Contacts of the strand formed by residues 285 - 292 (chain A) in PDB entry 1V9P
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 ALA 285 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A HIS* 4.7 4.9 - - + -
118A LYS 3.3 24.5 - - - +
120A ASP 4.6 0.2 - - - +
278A ARG* 4.1 17.9 + - - +
281A LEU* 4.5 11.9 - - + -
283A PHE* 3.4 21.4 + - + +
284A GLU* 1.3 75.2 - - - +
286A ASP* 1.3 63.7 + - - +
287A GLY 3.4 4.5 - - - +
316A PHE* 3.4 20.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 3.8 9.2 + - + +
120A ASP* 3.8 7.5 - - + +
278A ARG* 4.0 18.7 + - - -
284A GLU* 2.6 37.3 - - - +
285A ALA* 1.3 71.5 - - - +
287A GLY* 1.3 54.3 + - - +
315A LYS* 3.5 22.9 - - + +
316A PHE* 3.0 29.1 + - - +
318A ALA* 5.9 2.1 - - - -
700A AMP 5.0 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A HIS* 4.3 1.6 - - - +
118A LYS* 3.3 24.1 + - - +
285A ALA* 3.4 5.5 - - - +
286A ASP* 1.3 78.6 - - - +
288A VAL* 1.3 69.4 + - - +
314A TYR 3.3 12.1 - - - -
315A LYS* 3.6 2.2 - - - -
316A PHE* 3.4 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 4.0 17.7 - - + -
116A GLU 3.3 12.8 - - - +
117A HIS* 4.7 0.2 - - - -
118A LYS* 3.3 16.2 - - - +
267A VAL* 5.6 1.3 - - + -
271A TYR* 4.3 15.9 - - + -
274A PHE* 3.4 33.7 - - + -
287A GLY* 1.3 81.1 - - - +
289A VAL* 1.3 61.6 + - - +
290A VAL* 5.0 2.2 - - + -
313A ALA* 3.5 0.3 - - - -
314A TYR* 2.7 53.0 + - + +
316A PHE* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.3 34.5 - - + -
114A THR 3.2 15.9 - - - +
115A VAL* 3.5 3.4 - - - -
116A GLU* 2.9 34.0 + - + +
118A LYS* 3.2 31.9 - - + -
288A VAL* 1.3 74.1 - - - +
290A VAL* 1.3 58.6 + - - +
291A LYS* 3.4 29.2 + - + +
312A LEU 3.3 8.3 - - - +
313A ALA* 4.5 0.2 - - + -
700A AMP 4.2 17.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
94A VAL* 4.8 6.7 - - + -
97A PHE* 4.6 8.8 - - + -
113A TYR* 4.0 24.2 - - + -
114A THR 4.1 2.5 - - - -
115A VAL* 4.9 3.8 - - + -
267A VAL* 3.8 43.3 - - + -
288A VAL* 5.0 1.6 - - + -
289A VAL* 1.3 70.3 - - - +
291A LYS* 1.3 58.5 + - - +
292A LEU 4.2 0.4 + - - -
310A PHE 4.2 0.2 - - - +
311A ALA* 3.1 4.0 - - - +
312A LEU* 2.7 56.5 + - + +
314A TYR* 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 5.1 4.9 - - - +
113A TYR* 3.3 3.6 - - - -
114A THR* 2.9 40.8 + - - +
116A GLU* 4.1 8.1 - - - +
226A TYR* 4.9 8.6 - - - -
227A ALA* 5.2 5.7 - - - +
240A GLN* 3.4 38.6 - - + +
289A VAL* 3.8 19.0 - - + +
290A VAL* 1.3 72.6 - - - +
292A LEU* 1.3 70.9 + - - +
293A ASP* 3.8 0.9 - - - -
298A TRP* 4.4 18.5 - - + -
310A PHE* 3.8 4.3 - - - -
311A ALA* 3.9 16.0 - - + +
700A AMP 3.7 36.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.7 22.4 - - + -
111A PHE* 5.2 15.3 - - + -
112A LEU 3.9 8.1 - - - +
113A TYR* 3.3 23.9 - - + -
240A GLN* 4.4 0.5 - - - +
291A LYS* 1.3 73.0 - - - +
293A ASP* 1.3 72.3 + - - +
294A ASP* 3.6 22.9 - - + +
297A LEU* 4.8 13.2 - - + +
298A TRP* 3.0 29.0 + - + +
301A LEU* 3.5 31.4 - - + -
310A PHE* 2.6 29.3 + - + +
----------------------------------------------------------
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