Contacts of the strand formed by residues 289 - 294 (chain A) in PDB entry 2HVY
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 LEU 289 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLN* 3.5 31.2 - - - +
105A ALA* 4.0 15.3 - - - -
108A PRO* 4.9 11.0 - - + -
253A LEU* 3.9 30.1 - - + +
254A PRO* 3.4 24.4 - - - +
287A GLY 3.7 2.6 + - - -
288A ASP* 1.3 71.2 - - - +
290A VAL* 1.3 60.0 + - - +
302A LEU* 4.2 20.9 - - + -
303A GLY 3.4 15.5 - - - +
304A LYS* 4.9 0.9 - - - +
324A GLU* 4.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 4.6 2.5 - - - -
254A PRO* 3.4 21.5 - - + +
256A VAL* 4.5 11.0 - - + -
284A ILE* 4.0 32.8 - - + -
288A ASP 3.8 9.6 - - - +
289A LEU* 1.3 79.8 - - - +
291A ALA* 1.3 62.5 + - - +
292A ILE* 4.9 0.7 - - + -
302A LEU* 3.5 8.9 - - - +
303A GLY 2.9 42.2 + - - +
305A ALA* 4.2 4.3 - - + +
321A VAL* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL* 3.7 41.5 - - + -
253A LEU* 4.3 5.5 - - + +
254A PRO 3.0 7.6 + - - +
255A LYS* 3.3 12.3 - - + +
256A VAL* 2.9 26.1 + - - +
290A VAL* 1.3 73.8 - - - +
292A ILE* 1.3 62.5 + - - +
293A MET* 3.7 9.4 + - - +
299A LEU* 4.1 3.6 - - + -
301A ALA 3.7 3.6 - - - -
302A LEU* 4.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 3.5 20.2 - - + -
258A ILE* 3.8 38.6 - - + -
266A VAL* 4.6 4.5 - - + -
272A LEU* 4.1 10.3 - - + -
290A VAL* 4.9 2.5 - - + +
291A ALA* 1.3 71.3 - - - +
293A MET* 1.3 64.8 + - - +
299A LEU* 3.9 0.3 - - - +
300A VAL* 2.9 36.1 + - + -
301A ALA* 2.8 30.8 + - + +
303A GLY* 5.2 1.3 - - - +
321A VAL* 3.8 31.0 - - + -
323A VAL* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU* 4.1 10.5 - - + -
250A VAL* 3.9 27.1 - - + -
255A LYS* 3.8 38.1 - - + +
256A VAL 2.8 8.5 + - - +
257A TRP* 3.3 14.9 - - + +
258A ILE* 2.8 29.8 + - - +
291A ALA* 3.9 6.1 - - - +
292A ILE* 1.3 82.0 - - - +
294A THR* 1.3 68.1 + - - +
297A ASP* 3.6 30.7 - - + +
298A GLU 3.2 14.6 - - - +
299A LEU* 4.0 11.2 - - - +
300A VAL* 4.0 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 5.6 0.2 - - - -
257A TRP* 3.2 13.4 - - - -
258A ILE* 4.1 7.6 - - - -
260A ASP* 5.4 1.6 - - - -
263A VAL* 3.9 18.2 - - + -
293A MET* 1.3 75.8 - - - +
295A LEU* 1.3 59.9 + - - +
296A LYS 3.2 5.6 + - - -
297A ASP* 2.9 15.6 + - - -
298A GLU* 2.8 48.0 + - - +
300A VAL* 3.5 22.2 - - + -
328A MET* 3.7 13.5 - - + -
333A TYR* 3.8 12.1 - - + +
----------------------------------------------------------
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