Contacts of the helix formed by residues 366 - 375 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B PRO* 3.5 20.4 + - + +
365B LEU* 1.3 83.8 - - - +
367B GLN* 1.3 67.1 + - - +
368B GLU* 3.4 4.9 - - + +
369B TRP* 3.4 15.7 + - + +
370B MET* 3.0 21.8 + - - +
540B LEU* 3.9 5.4 - - - -
541B PRO* 3.7 19.7 - - + -
544B ASP* 3.2 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 1.3 71.1 - - - +
368B GLU* 1.3 66.1 + - - +
370B MET* 2.9 7.8 + - - +
371B TRP* 2.8 54.8 + - + +
390B THR* 3.0 39.8 + - - +
469B LEU* 4.0 3.7 - - - +
471B ASN* 4.3 6.5 - - - +
540B LEU* 3.7 29.4 - - + +
544B ASP* 2.7 47.2 + - + +
545B ALA 4.3 0.4 - - - -
546B PRO* 3.5 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 3.4 3.6 - - + +
367B GLN* 1.3 79.0 - - - +
369B TRP* 1.3 65.9 + - - +
371B TRP* 3.6 6.0 + - - +
372B ASN* 3.3 20.9 + - + +
397B GLN* 5.9 5.1 - - + +
544B ASP* 4.9 1.8 + - - -
545B ALA 5.6 1.3 + - - +
546B PRO* 5.6 7.1 - - + +
547B GLN* 3.3 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ASN* 2.9 48.7 + - + +
357B ALA 4.7 2.7 + - - -
359B VAL* 4.3 17.7 - - + +
365B LEU* 3.4 30.1 - - + -
366B LYS* 3.4 19.5 + - + +
368B GLU* 1.3 80.9 - - - +
370B MET* 1.3 75.5 + - - +
373B GLN* 2.9 59.1 + - + +
515B THR* 3.6 33.7 + - - -
518B TRP* 3.6 24.0 - + - -
519B ASP* 3.8 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 5.1 3.4 - - + -
366B LYS 3.0 13.5 + - - +
367B GLN* 2.9 9.6 + - - +
369B TRP* 1.3 88.5 - - + +
371B TRP* 1.3 104.4 + - + +
373B GLN* 3.1 2.3 + - - +
374B LEU* 2.8 29.4 + - + +
441B PHE* 4.4 2.5 - - + -
469B LEU* 4.1 17.7 - - + -
518B TRP* 3.7 43.2 - - + -
538B VAL* 3.9 19.7 - - - -
540B LEU* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B GLN* 2.8 58.3 + - + +
368B GLU* 4.4 4.5 - - - +
370B MET* 1.3 90.6 - - + +
372B ASN* 1.3 62.7 + - - +
374B LEU* 3.6 19.6 + - + -
391B SER* 3.6 34.3 - - - -
394B GLY* 3.4 36.4 - - - +
395B ILE* 3.9 16.2 - - + -
397B GLN* 4.1 12.8 - - + -
398B THR* 2.8 37.7 + - - +
441B PHE* 3.6 39.7 - + + -
469B LEU* 3.8 9.4 - - + -
546B PRO* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B THR* 3.5 28.7 - - - +
354B PRO 3.1 23.4 + - - +
355B ALA* 3.8 2.4 - - - +
356B ASN* 3.0 32.1 + - - +
368B GLU* 3.3 17.1 + - + +
369B TRP 3.3 3.3 + - - +
370B MET 3.2 0.6 - - - -
371B TRP* 1.3 81.4 - - - +
373B GLN* 1.3 61.1 + - - +
374B LEU 3.4 0.7 + - - -
375B GLY* 3.7 8.3 + - - -
376B ASN* 5.0 2.6 + - - +
397B GLN* 4.4 13.0 + - + +
398B THR* 5.3 0.2 - - - +
399B THR* 5.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ALA* 5.9 0.3 - - - +
356B ASN* 2.8 29.6 + - - +
369B TRP* 2.9 48.9 + - + +
370B MET 3.7 3.6 - - - +
372B ASN* 1.3 77.3 - - - +
374B LEU* 1.3 64.5 - - - +
376B ASN* 3.0 42.2 + - + +
377B PHE* 4.2 0.7 + - - +
518B TRP* 3.8 11.7 + - - +
519B ASP* 2.8 34.5 + - - +
523B GLN* 5.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B MET* 2.8 16.8 + - + +
371B TRP* 3.7 16.8 - - + +
372B ASN 3.3 1.0 - - - -
373B GLN* 1.3 77.4 - - - +
375B GLY* 1.3 63.1 + - - +
376B ASN 3.0 0.2 - - - -
377B PHE* 2.9 36.2 + - + +
378B LEU* 3.4 18.2 + - + +
384B VAL* 5.3 1.1 - - + -
395B ILE* 3.7 27.6 - - + -
398B THR* 3.8 11.7 - - + +
441B PHE* 3.7 42.4 - - + -
518B TRP* 4.0 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ASN 3.7 8.1 + - - -
373B GLN 3.1 2.0 + - - -
374B LEU* 1.3 77.5 - - - +
376B ASN* 1.3 62.0 + - - +
377B PHE 3.3 0.2 - - - -
378B LEU* 3.7 16.3 + - - +
398B THR* 3.9 7.3 - - - +
399B THR* 3.5 29.8 - - - +
401B PRO* 5.1 3.1 - - - +
----------------------------------------------------------
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