Contacts of the helix formed by residues 263 - 276 (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 GLY 263 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 3.0 21.8 - - - -
110A PRO* 3.7 8.7 - - - -
111A PHE 3.0 21.5 + - - +
113A TYR* 4.2 1.5 - - - -
261A ALA 4.1 0.2 + - - -
262A LEU* 1.3 81.0 - - - +
264A ALA* 1.3 70.8 + - - +
265A GLU* 3.2 7.9 - - - -
266A GLY 2.8 4.2 + - - -
267A VAL* 2.9 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.7 22.2 - - + +
94A VAL* 3.1 30.0 - - + +
95A LEU* 3.9 12.3 - - + -
98A GLU* 2.6 22.2 + - - +
113A TYR* 4.3 1.7 - - - -
263A GLY* 1.3 67.0 - - - -
265A GLU* 1.3 69.6 + - - +
267A VAL* 2.8 14.2 + - - +
268A GLU* 2.7 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.1 20.8 + - + +
109A ARG* 2.5 47.6 + - - -
110A PRO* 5.4 2.6 - - - +
262A LEU 4.9 0.4 - - - +
263A GLY* 3.8 6.2 - - - -
264A ALA* 1.3 81.6 + - - +
266A GLY* 1.3 62.7 + - - +
268A GLU* 3.1 16.4 + - - +
269A GLU* 3.2 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ALA* 4.1 7.4 - - - +
262A LEU 3.1 19.3 + - - -
263A GLY 2.8 9.9 + - - -
265A GLU* 1.3 72.4 - - - +
267A VAL* 1.3 56.5 + - - +
269A GLU* 2.7 38.6 + - - +
270A VAL* 3.3 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 4.4 9.4 - - + -
113A TYR* 3.4 34.3 - - + -
115A VAL* 4.3 20.6 - - + +
261A ALA* 3.9 12.6 - - + +
263A GLY 2.9 11.1 + - - +
264A ALA* 2.8 16.3 + - - +
266A GLY* 1.3 69.6 - - - +
268A GLU* 1.3 55.2 + - - +
269A GLU 2.7 11.1 + - - -
270A VAL* 2.9 14.2 + - - +
271A TYR* 2.9 10.9 + - + +
288A VAL* 5.6 1.1 - - + -
290A VAL* 3.8 34.1 - - + -
314A TYR* 4.6 9.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
91A TYR* 3.3 41.1 - - + +
94A VAL* 6.1 0.2 - - + -
264A ALA 2.7 8.1 + - - -
265A GLU* 3.2 12.8 - - - +
267A VAL* 1.3 73.9 - - - +
269A GLU* 1.3 60.3 + - - +
271A TYR* 3.7 15.4 - - - +
272A ARG* 3.7 32.5 + - - +
314A TYR* 2.9 39.0 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
265A GLU 3.2 6.2 + - - +
266A GLY* 2.7 29.5 + - - +
268A GLU* 1.3 70.0 - - - +
270A VAL* 1.3 64.6 + - + +
271A TYR 3.1 1.5 + - - -
272A ARG* 3.3 5.5 + - - +
273A ARG* 2.9 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.9 17.9 - - + -
259A GLU* 3.7 18.8 - - + +
260A LYS 4.2 2.2 - - - +
261A ALA* 3.8 28.7 - - + -
266A GLY 4.0 3.1 - - - +
267A VAL 2.9 5.9 + - - +
269A GLU* 1.3 74.2 - - + +
271A TYR* 1.3 68.2 + - - +
273A ARG* 3.2 23.7 + - - +
274A PHE* 2.8 65.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE 4.9 3.3 + - - -
115A VAL* 5.5 0.6 - - - +
267A VAL* 2.9 15.1 + - + +
268A GLU* 3.7 19.5 - - - +
270A VAL* 1.3 76.9 - - - +
272A ARG* 1.3 67.8 + - + +
274A PHE* 2.9 10.0 - - - +
275A LEU* 2.7 49.5 + - + +
288A VAL* 4.3 18.4 - - + -
314A TYR* 3.3 59.7 + + + -
315A LYS 3.5 15.3 + - - -
316A PHE* 3.7 31.4 - + - -
317A PRO* 3.8 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 3.7 22.6 + - - +
269A GLU* 3.3 7.4 + - - +
271A TYR* 1.3 91.9 - - + +
273A ARG* 1.3 64.3 + - - +
274A PHE 2.8 5.8 + - - -
275A LEU* 3.9 12.1 - - + +
276A ALA* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU* 2.7 38.4 + - - -
269A GLU* 2.9 58.4 + - - +
270A VAL* 3.7 17.1 - - - +
272A ARG* 1.3 75.5 - - - +
274A PHE* 1.3 64.8 + - + +
276A ALA* 4.0 6.9 - - - +
277A GLN* 3.2 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 4.8 2.9 - - + -
116A GLU* 4.1 6.5 - - - -
117A HIS* 3.4 57.2 + + - +
257A GLY 4.8 6.1 - - - -
258A TYR 5.3 0.4 - - - -
259A GLU* 3.1 29.2 - - + -
270A VAL* 2.8 34.2 + - + +
271A TYR 2.9 13.5 - - - +
272A ARG 2.8 0.6 - - - -
273A ARG* 1.3 84.8 - - + +
275A LEU* 1.3 49.7 + - - +
276A ALA 2.5 6.0 + - - -
277A GLN* 2.4 38.8 + - - +
278A ARG* 3.2 7.3 + - - -
288A VAL* 3.4 27.4 - - + -
316A PHE* 4.1 6.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A TYR* 2.7 38.9 + - + +
272A ARG* 3.2 14.6 + - + +
274A PHE* 1.3 70.7 - - - +
276A ALA* 1.3 56.2 + - - +
277A GLN 3.3 0.4 - - - -
278A ARG* 3.3 40.6 - - - +
316A PHE* 3.7 27.7 - - + -
317A PRO* 4.3 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG 3.2 14.7 + - - +
273A ARG* 4.0 8.7 - - - +
274A PHE 2.5 5.5 + - - -
275A LEU* 1.3 76.4 - - - +
277A GLN* 1.3 61.6 + - + +
278A ARG* 3.3 2.0 + - - -
279A HIS 5.1 0.7 + - - -
280A ALA* 5.1 1.4 - - - +
----------------------------------------------------------
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