Contacts of the strand formed by residues 191 - 195 (chain B) in PDB entry 3GYQ
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 GLN 191 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLY 4.0 1.0 + - - +
190B MET* 1.3 70.5 - - - +
192B LEU* 1.3 61.8 + - - +
193B MET* 3.3 31.3 + - - +
209B ASN* 2.9 34.0 + - - +
211B ASP* 3.6 16.8 - - + +
212B ARG 3.1 9.0 + - - +
213B LEU* 3.7 9.9 - - + +
214B ALA* 3.1 18.8 + - - -
233B SER* 3.2 29.3 + - - +
234B ALA* 5.0 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B VAL* 5.1 1.1 - - + -
182B ILE* 5.5 0.9 - - + -
185B ILE* 4.1 26.2 - - + +
190B MET 3.7 4.8 + - - -
191B GLN* 1.3 70.6 - - - +
193B MET* 1.3 61.2 + - - +
214B ALA* 3.3 29.2 - - + +
216B LEU* 3.8 26.2 - - + -
228B PHE* 4.1 21.8 - - + +
231B ALA* 3.6 27.4 - - + +
232B SER* 3.6 30.0 - - - +
233B SER* 2.9 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLN* 3.5 47.1 - - - +
192B LEU* 1.3 74.6 - - - +
194B THR* 1.3 62.5 + - - +
195B LEU* 3.6 2.1 + - + +
201B ILE* 5.6 5.2 - - + -
206B LEU* 4.1 11.4 - - + -
209B ASN* 4.5 7.9 - - - +
213B LEU* 3.7 20.4 - - + -
214B ALA 2.9 11.2 + - - +
215B LEU* 3.6 14.2 - - + -
216B LEU* 2.8 29.8 + - - -
234B ALA* 3.6 22.0 - - + -
236B VAL* 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 4.8 0.7 - - - +
193B MET* 1.3 70.6 - - - +
195B LEU* 1.3 63.4 + - - +
196B LYS* 3.6 8.3 + - + -
216B LEU* 3.9 16.6 - - + +
224B PRO* 3.9 30.3 - - + -
228B PHE* 5.3 1.3 - - + +
229B GLU* 4.7 10.2 + - - +
232B SER* 2.7 32.8 + - - -
234B ALA 2.8 10.7 + - - -
235B SER* 3.0 10.4 - - - -
236B VAL 2.7 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B MET 3.8 15.0 - - - +
194B THR* 1.3 75.6 - - - +
196B LYS* 1.3 58.2 + - - +
203B VAL* 4.8 1.1 - - + -
206B LEU* 5.1 1.1 - - + -
215B LEU* 3.8 22.7 - - + -
216B LEU 3.2 17.1 + - - +
217B PHE* 3.6 30.7 - - + -
223B GLY 4.8 1.0 - - - +
224B PRO* 4.9 0.5 - - - +
236B VAL* 3.1 26.5 - - + -
238B ILE* 4.6 5.4 - - + -
252B SER 4.4 3.4 - - - +
256B ALA* 3.4 29.6 - - + -
270B SAM 2.7 46.6 + - + +
----------------------------------------------------------
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