Contacts of the helix formed by residues 367 - 376 (chain H) in PDB entry 2W3S
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 367 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H ARG* 1.3 73.3 - - - +
368H PRO* 1.4 72.7 - - - +
369H ALA* 3.2 12.9 + - - +
370H GLU* 3.7 25.5 + - + +
371H LEU* 2.8 30.8 + - - +
427H PHE* 5.4 0.5 - - - -
431H ARG* 2.5 40.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 368 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357H ILE* 5.8 0.2 - - - +
358H GLU* 3.4 33.9 - - - +
361H ALA* 3.5 25.8 - - + -
362H ARG* 4.1 18.8 - - - +
366H ARG 3.3 6.4 - - - +
367H ASP* 1.4 93.0 - - - +
369H ALA* 1.3 49.6 + - - +
371H LEU* 3.4 2.6 + - + +
372H ARG* 2.7 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 369 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367H ASP* 3.2 13.4 + - - +
368H PRO* 1.3 76.4 - - - +
370H GLU* 1.3 66.4 + - - +
372H ARG* 3.3 10.0 + - - +
373H ALA* 3.0 26.7 + - - +
418H VAL* 6.0 0.9 - - - +
422H GLN* 4.0 12.4 + - - +
427H PHE* 3.9 29.4 - - + -
450H LEU* 4.8 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 370 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H ARG* 2.7 54.2 + - - +
367H ASP* 3.2 22.6 + - + +
369H ALA* 1.3 79.1 - - - +
371H LEU* 1.3 63.1 + - - +
373H ALA* 3.4 4.8 + - - +
374H LEU* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H ALA* 5.3 0.7 - - + -
284H GLY* 3.4 32.1 - - - +
286H LEU* 5.9 1.1 - - + -
357H ILE* 3.9 22.6 - - + +
360H LEU* 4.4 4.7 - - + -
361H ALA* 3.7 32.5 - - + +
364H MET* 3.7 26.0 - - + -
366H ARG* 4.7 15.7 - - + +
367H ASP 2.8 16.8 + - - +
368H PRO* 3.6 4.9 - - + +
370H GLU* 1.3 82.2 - - - +
372H ARG* 1.3 60.5 + - - +
374H LEU* 3.4 8.9 - - + +
375H ASN* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 372 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H TYR* 3.0 28.7 - - + +
354H GLU* 2.7 50.7 + - - -
357H ILE* 3.5 17.4 - - + +
358H GLU* 2.9 23.2 + - - -
368H PRO* 2.7 41.3 + - - +
369H ALA* 3.8 6.0 - - - +
371H LEU* 1.3 69.1 - - - +
373H ALA* 1.3 60.2 + - - +
374H LEU 3.1 1.3 - - - -
375H ASN* 2.8 19.4 + - - -
376H PHE* 3.1 25.5 + - + -
449H ALA* 6.3 0.6 - - - +
450H LEU* 3.8 21.0 + - + +
452H PRO* 3.9 13.2 - - - +
741H LEU* 3.2 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H ALA 3.0 16.8 + - - +
370H GLU* 3.9 4.7 - - - +
372H ARG* 1.3 76.6 - - - +
374H LEU* 1.3 61.7 + - - +
375H ASN 3.2 0.5 + - - -
376H PHE* 3.6 35.0 + - + +
415H GLY* 5.9 1.5 - - - -
418H VAL* 5.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H SER* 3.6 15.0 - - - +
284H GLY* 3.4 35.0 - - - +
285H LYS* 3.4 39.9 + - + +
366H ARG* 4.2 2.7 - - - +
370H GLU* 3.0 29.0 + - - +
371H LEU* 3.4 12.1 - - + +
372H ARG 3.1 0.4 - - - -
373H ALA* 1.3 77.0 - - - +
375H ASN* 1.3 62.5 + - - +
376H PHE 4.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 375 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H GLY 3.1 23.4 + - - -
285H LYS* 3.8 8.8 - - - +
286H LEU* 2.9 50.8 + - + +
319H TYR* 3.1 11.9 - - + -
320H PHE* 3.1 27.1 + - - +
357H ILE* 4.6 2.6 - - + +
371H LEU* 2.9 24.6 + - - +
372H ARG 2.8 8.4 + - - +
374H LEU* 1.3 86.2 - - - +
376H PHE* 1.3 67.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 376 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318H SER 3.3 15.3 - - - +
319H TYR* 3.7 11.9 - + - -
320H PHE* 4.8 2.1 + - - +
372H ARG* 3.1 14.2 + - + -
373H ALA* 3.6 36.1 - - + +
374H LEU 3.6 4.1 - - - +
375H ASN* 1.3 82.6 - - - +
377H TYR* 1.3 70.4 - - - +
378H ASP* 3.7 3.6 + - - +
401H GLN* 4.6 2.6 + - - +
414H LEU* 4.0 15.9 - - + -
415H GLY* 3.9 23.1 - - - +
418H VAL* 3.7 39.5 - - + -
450H LEU* 5.4 3.1 - - + -
452H PRO* 3.4 35.2 - - + -
----------------------------------------------------------
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