Contacts of the strand formed by residues 338 - 343 (chain A) in PDB entry 6GR2
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 VAL 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA* 3.4 28.9 - - - +
333A LEU* 4.6 8.8 - - + +
335A VAL* 3.4 32.9 + - + +
336A PRO 3.3 0.8 - - - -
337A GLY* 1.3 77.6 + - - +
339A TYR* 1.3 65.1 + - - +
340A GLY* 3.6 15.3 - - - +
354A THR* 3.6 24.7 - - + -
356A LEU* 3.7 25.1 - - + -
360A ALA* 5.4 0.2 - - + -
364A ALA* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LYS 5.4 2.0 + - - -
218A LEU* 4.0 11.4 - - + -
300A TYR* 3.6 47.2 - + + +
301A ARG* 3.6 39.8 - - + +
304A GLY* 3.2 20.7 - - - +
305A ARG* 4.0 2.1 + - - +
308A VAL* 4.6 2.4 - - - +
333A LEU* 5.0 1.7 - - - +
337A GLY 4.1 1.3 - - - -
338A VAL* 1.3 76.1 - - - +
340A GLY* 1.3 55.5 + - - +
355A LEU* 2.7 26.4 + - + +
356A LEU* 3.6 9.9 - - - -
357A GLU* 3.5 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLY* 3.6 19.0 - - - -
307A MET* 3.9 7.2 - - - -
308A VAL* 3.8 7.6 - - - -
333A LEU* 3.9 5.8 - - - -
338A VAL* 3.6 4.7 - - - -
339A TYR* 1.3 80.7 - - - +
341A SER* 1.3 65.0 + - - -
354A THR* 3.4 5.9 - - - +
355A LEU* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET* 3.9 10.0 - - - +
308A VAL* 4.0 10.6 - - - +
311A HIS* 4.0 0.5 - - - +
329A VAL* 3.4 26.9 - - - +
332A ALA* 3.9 22.0 - - - +
333A LEU* 3.9 7.3 - - - +
340A GLY* 1.3 76.2 - - - -
342A ARG* 1.3 69.8 + - - +
352A THR* 3.4 12.5 + - - +
353A VAL 3.3 8.4 + - - -
354A THR* 2.7 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 3.2 17.7 + - - +
40A LEU 3.0 17.8 + - - -
41A ILE* 3.3 22.0 - - - +
42A GLY 3.9 0.4 - - - +
43A GLU* 2.6 30.2 + - - +
307A MET* 3.4 31.9 - - + +
310A SER* 3.3 16.5 + - - -
311A HIS* 3.4 19.7 - - + -
314A LEU* 3.1 27.1 - - - +
329A VAL* 3.8 3.1 - - - -
341A SER* 1.3 82.1 + - - +
343A MET* 1.3 84.4 + - - +
352A THR* 3.0 16.3 + - - -
353A VAL* 3.0 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 3.6 2.9 - - + +
311A HIS* 3.4 24.6 + - + +
314A LEU* 3.9 22.2 - - + +
320A VAL* 3.9 22.0 - - + +
321A SER* 3.8 25.6 - - - -
325A LEU* 3.7 22.7 - - + -
329A VAL* 5.1 0.2 - - - -
342A ARG* 1.3 106.8 + - - +
344A THR* 1.3 59.0 + - - +
345A GLY 3.5 24.5 - - - +
346A GLY 3.9 4.3 - - - +
347A GLY* 3.5 21.3 - - - +
351A CYS 3.7 7.0 - - - +
352A THR* 4.0 2.6 + - - +
----------------------------------------------------------
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