 41.0 + - - +
310A LEU* 5.7 0.7 - - - +
319A PHE* 5.1 2.7 - - + -
----------------------------------------------------------
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