Contacts of the strand formed by residues 192 - 197 (chain P) in PDB entry 4R2G
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 TYR 192 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P LEU* 4.1 2.3 - - - +
133P LEU* 3.9 21.1 - - + -
149P TRP* 5.3 1.3 - + + -
151P ALA* 3.8 26.5 - - + -
152P ASP 4.0 2.0 - - - +
156P VAL* 5.0 1.3 - - + -
179P LEU* 3.9 22.4 - - + -
181P LEU* 3.3 32.6 - - + +
185P GLN* 3.3 17.2 + - - +
186P TRP* 3.6 44.2 - + - -
189P HIS* 3.8 21.2 + + + -
190P LYS 5.6 0.4 - - - -
191P SER* 1.3 83.1 - - - +
193P SER* 1.3 60.7 + - - +
205P LYS 3.8 0.7 - - - +
206P THR* 3.2 5.4 - - - -
207P VAL* 2.9 39.6 + - + +
209P PRO* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P TRP* 3.0 5.9 - - - +
150P LYS* 1.6 96.9 + - - +
151P ALA 3.6 2.0 + - - +
152P ASP* 4.3 1.2 - - - +
191P SER* 5.1 1.3 + - - -
192P TYR* 1.3 73.6 - - - +
194P CYS* 1.3 54.4 + - - +
195P GLN* 4.1 0.9 + - - -
204P GLU* 3.4 12.2 + - - -
205P LYS 3.2 5.8 - - - -
206P THR* 3.4 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 194 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P VAL* 4.7 5.0 - - - +
118P LEU* 4.0 9.6 - - + +
135P CYS* 2.0 47.6 - - - -
147P VAL* 5.1 3.1 - - + -
148P ALA 3.6 5.8 - - - +
149P TRP* 3.4 34.3 - - + +
193P SER* 1.3 74.1 - - - +
195P GLN* 1.3 59.9 + - - +
196P VAL* 4.2 8.2 - - - +
203P VAL 4.1 1.0 - - - +
204P GLU* 3.8 0.9 - - - -
205P LYS 3.1 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 4.5 26.4 - - + +
214A PRO 4.8 5.5 + - - -
146P THR 3.7 0.9 - - - +
147P VAL* 3.6 3.6 - - - +
148P ALA* 2.9 42.9 + - - +
150P LYS* 2.9 50.7 + - + +
194P CYS* 1.3 73.6 - - - +
196P VAL* 1.3 61.7 + - - +
197P THR* 5.0 0.7 + - - -
202P THR* 3.7 19.6 - - + +
203P VAL 3.5 3.8 - - - -
204P GLU* 3.6 35.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P PRO* 3.8 19.7 - - + -
116P VAL* 3.6 30.3 - - + -
135P CYS* 4.1 16.8 - - - -
137P ILE* 3.6 23.1 - - + -
145P VAL* 3.8 17.9 - - + -
146P THR 3.3 5.2 - - - +
147P VAL* 4.2 6.5 - - + -
194P CYS* 4.2 1.8 - - - -
195P GLN* 1.3 78.1 - - - +
197P THR* 1.3 61.5 + - - +
201P SER 4.0 0.3 - - - +
202P THR* 3.4 3.3 - - - +
203P VAL* 2.9 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLU* 3.6 29.5 + - + +
212A PRO 5.9 1.3 - - - +
213A ILE* 3.4 17.8 - - + +
144P ALA 4.2 0.7 - - - +
145P VAL* 3.5 6.2 - - - +
146P THR* 2.9 44.1 + - - -
195P GLN 5.0 0.9 + - - -
196P VAL* 1.3 76.1 - - - +
198P HIS* 1.3 64.7 + - - +
199P GLU 4.4 0.2 + - - -
200P GLY* 3.8 4.7 - - - -
201P SER 3.5 19.7 - - - +
202P THR* 3.0 22.8 + - - +
----------------------------------------------------------
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