Contacts of the helix formed by residues 365 - 377 (chain A) in PDB entry 2WO6
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 ASN 365 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PTR 5.1 0.7 - - - -
325A ARG* 3.4 15.0 - - - +
363A GLY 3.3 0.8 - - - -
364A ALA* 1.3 86.1 + - - +
366A GLU* 1.3 53.6 + - - +
367A VAL* 3.4 10.1 + - - +
368A ASP* 2.9 37.3 + - - +
369A GLN* 2.6 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN 4.9 1.4 - - - +
321A PTR 3.8 24.7 + - + +
325A ARG* 4.0 1.5 - - + +
328A ARG* 2.8 37.5 + - - +
332A VAL 4.8 0.7 - - - +
333A LEU* 3.6 21.4 - - + +
365A ASN* 1.3 74.6 - - - +
367A VAL* 1.3 57.5 + - - +
369A GLN* 3.5 7.5 - - - +
370A MET* 2.9 24.9 + - - +
390A LYS* 2.8 24.0 + - - -
393A LYS* 2.4 42.9 + - - +
394A PHE* 3.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASN* 3.3 8.8 + - - +
366A GLU* 1.3 77.9 - - - +
368A ASP* 1.3 56.5 + - - +
370A MET* 3.8 1.2 - - - +
371A ASN* 2.9 48.6 + - - +
393A LYS* 4.3 32.3 - - + +
394A PHE* 3.9 17.0 - - + -
406A LYS 6.0 1.1 - - - +
408A THR* 4.7 14.8 - - - +
415A TYR* 5.3 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLY* 3.3 2.0 - - - -
364A ALA* 2.9 27.2 + - + +
365A ASN* 2.9 28.7 + - - +
367A VAL* 1.3 76.6 - - - +
369A GLN* 1.3 57.0 + - - +
371A ASN* 3.4 0.7 + - - +
372A LYS* 2.9 55.7 + - - +
413A ARG* 4.2 6.7 + - - +
415A TYR* 2.5 41.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
325A ARG* 3.1 39.3 + - + +
326A PHE* 3.4 8.4 + - - -
328A ARG 4.9 1.4 + - - +
333A LEU* 4.1 20.6 - - + -
345A TRP* 6.2 0.2 - - - +
361A PHE* 3.0 38.7 + - - +
363A GLY* 2.8 31.4 + - - +
365A ASN 2.6 21.2 + - - +
366A GLU* 3.5 10.3 - - - +
368A ASP* 1.3 73.4 - - - +
370A MET* 1.3 61.3 + - - +
372A LYS* 3.3 3.8 + - - +
373A ILE* 3.1 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PRO* 4.3 9.0 - - + +
333A LEU* 3.9 28.4 - - + +
334A LEU* 3.8 38.1 - - + -
366A GLU 2.9 16.8 + - - +
367A VAL 3.8 0.7 - - - +
369A GLN* 1.3 73.8 - - - +
371A ASN* 1.3 62.4 + - - +
373A ILE* 3.2 17.3 + - - +
374A VAL* 2.9 33.7 + - + +
380A PRO* 4.6 6.7 - - + -
394A PHE* 3.5 36.3 - - + -
395A PHE* 4.0 20.2 - - + -
405A LEU* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 2.9 43.3 + - - +
368A ASP 3.8 0.9 - - - +
370A MET* 1.3 77.9 - - - +
372A LYS* 1.3 56.2 + - - +
374A VAL* 3.2 7.3 + - - +
375A GLU* 3.0 32.4 + - - +
394A PHE* 5.5 4.4 + - - +
405A LEU* 3.3 38.4 - - - +
406A LYS 4.9 7.8 + - - +
415A TYR* 3.3 46.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU 5.7 0.4 - - - +
361A PHE* 3.4 27.4 - - + -
362A SER* 2.8 47.8 + - - +
363A GLY 4.0 0.2 - - - +
364A ALA 4.9 0.2 - - - +
368A ASP* 2.9 42.5 + - - +
369A GLN* 3.7 4.9 - - - +
370A MET 3.2 0.4 - - - -
371A ASN* 1.3 72.3 - - - +
373A ILE* 1.3 66.0 + - - +
375A GLU* 3.4 32.6 + - - +
376A VAL* 3.7 3.6 + - - +
413A ARG* 3.6 25.2 - - - +
415A TYR* 4.5 4.3 - - + -
421A ARG* 5.0 5.0 + - - +
316B GLN* 5.3 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG 4.0 6.5 - - - +
330A PRO* 4.8 4.5 - - + -
333A LEU* 3.5 31.9 - - + -
345A TRP* 3.8 35.2 - - + -
361A PHE* 3.5 29.8 - - + -
369A GLN* 3.1 19.2 + - - +
370A MET* 3.2 11.4 + - - +
372A LYS* 1.3 76.5 - - - +
374A VAL* 1.3 56.7 + - - +
376A VAL* 3.2 5.4 + - - +
377A LEU* 3.0 30.7 + - + +
462A TYR* 3.4 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A MET* 2.9 23.3 + - - +
371A ASN* 3.2 7.4 + - - +
373A ILE* 1.3 75.0 - - - +
375A GLU* 1.3 65.1 + - - +
378A GLY 3.1 27.9 + - - +
379A ILE* 3.7 24.0 - - + -
380A PRO* 4.1 2.9 - - + -
395A PHE* 4.0 28.0 - - + -
405A LEU* 4.0 13.5 - - + -
416A LYS 6.0 0.4 - - - +
418A PRO* 3.5 14.1 - - + +
419A GLY 3.0 17.8 + - - -
462A TYR* 3.8 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ASN 3.0 17.3 + - - +
372A LYS* 3.6 26.8 - - - +
373A ILE 3.3 0.6 - - - -
374A VAL* 1.3 77.0 - - - +
376A VAL* 1.3 57.1 + - - +
413A ARG* 4.6 8.5 + - - -
415A TYR* 3.6 20.6 - - + -
416A LYS* 2.8 60.7 + - + +
417A PRO 3.9 0.3 - - - +
419A GLY 3.1 2.2 + - - +
420A THR 3.0 13.0 + - - -
421A ARG* 2.9 46.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 4.6 2.2 - - + -
361A PHE* 3.6 31.9 - - + -
372A LYS 3.7 2.0 + - - +
373A ILE 3.2 1.0 + - - -
375A GLU* 1.3 79.8 - - - +
377A LEU* 1.3 76.8 + - + +
378A GLY 3.6 0.7 - - - -
419A GLY* 3.8 10.6 - - - +
421A ARG* 3.2 52.4 - - - +
422A LYS* 5.1 3.5 - - - +
423A LEU* 4.2 24.0 - - + +
426A ILE* 4.1 8.1 - - + -
457A LEU* 5.7 0.7 - - + -
460A LEU* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A TRP* 3.6 24.5 - - + -
361A PHE* 4.3 7.2 - - + -
373A ILE* 3.0 19.7 + - + +
376A VAL* 1.3 93.8 - - + +
378A GLY* 1.3 61.9 + - - +
379A ILE 4.9 0.7 - - - +
419A GLY* 4.4 2.0 - - - -
457A LEU* 3.9 28.3 - - + -
460A LEU* 3.5 37.9 - - + +
462A TYR* 3.7 23.4 - - + -
----------------------------------------------------------
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