Contacts of the strand formed by residues 319 - 326 (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 ILE 319 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ASP* 3.8 36.1 - - + +
272A LEU 3.6 4.3 - - - +
273A ALA* 4.4 4.3 - - + -
306A MET* 3.5 28.2 - - + +
307A MET* 3.4 13.9 - - - +
318A GLY* 1.3 70.1 - - - -
320A ALA* 1.3 60.6 + - - +
321A VAL 3.7 26.5 - - - +
322A ASP* 4.3 1.8 - - + +
59E C 3.6 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 2.8 14.3 + - + +
273A ALA 4.5 0.4 - - - -
274A VAL* 4.0 13.0 - - + +
277A ILE* 3.7 30.1 - - + -
306A MET* 2.7 28.5 + - - -
307A MET* 3.4 13.4 + - - -
312A MET* 3.4 24.9 - - + +
318A GLY 3.5 2.0 + - - -
319A ILE* 1.3 73.9 - - - +
321A VAL* 1.3 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 4.2 8.7 - - + -
271A ASP* 3.6 4.3 - - - +
272A LEU* 3.1 50.2 + - + -
290A VAL* 3.7 24.9 - - + -
292A ILE* 3.8 13.5 - - + -
303A GLY* 3.7 27.8 - - - -
304A LYS 3.6 6.7 - - - +
305A ALA* 4.6 1.6 - - - -
312A MET* 4.0 13.7 - - + -
319A ILE* 3.7 4.8 - - - +
320A ALA* 1.3 86.5 - - + +
322A ASP* 1.3 65.4 + - - +
323A VAL* 3.4 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ASP* 3.8 18.6 - - - +
303A GLY* 3.2 1.2 - - - -
304A LYS* 2.8 49.5 + - + +
306A MET* 3.6 28.6 - - + +
319A ILE* 4.7 1.8 - - + +
321A VAL* 1.3 70.1 - - - +
323A VAL* 1.3 73.3 + - - +
324A GLU* 3.4 8.2 + - - +
4E U 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A VAL* 3.8 10.5 - - + +
269A GLY 5.8 2.0 - - - +
270A ALA 3.6 21.5 - - - +
271A ASP* 3.0 22.2 + - - +
272A LEU 3.9 4.5 - - - +
292A ILE* 3.8 24.5 - - + -
301A ALA* 3.8 16.4 - - + -
302A LEU 4.1 3.4 - - - +
303A GLY* 4.3 1.3 - - - -
321A VAL 4.1 0.7 - - - +
322A ASP* 1.3 79.7 - - - +
324A GLU* 1.3 61.2 + - - +
325A LYS 4.4 1.6 - - - +
326A VAL* 3.7 30.3 - - + -
3E G 4.7 1.8 - - - +
4E U 3.8 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLN* 4.6 11.2 + - - +
289A LEU* 4.4 10.9 - - - +
302A LEU* 2.9 11.6 + - + +
303A GLY* 3.8 5.4 - - - +
304A LYS* 3.7 36.9 + - + +
322A ASP* 3.7 17.3 - - - +
323A VAL* 1.3 76.5 - - - +
325A LYS* 1.3 72.2 + - + +
4E U 4.0 16.0 + - - +
5E C 4.2 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.6 64.0 + - + +
104A GLN* 3.8 32.7 - - + +
301A ALA* 3.1 4.4 - - - -
302A LEU* 2.8 42.3 + - + -
324A GLU* 1.3 87.4 - - + +
326A VAL* 1.3 63.5 + - - +
327A PHE* 3.7 17.3 - - + -
5E C 3.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 2.9 20.3 + - - -
266A VAL 3.6 16.8 - - - +
267A THR* 3.8 22.9 - - + +
300A VAL 3.7 10.8 - - - +
301A ALA* 4.1 2.7 - - + -
323A VAL* 3.7 22.0 - - + -
325A LYS* 1.3 72.5 - - - +
327A PHE* 1.3 63.4 + - - +
328A MET 3.6 19.7 - - - +
4E U 3.5 33.4 - - - +
5E C 2.9 19.0 + - - +
----------------------------------------------------------
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