Contacts of the helix formed by residues 366 - 384 (chain A) in PDB entry 4M83
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 ASP 366 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ALA 4.0 10.6 - - - +
363A LEU 3.7 7.3 + - - +
364A VAL 3.5 4.7 + - - +
365A ASP* 1.3 76.8 - - - +
367A PRO* 1.3 70.4 - - - +
368A GLU* 3.0 25.2 + - - +
369A VAL* 3.3 33.0 - - + +
370A ALA* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASP 4.4 2.7 - - - +
366A ASP* 1.3 89.9 - - - +
368A GLU* 1.3 62.3 + - + +
370A ALA* 3.6 8.4 - - + +
371A ARG* 2.7 31.5 + - - +
374A ARG* 4.7 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASP* 3.0 13.0 - - - +
367A PRO* 1.3 85.6 - - + +
369A VAL* 1.3 60.8 + - - +
370A ALA 3.1 1.1 - - - -
371A ARG* 2.9 44.1 + - - +
372A ARG* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 4.0 30.3 - - + -
341A GLY 3.5 19.7 - - - +
342A VAL* 4.2 13.2 - - - +
362A ALA 5.3 0.2 - - - +
363A LEU* 4.1 20.6 - - + +
366A ASP* 3.2 35.0 + - + +
368A GLU* 1.3 76.7 - - - +
370A ALA* 1.3 63.8 + - - +
372A ARG* 3.1 5.6 + - - +
373A LEU* 3.0 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 6.0 0.9 - - - -
366A ASP 3.1 13.0 + - - +
367A PRO* 3.6 10.8 - - + +
369A VAL* 1.3 78.8 - - - +
371A ARG* 1.3 55.3 + - - +
373A LEU* 3.2 11.7 + - - +
374A ARG* 2.9 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A PRO 2.7 21.0 + - - +
368A GLU* 2.9 43.9 + - - +
370A ALA* 1.3 74.9 - - - +
372A ARG* 1.3 102.2 + - - +
374A ARG* 4.3 8.7 - - - +
375A ARG* 3.4 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU 3.8 21.5 + - - +
341A GLY* 4.2 12.1 - - - +
342A VAL* 3.5 19.5 - - + -
368A GLU* 2.8 25.6 + - - +
369A VAL* 3.1 3.1 + - - +
371A ARG* 1.3 117.3 - - - +
373A LEU* 1.3 61.9 + - - +
375A ARG* 3.3 5.5 + - - +
376A ILE* 3.0 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 4.1 20.1 - - + +
318A ALA* 3.6 34.9 - - + +
319A THR 4.3 8.3 - - - +
320A PRO* 3.5 39.3 - - + -
321A MET* 4.9 0.2 - - + -
342A VAL* 3.6 28.0 - - + -
369A VAL* 3.0 23.6 + - + +
370A ALA* 3.2 9.4 + - - +
372A ARG* 1.3 75.1 - - - +
374A ARG* 1.3 65.3 + - - +
376A ILE* 3.2 6.3 + - + +
377A GLN* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA* 5.0 5.3 - - + +
367A PRO* 4.7 2.4 + - - +
370A ALA* 2.9 48.7 + - - +
371A ARG* 4.1 7.5 - - - +
372A ARG 3.3 0.2 - - - -
373A LEU* 1.3 77.1 - - - +
375A ARG* 1.3 60.1 + - - +
377A GLN* 3.4 19.0 + - - +
378A ALA* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ARG 3.4 12.5 + - - +
372A ARG* 3.3 9.6 + - - +
374A ARG* 1.3 79.2 - - - +
376A ILE* 1.3 62.1 + - + +
378A ALA* 3.5 8.0 + - + +
379A GLU* 3.1 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA* 4.3 9.9 - - + -
315A LEU* 3.7 39.0 - - + +
340A LEU* 3.6 40.4 - - + +
342A VAL* 4.5 8.1 - - + -
372A ARG* 3.0 16.8 + - + +
373A LEU* 3.2 9.4 + - - +
375A ARG* 1.3 74.9 - - - +
377A GLN* 1.3 60.2 + - - +
379A GLU* 3.0 16.3 + - - +
380A MET* 2.8 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ARG* 5.7 6.9 - - - +
315A LEU 3.5 15.3 - - - +
316A ALA 3.1 22.7 + - - +
317A THR* 3.8 3.2 - - - +
318A ALA* 3.3 27.9 - - + +
373A LEU 3.0 12.2 + - - +
374A ARG* 3.8 20.6 - - - +
376A ILE* 1.3 76.5 - - - +
378A ALA* 1.3 57.8 + - - +
380A MET* 3.3 10.0 + - - +
381A ALA* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG 3.2 14.0 + - - +
375A ARG* 3.7 10.5 - - + +
377A GLN* 1.3 78.8 - - - +
379A GLU* 1.3 63.3 + - + +
381A ALA* 3.5 8.0 + - - +
382A GLN* 3.4 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA* 6.0 1.0 - - - +
375A ARG* 3.1 31.6 + - + +
376A ILE* 3.0 20.3 + - - +
378A ALA* 1.3 77.0 - - + +
380A MET* 1.3 64.8 + - + +
382A GLN* 3.2 17.5 + - - +
383A GLU* 3.3 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PRO* 4.1 27.6 - - + -
195A ALA* 6.0 0.7 - - + -
212A GLY* 6.2 0.9 - - - -
213A ALA 5.8 1.8 - - - +
217A ASP* 6.1 0.7 - - - +
312A GLN* 3.4 31.4 - - - +
315A LEU* 3.8 14.1 - - - +
316A ALA* 3.8 24.7 - - + +
376A ILE* 2.8 44.5 + - + +
377A GLN* 3.7 5.8 - - - +
379A GLU* 1.3 71.0 - - + +
381A ALA* 1.3 60.9 + - - +
383A GLU* 2.9 32.4 + - - +
384A GLY* 3.1 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLN 2.8 21.2 + - - +
378A ALA* 3.6 9.9 - - - +
379A GLU 3.3 0.2 - - - -
380A MET* 1.3 73.5 - - - +
382A GLN* 1.3 61.6 + - + +
384A GLY* 3.0 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ALA 3.4 16.3 + - - +
379A GLU* 3.2 10.4 + - - +
380A MET 3.1 0.8 - - - -
381A ALA* 1.3 79.1 - - - +
383A GLU* 1.3 60.9 + - - +
384A GLY 2.9 5.6 + - - -
388A ARG* 3.1 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PRO* 3.3 22.8 - - - +
194A LYS* 3.0 32.0 + - - +
195A ALA 4.7 0.5 + - - -
210A PHE* 3.5 20.6 - - + +
211A VAL* 3.1 20.5 - - - +
212A GLY* 3.4 14.1 + - - -
379A GLU* 3.5 15.3 - - - +
380A MET* 2.9 22.6 + - - +
382A GLN* 1.3 75.6 - - - +
384A GLY* 1.3 56.3 + - - +
385A GLY 3.0 9.2 + - - -
388A ARG* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A MET 3.1 6.4 + - - -
381A ALA* 3.0 17.9 + - - +
382A GLN 2.9 2.6 - - - -
383A GLU* 1.3 73.7 - - - +
385A GLY* 1.3 57.5 + - - -
388A ARG* 3.6 17.7 - - - -
----------------------------------------------------------
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