Contacts of the helix formed by residues 360 - 371 (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 ALA 360 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 4.5 2.2 - - + +
336A PRO 3.4 25.4 - - - +
337A GLY* 4.0 16.4 - - - -
338A VAL 4.8 0.2 - - - +
356A LEU* 4.3 7.0 - - + -
357A GLU* 2.8 23.6 + - + +
359A SER* 1.3 73.8 + - - +
361A ALA* 1.3 62.8 + - - -
362A PRO 3.4 0.7 - - - -
363A HIS* 3.3 10.2 + - + +
364A ALA* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ALA* 4.8 2.0 - - + -
221A LEU* 5.3 1.1 - - + -
356A LEU* 4.0 19.7 - - + -
357A GLU 3.6 2.4 + - - -
358A ALA 3.2 11.5 + - - +
360A ALA* 1.3 75.6 - - - +
362A PRO* 1.3 73.8 - - + +
364A ALA* 3.1 2.1 + - - +
365A MET* 3.0 29.0 + - - +
380A LEU* 3.9 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ALA 4.0 3.8 - - - +
359A SER* 3.6 15.7 - - - +
360A ALA 3.7 0.2 - - - -
361A ALA* 1.3 95.4 - - + +
363A HIS* 1.3 61.4 + - - +
365A MET* 3.5 9.2 + - + +
366A ARG* 3.3 43.7 + - - +
380A LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 3.6 16.7 - - + +
336A PRO* 3.9 26.8 + - + +
359A SER 5.2 0.6 + - - +
360A ALA* 3.3 10.6 + - - +
361A ALA 3.3 0.8 - - - -
362A PRO* 1.3 77.6 - - - +
364A ALA* 1.3 59.6 + - - +
366A ARG* 3.1 23.4 + - + +
367A HIS* 2.8 50.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 4.0 8.1 - - + -
335A VAL* 3.7 25.9 - - + +
338A VAL* 4.5 2.7 - - + -
356A LEU* 3.5 25.8 - - + -
360A ALA 2.9 17.4 + - - +
361A ALA 3.6 2.9 - - - +
363A HIS* 1.3 77.5 - - - +
365A MET* 1.3 58.3 + - - +
367A HIS* 3.9 0.2 - - - +
368A ILE* 2.9 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 54.5 - - + +
221A LEU* 3.9 14.6 - - + -
361A ALA 3.0 19.0 + - - +
362A PRO* 3.9 7.4 - - - +
364A ALA* 1.3 74.9 - - - +
366A ARG* 1.3 63.4 + - + +
369A GLN* 3.1 27.0 + - - +
378A PHE* 3.4 52.3 - - + -
380A LEU* 4.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PRO* 3.3 26.4 + - - +
363A HIS* 3.1 37.9 + - + +
365A MET* 1.3 80.0 - - + +
367A HIS* 1.3 62.3 + - - +
369A GLN* 4.0 2.9 - - - +
370A GLU* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA* 3.3 32.7 + - + -
334A ALA* 3.8 19.5 - - + +
335A VAL* 3.5 17.9 - - + +
363A HIS* 2.8 38.4 + - - +
366A ARG* 1.3 70.8 - - - +
368A ILE* 1.3 66.3 + - - +
370A GLU* 3.3 3.9 + - - -
371A HIS* 3.0 66.6 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 4.3 17.9 - - + -
223A THR* 4.3 11.9 - - + +
328A LEU* 3.7 32.1 - - + +
331A ALA* 4.2 10.1 - - + +
332A ALA* 3.7 42.0 - - + +
335A VAL* 4.9 1.8 - - + -
352A THR* 5.7 1.1 - - + -
354A THR* 5.0 3.8 - - + +
364A ALA* 2.9 28.0 + - + +
365A MET 4.2 1.6 - - - +
367A HIS* 1.3 76.0 - - - +
369A GLN* 1.3 65.4 + - - +
371A HIS 3.3 2.1 + - - -
372A TYR* 3.2 25.8 + - - +
376A ALA* 5.1 0.7 - - + -
378A PHE* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A MET 3.1 20.8 + - - +
366A ARG* 4.0 3.6 - - - +
368A ILE* 1.3 81.1 - - - +
370A GLU* 1.3 63.0 + - - +
371A HIS 3.4 0.2 + - - -
372A TYR* 3.4 12.0 + - - +
374A GLY 3.0 24.2 + - - -
375A THR* 3.9 6.8 - - - +
376A ALA* 2.9 41.5 + - - +
378A PHE* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ARG 3.1 17.7 + - - +
367A HIS* 3.9 4.5 - - - +
369A GLN* 1.3 79.4 - - - +
371A HIS* 1.3 72.7 + - + +
372A TYR 3.4 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLN* 3.2 17.9 - - - +
331A ALA* 4.3 15.4 - - + +
367A HIS* 3.0 58.3 + + - +
368A ILE 3.6 1.8 - - - -
370A GLU* 1.3 86.6 - - + +
372A TYR* 1.3 58.4 + - - +
----------------------------------------------------------
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