Contacts of the helix formed by residues 257 - 269 (chain D) in PDB entry 2GVG
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 HIS 257 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D TRP* 3.3 39.2 + + + +
254D GLY* 3.0 8.8 + - - -
256D ASP* 1.3 99.6 + - + +
258D GLU* 1.3 65.1 + - - +
259D LYS* 3.2 3.6 - - - +
260D ASP* 2.8 30.8 + - + +
261D ALA 3.1 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ILE* 4.0 10.5 - - + -
254D GLY 4.1 2.7 + - - -
255D LYS 4.3 3.0 + - - +
256D ASP 3.8 1.6 - - - -
257D HIS* 1.3 76.9 - - - +
259D LYS* 1.3 58.3 + - - +
261D ALA* 3.3 6.2 + - - +
262D PHE* 2.9 70.8 + - + -
278D SER 4.0 12.5 - - - +
280D SER* 4.2 10.6 + - - -
281D TYR* 3.4 38.6 + - + +
282D ASP 5.0 2.8 + - - +
285D ASN* 4.6 5.7 + - - -
286D ALA* 4.3 4.2 - - - +
290D ILE* 3.5 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D HIS* 3.2 1.3 - - - -
258D GLU* 1.3 77.3 - - - +
260D ASP* 1.3 69.5 + - - +
262D PHE* 3.3 1.8 + - - +
263D GLU* 2.8 31.8 + - - +
290D ILE* 4.0 21.6 - - + +
294D ASP* 3.3 44.7 + - + +
295D LEU* 3.6 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D TRP* 4.0 20.3 - - + -
257D HIS* 2.8 41.7 + - + +
259D LYS* 1.3 82.8 - - - +
261D ALA* 1.3 61.1 + - - +
263D GLU* 3.8 13.3 - - - +
264D HIS* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D THR 4.3 0.7 - - - +
250D ILE* 3.8 25.8 - - + +
253D TRP* 3.3 41.2 - - + +
257D HIS 3.1 9.9 + - - +
258D GLU 3.5 8.7 - - - +
260D ASP* 1.3 78.2 - - - +
262D PHE* 1.3 57.3 - - - +
264D HIS* 3.7 0.7 - - - +
265D ILE* 2.7 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ILE* 3.6 26.9 - - + -
258D GLU* 2.9 52.9 + - + +
259D LYS 3.5 1.1 - - - +
260D ASP 3.3 0.2 - - - -
261D ALA* 1.3 76.2 - - - +
263D GLU* 1.3 63.1 + - - +
265D ILE* 3.4 4.0 + - - +
266D VAL* 3.1 30.6 + - - +
276D VAL* 3.8 7.9 - - + -
277D VAL 3.8 16.6 - - - -
278D SER* 4.0 10.3 - - - -
286D ALA* 4.1 13.2 - - + -
290D ILE* 3.5 22.2 - - + -
291D TRP* 3.4 38.4 - + + -
295D LEU* 3.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D LYS* 2.8 24.0 + - - +
260D ASP* 3.8 14.3 - - - +
262D PHE* 1.3 73.5 - - - +
264D HIS* 1.3 62.8 + - - +
266D VAL* 3.3 6.3 - - - +
267D THR* 2.8 34.7 + - - +
295D LEU* 3.4 27.0 - - + +
297D HIS* 4.8 6.1 + - - -
298D LEU* 3.6 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D TRP* 3.5 30.8 - + + -
260D ASP 2.8 19.1 + - - +
261D ALA 3.7 1.6 - - - +
263D GLU* 1.3 78.9 - - - +
265D ILE* 1.3 57.5 + - - +
267D THR* 3.3 7.4 + - + -
268D GLN* 2.9 55.3 + - + +
24E LYS 2.9 29.5 + - - -
25E GLN* 4.0 5.7 + - - -
26E TYR 4.0 15.6 + - - -
28E PRO* 5.8 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ALA* 4.5 4.3 - - + +
249D THR* 3.9 9.9 - - + +
250D ILE* 4.5 9.6 - - + -
253D TRP* 4.9 0.2 - - - +
261D ALA 2.7 28.0 + - - +
262D PHE* 3.8 6.3 - - - +
264D HIS* 1.3 76.2 - - - +
266D VAL* 1.3 64.3 + - - +
268D GLN* 3.1 6.3 + - - -
269D PHE* 3.1 27.2 + - + +
274D VAL* 4.3 17.7 - - + -
276D VAL* 4.4 13.5 - - + -
25E GLN* 3.2 68.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D PHE 3.1 18.6 + - - +
263D GLU* 3.3 14.1 - - - +
265D ILE* 1.3 76.3 - - - +
267D THR* 1.3 61.8 + - - +
270D SER* 3.1 14.4 + - - -
274D VAL* 4.5 7.4 - - + -
276D VAL* 4.2 7.6 - - + -
291D TRP* 3.5 32.1 - - + -
295D LEU* 5.2 0.2 - - + -
298D LEU* 4.2 21.1 - - + +
299D ILE* 4.7 4.9 - - + -
302D ARG* 2.7 35.5 + - - +
308D LEU* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D GLU* 2.8 27.8 + - - +
264D HIS* 3.6 7.2 - - + +
265D ILE 3.1 0.6 - - - -
266D VAL* 1.3 78.6 - - - +
268D GLN* 1.3 69.4 + - + +
269D PHE 3.1 0.8 + - - -
270D SER* 3.7 18.8 + - - -
298D LEU* 4.4 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D HIS* 2.9 50.7 + - + +
265D ILE* 3.1 6.5 + - - +
267D THR* 1.3 78.6 - - + +
269D PHE* 1.3 81.5 + - + +
270D SER 3.7 0.9 + - - -
24E LYS* 3.6 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D PRO* 3.5 32.1 - - + -
265D ILE* 3.1 19.9 + - + +
268D GLN* 1.3 94.9 - - + +
270D SER* 1.3 52.0 + - - +
271D SER 3.3 3.1 - - - +
272D VAL* 3.3 21.6 - - + +
274D VAL* 3.9 20.3 - - + +
302D ARG* 2.5 30.7 + - - -
21E THR* 3.8 16.8 - - - -
24E LYS* 3.5 42.8 - - + -
25E GLN* 3.7 27.1 - - + -
93E ASP* 5.8 0.2 - - - -
95E VAL* 4.1 7.6 - - + -
----------------------------------------------------------
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