Contacts of the helix formed by residues 366 - 374 (chain D) in PDB entry 2W93
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 LYS 366 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D PRO* 3.6 14.7 + - + +
365D LEU* 1.3 83.8 - - - +
367D GLN* 1.3 66.3 + - - +
368D GLU* 3.4 5.6 - - + +
369D TRP* 3.4 15.6 + - + +
370D MET* 3.0 22.2 + - - +
540D LEU* 3.9 4.7 - - - -
541D PRO* 4.0 13.9 - - + -
544D ASP* 3.3 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 367 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D LYS* 1.3 70.7 - - - +
368D GLU* 1.3 65.4 + - - +
370D MET* 2.9 7.2 + - - +
371D TRP* 2.7 65.4 + - + +
390D THR* 2.9 32.9 + - - +
469D LEU* 4.1 3.2 - - - +
471D ASN* 4.2 7.1 - - - +
540D LEU* 3.8 29.3 - - + +
544D ASP* 2.7 46.9 + - + +
545D ALA 4.0 0.7 - - - +
546D PRO* 3.5 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D LYS* 3.4 3.6 - - + +
367D GLN* 1.3 80.8 - - - +
369D TRP* 1.3 66.1 + - - +
371D TRP* 3.6 6.0 + - - +
372D ASN* 3.2 20.8 + - + +
397D GLN* 5.9 3.1 - - + +
544D ASP* 5.1 1.2 + - - -
545D ALA 6.1 0.4 - - - +
546D PRO* 5.6 8.5 - - + +
547D GLN* 4.9 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 369 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D ASN* 3.0 50.6 + - + +
357D ALA 4.6 2.0 + - - -
359D VAL* 4.3 16.9 - - + +
365D LEU* 3.5 30.7 - - + -
366D LYS* 3.4 19.8 + - + +
367D GLN 3.3 0.2 - - - -
368D GLU* 1.3 78.4 - - - +
370D MET* 1.3 74.8 + - - +
372D ASN 3.2 1.7 + - - -
373D GLN* 2.8 59.6 + - + +
515D THR* 3.5 33.5 + - - -
518D TRP* 3.6 24.7 - + - -
519D ASP* 3.7 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D LEU* 5.0 4.0 - - + -
366D LYS 3.0 16.5 + - - +
367D GLN* 2.9 5.8 + - - +
369D TRP* 1.3 89.1 - - + +
371D TRP* 1.3 105.6 + - + +
373D GLN* 3.0 2.9 + - - +
374D LEU* 2.8 30.1 + - + +
441D PHE* 4.4 2.9 - - + -
469D LEU* 4.1 16.6 - - + -
518D TRP* 3.6 43.5 - - + -
538D VAL* 3.8 20.4 - - - -
540D LEU* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D GLN* 2.7 62.9 + - + +
368D GLU* 4.3 5.4 - - - +
370D MET* 1.3 96.1 - - + +
372D ASN* 1.3 62.5 + - - +
374D LEU* 3.6 17.7 + - + -
391D SER* 3.6 36.8 - - - -
394D GLY* 3.3 39.7 - - - +
395D ILE* 3.9 11.4 - - + -
397D GLN* 4.2 12.6 - - + -
398D THR* 2.8 38.9 + - - +
441D PHE* 3.9 31.6 - + + -
469D LEU* 3.9 5.2 - - + -
546D PRO* 4.0 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D THR* 4.2 23.3 - - - +
354D PRO 2.9 28.6 + - - +
355D ALA* 5.0 2.6 - - - -
356D ASN* 3.1 29.3 + - - +
368D GLU* 3.2 16.7 + - + +
369D TRP 3.2 3.9 + - - +
370D MET 3.2 0.6 - - - -
371D TRP* 1.3 80.4 - - - +
373D GLN* 1.3 61.8 + - - +
374D LEU 3.6 0.5 + - - -
375D GLY* 4.0 6.1 + - - -
376D ASN* 5.0 3.5 - - - +
397D GLN* 4.3 12.3 + - + +
399D THR* 5.6 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D ALA* 6.0 0.2 - - - +
356D ASN* 2.7 34.7 + - - +
369D TRP* 2.8 51.3 + - + +
370D MET 3.0 4.4 + - - +
372D ASN* 1.3 78.7 - - - +
374D LEU* 1.3 64.6 + - - +
375D GLY 3.2 0.2 - - - -
376D ASN* 3.0 42.4 + - + +
377D PHE* 4.3 0.7 + - - +
518D TRP* 3.9 11.4 + - - +
519D ASP* 2.8 31.1 + - - +
523D GLN* 5.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D MET* 2.8 20.0 + - + +
371D TRP* 3.8 15.7 - - + +
372D ASN 3.4 1.2 - - - -
373D GLN* 1.3 73.1 - - - +
375D GLY* 1.3 62.3 + - - +
377D PHE* 3.0 36.5 + - + +
378D LEU* 3.3 20.0 + - + +
384D VAL* 5.2 0.7 - - + -
395D ILE* 3.7 27.8 - - + -
398D THR* 3.8 10.5 - - + +
441D PHE* 3.6 42.2 - - + -
518D TRP* 4.0 18.2 - - + +
----------------------------------------------------------
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