Contacts of the helix formed by residues 286 - 296 (chain A) in PDB entry 1V0D
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 286 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU 3.7 2.0 + - - -
285A VAL* 1.3 70.0 - - - +
287A TRP* 1.3 57.9 + - - +
288A GLU* 3.3 14.0 + - - +
289A TYR* 2.8 33.2 + - - +
290A PHE* 3.9 2.9 - - - -
321A ARG* 2.9 25.2 + - - +
322A ILE 2.8 19.1 + - - +
323A TYR 3.9 15.4 + - - -
324A ARG* 3.1 28.1 + - + +
325A PRO* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ARG* 4.0 27.9 - - - +
192A VAL* 3.6 28.9 - - + -
195A SER* 3.8 26.4 - - - -
196A MET* 3.8 29.6 - - + +
199A LYS* 4.1 26.9 - - + -
285A VAL* 2.9 18.7 + - + +
286A ASN* 1.3 70.3 - - - +
288A GLU* 1.3 94.3 + - + +
289A TYR 3.1 0.2 - - - -
290A PHE* 3.1 16.9 + - + +
291A TYR* 3.0 22.8 + - + +
324A ARG* 3.2 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LYS* 4.4 15.3 - - - +
286A ASN* 2.9 8.0 + - - +
287A TRP* 1.3 118.6 + - + +
289A TYR* 1.3 60.8 + - - +
291A TYR* 3.2 7.5 - - - +
292A SER* 3.0 24.8 + - - -
324A ARG* 2.7 35.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ILE* 4.5 5.2 - - - +
286A ASN* 2.8 29.4 + - - +
288A GLU* 1.3 78.5 - - - +
290A PHE* 1.3 67.8 + + - +
292A SER* 3.2 11.7 + - - -
293A LEU* 3.1 56.5 + - + +
317A CYS* 3.9 7.0 - - + -
318A ASP* 3.0 39.0 + - + +
321A ARG* 3.4 67.9 + - + +
322A ILE* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A MET* 5.0 2.5 - - - -
271A VAL* 4.0 15.0 - - + -
274A THR* 3.7 15.0 - - + -
275A LEU* 3.4 55.2 - - + -
278A ALA* 4.0 4.5 - - + -
285A VAL* 3.7 24.2 - - + -
286A ASN 3.9 10.5 - - - -
287A TRP* 3.1 8.2 + - - +
289A TYR* 1.3 77.1 - + - +
291A TYR* 1.3 60.2 + - - +
293A LEU* 3.3 8.8 + - + +
294A LEU* 2.8 46.5 + - + +
317A CYS* 4.5 7.6 - - - -
322A ILE* 3.7 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A MET* 3.8 23.3 - - + -
199A LYS* 3.5 45.0 + - + +
200A LEU* 3.4 31.1 - - + +
203A VAL* 3.7 15.8 - - - +
206A ASN* 4.4 3.7 + - - -
287A TRP* 3.0 18.2 + + + +
288A GLU* 3.2 15.7 - - - +
289A TYR 3.2 0.2 - - - -
290A PHE* 1.3 76.7 - - - +
292A SER* 1.3 68.9 + - - +
294A LEU 3.0 1.7 + - - -
295A PHE* 2.8 58.4 + + + -
296A THR* 3.9 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU 3.0 11.9 + - - -
289A TYR* 3.2 14.5 + - - -
291A TYR* 1.3 82.1 - - - +
293A LEU* 1.3 68.3 + - - +
296A THR* 3.1 40.8 + - - +
298A GLU* 3.0 35.3 + - - -
299A ASN* 4.0 4.2 + - - +
321A ARG* 4.9 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A HIS* 3.3 8.2 - - - -
265A ILE* 4.5 11.9 - - + -
271A VAL* 3.9 20.0 - - + -
289A TYR* 3.1 62.0 + - + +
290A PHE* 3.5 12.3 - - + +
292A SER* 1.3 85.7 - - - +
294A LEU* 1.3 60.3 + - - +
296A THR 4.9 0.3 + - - -
298A GLU* 6.0 2.0 - - + -
299A ASN* 2.7 47.6 + - + +
300A LEU* 4.8 0.9 - - - +
317A CYS* 3.9 18.2 - - - -
321A ARG* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR* 4.0 8.2 - - + +
174A VAL* 4.0 18.2 - - + -
196A MET* 4.0 21.5 - - + -
263A HIS* 3.0 21.5 + - - -
267A LYS* 4.1 16.6 - - + -
271A VAL* 3.7 22.0 - - + -
272A VAL* 3.9 23.8 - - + -
275A LEU* 5.1 6.3 - - + -
290A PHE* 2.8 36.1 + - + +
293A LEU* 1.3 75.2 - - - +
295A PHE* 1.3 84.3 + - + +
300A LEU* 4.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 4.1 25.9 - - + +
170A TYR* 4.0 9.0 - - + -
171A LEU* 3.7 46.0 - - + -
174A VAL* 4.6 4.5 - - + -
196A MET* 4.0 20.2 - - + -
200A LEU* 4.0 31.6 - - + -
206A ASN* 3.1 16.3 - - - +
209A TYR* 4.2 1.0 - - - -
291A TYR* 2.8 51.0 + + + +
294A LEU* 1.3 102.0 - - + +
296A THR* 1.3 61.6 + - - +
300A LEU* 4.1 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASN* 4.5 3.0 + - - -
209A TYR* 3.5 12.6 - - - +
291A TYR* 3.9 17.7 - - - -
292A SER* 3.1 25.3 + - - +
294A LEU 3.9 0.4 - - - -
295A PHE* 1.3 80.6 + - - +
297A ALA* 1.3 71.9 + - + +
298A GLU* 2.8 42.1 + - + +
299A ASN* 3.1 11.4 + - - +
300A LEU* 3.1 17.1 - - - +
----------------------------------------------------------
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