Contacts of the helix formed by residues 266 - 278 (chain A) in PDB entry 1WLZ
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 SER 266 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ILE* 1.3 76.4 - - - +
267A ARG* 1.3 60.1 + - - +
268A GLU* 3.5 14.7 + - - +
269A GLU* 2.9 46.8 + - - +
270A PHE* 2.9 28.1 + - - +
290A TRP* 4.8 0.9 - - - -
300A ARG* 3.6 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ILE 4.0 0.2 + - - -
266A SER* 1.3 74.3 - - - +
268A GLU* 1.3 71.0 + - - +
270A PHE* 3.2 4.0 + - - +
271A ARG* 2.9 26.4 + - - +
286A PHE* 3.5 31.3 - - + -
287A ASP* 2.8 42.4 + - - +
290A TRP* 3.2 64.5 - - + +
299A GLY 4.2 10.7 + - - +
283C ASP* 3.9 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 3.8 15.3 + - - +
267A ARG* 1.3 91.1 + - - +
269A GLU* 1.3 60.6 + - - +
271A ARG* 3.3 10.6 + - - +
272A ALA* 3.0 25.8 + - - +
286A PHE* 5.8 0.2 - - - -
271C ARG* 3.6 17.7 - - - +
275C ASN* 4.9 1.9 + - - -
280C ILE* 3.7 21.1 - - + +
281C LEU 3.5 19.1 - - - +
282C THR* 3.9 18.8 - - - +
283C ASP* 3.9 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PHE* 3.5 48.7 - - + +
265A ILE* 3.4 15.5 - - + +
266A SER* 2.9 45.5 + - - +
268A GLU* 1.3 72.8 - - - +
270A PHE* 1.3 65.8 + - - +
272A ALA* 3.1 12.5 + - - +
273A ILE* 3.1 16.6 + - - +
300A ARG* 4.9 2.0 + - - -
280C ILE* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 4.6 5.8 - - + -
254A PHE* 4.2 9.2 - + - -
265A ILE* 3.6 11.6 - - + +
266A SER 2.9 13.6 + - - +
267A ARG 3.5 7.0 - - - +
269A GLU* 1.3 77.8 - - - +
271A ARG* 1.3 61.3 + - - +
273A ILE* 3.1 10.6 + - + +
274A CYS* 3.0 45.2 + - - -
286A PHE* 3.8 13.2 - + - -
289A LEU* 4.3 5.2 - - + -
290A TRP* 3.6 26.2 - + + -
293A MET* 3.8 36.1 - - + -
301A LEU* 3.5 21.5 - - + -
306A PHE* 3.8 27.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 2.9 10.8 + - - +
268A GLU* 3.5 12.8 - - - +
269A GLU 3.2 0.2 - - - -
270A PHE* 1.3 78.5 - - - +
272A ALA* 1.3 56.5 + - - +
274A CYS* 3.1 4.5 + - + +
275A ASN* 2.8 46.8 + - - +
281A LEU* 3.1 27.3 + - + +
282A THR 3.5 0.6 - - - -
283A ASP* 2.7 43.2 + - - +
286A PHE* 3.5 56.6 - - + +
287A ASP* 5.7 0.8 + - - -
268C GLU* 3.5 9.2 - - - +
271C ARG* 4.0 32.2 - - - +
275C ASN* 5.9 0.4 - - - +
283C ASP* 4.9 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PHE* 4.8 3.8 - - + -
268A GLU 3.0 14.2 + - - +
269A GLU 3.1 10.0 + - - +
271A ARG* 1.3 77.6 - - - +
273A ILE* 1.3 61.3 + - - +
275A ASN* 3.3 17.6 - - - +
276A ARG* 3.5 8.3 + - - +
275C ASN* 3.9 26.4 - - + +
280C ILE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 6.5 0.4 - - + -
250A ILE* 4.5 14.4 - - + +
253A GLU* 3.7 35.0 - - + +
254A PHE* 3.7 37.7 - - + -
257A PHE* 3.9 23.1 - - + -
265A ILE* 4.1 2.7 - - + -
269A GLU 3.1 11.1 + - - +
270A PHE* 3.1 13.1 + - + +
272A ALA* 1.3 75.0 - - - +
274A CYS* 1.3 67.0 + - - +
276A ARG* 3.2 4.3 + - - +
277A ARG* 2.9 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 4.7 11.4 - - - -
270A PHE* 3.0 52.2 + - - -
271A ARG* 3.1 11.0 + - + +
273A ILE* 1.3 77.4 - - - +
275A ASN* 1.3 63.7 + - - +
277A ARG* 4.9 0.4 - - - -
278A VAL* 2.9 30.9 + - + +
279A GLN 3.0 11.1 + - - +
281A LEU* 4.3 17.7 - - + -
286A PHE* 4.7 1.3 - - + -
289A LEU* 4.0 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 2.8 33.6 + - - +
272A ALA* 3.3 9.6 - - - +
273A ILE 3.2 0.2 - - - -
274A CYS* 1.3 78.9 - - - +
276A ARG* 1.3 59.0 + - - +
279A GLN* 3.4 21.2 + - - -
280A ILE* 3.6 34.9 + - + +
281A LEU* 4.0 5.7 - - - +
268C GLU 5.1 1.0 - - - +
271C ARG* 5.3 0.5 - - - +
272C ALA* 3.8 21.7 + - + +
275C ASN* 3.6 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU* 4.6 11.9 + - - +
272A ALA 3.5 7.0 + - - +
273A ILE* 3.2 6.6 + - - +
275A ASN* 1.3 80.8 - - + +
277A ARG* 1.3 114.8 + - + +
278A VAL 5.1 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ARG 5.2 0.2 - - - +
239A LEU* 5.8 1.6 - - + -
242A ALA* 3.6 26.7 - - + +
246A HIS* 3.6 42.0 + - - +
249A ALA* 3.6 21.2 - - - +
250A ILE* 3.9 17.5 - - + +
253A GLU* 3.1 26.0 + - - +
273A ILE* 2.9 34.4 + - + +
274A CYS* 4.9 0.4 - - - -
276A ARG* 1.3 124.4 - - + +
278A VAL* 1.3 64.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ILE* 4.4 22.2 - - + +
238A ARG* 3.5 35.2 + - + +
239A LEU* 3.5 41.7 - - + -
242A ALA* 4.4 4.5 - - + -
274A CYS* 2.9 18.8 + - + +
275A ASN 4.6 0.4 - - - -
276A ARG 5.1 0.9 - - - -
277A ARG* 1.3 86.5 - - + +
279A GLN* 1.3 75.6 + - + +
281A LEU* 5.4 2.2 - - + -
----------------------------------------------------------
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