Contacts of the helix formed by residues 261 - 278 (chain A) in PDB entry 2XTJ
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 VAL 261 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A THR* 1.3 72.0 - - - +
262A SER* 1.3 58.0 + - - +
264A THR* 3.2 6.4 + - - -
265A LEU* 2.9 34.8 + - + +
291A GLY* 5.9 1.3 - - - -
292A GLY 5.5 2.2 - - - +
294A SER* 4.0 28.9 - - - +
296A VAL* 4.0 17.9 - - + -
297A LEU* 4.4 12.8 - - + +
79P VAL* 5.3 3.1 - - + -
144P GLU* 4.2 3.8 - - - +
146P ASP* 3.6 9.6 - - - +
147P SER* 2.8 40.4 + - - +
148P SER 4.9 0.4 - - - +
149P VAL* 4.1 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASN* 5.3 1.2 + - - -
260A THR* 3.2 4.7 + - - +
261A VAL* 1.3 76.2 - - - +
263A GLY* 1.3 58.4 + - - +
265A LEU* 3.2 15.3 + - - +
266A ILE* 3.0 32.5 + - - +
77P THR* 4.8 0.5 - - - +
79P VAL* 4.5 4.7 - - - -
115P PHE* 4.6 1.2 - - - -
123P LEU* 3.5 37.7 - - - +
146P ASP* 2.6 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 3.7 9.9 - - - -
207A ASN* 3.6 34.3 - - - -
252A VAL* 3.8 11.5 - - - +
260A THR* 2.8 21.6 + - - -
262A SER* 1.3 72.7 + - - +
264A THR* 1.3 62.9 + - - +
266A ILE* 3.4 1.1 + - - -
267A GLY 3.1 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.2 6.1 - - + +
252A VAL* 4.2 17.7 - - + +
260A THR 2.7 19.0 + - - +
261A VAL* 3.4 10.3 - - - -
263A GLY* 1.3 77.1 - - - +
265A LEU* 1.3 50.2 + - - +
267A GLY* 3.2 2.3 + - - -
268A LEU* 2.8 35.7 + - + +
287A LEU* 4.3 23.1 - - + -
289A LEU* 4.5 13.3 - - + +
297A LEU* 3.8 23.6 - - + -
149P VAL* 3.6 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL* 2.9 25.2 + - + +
262A SER* 3.2 16.6 + - - +
264A THR* 1.3 75.2 - - - +
266A ILE* 1.3 58.4 + - - +
268A LEU* 3.2 9.7 + - - +
269A GLU* 2.9 28.4 + - - +
296A VAL* 3.7 42.6 - - + +
297A LEU* 4.2 7.4 - - + -
300A ALA* 3.7 27.6 - - + -
79P VAL* 4.2 12.1 - - + -
115P PHE* 3.7 26.9 - - + -
118P LEU* 4.1 3.2 - - + +
119P LEU* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 3.4 21.3 - - + -
207A ASN* 3.6 22.4 - - - +
262A SER* 3.0 21.6 + - - +
263A GLY 3.9 4.3 - - - +
264A THR 3.2 0.2 - - - -
265A LEU* 1.3 75.3 - - - +
267A GLY* 1.3 57.8 + - - +
269A GLU* 3.1 8.8 + - + +
270A PHE* 2.8 25.0 + - + +
112P LEU* 6.1 0.2 - - + -
113P HIS* 3.7 55.0 - - + +
115P PHE* 3.8 8.7 - - + -
123P LEU* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.2 10.3 - - - -
205A PHE* 3.2 25.2 - - - -
250A LEU* 3.5 15.7 - - - +
252A VAL* 4.7 0.2 - - - -
263A GLY 3.1 11.6 + - - -
264A THR 3.2 4.0 + - - -
266A ILE* 1.3 73.9 - - - +
268A LEU* 1.3 64.7 + - - +
270A PHE* 3.2 4.9 + - - +
271A ILE* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.1 8.0 - - + +
264A THR* 2.8 22.0 + - + +
265A LEU* 3.2 8.3 + - - +
267A GLY* 1.3 72.6 - - - +
269A GLU* 1.3 62.7 + - - +
271A ILE* 3.2 10.4 + - + +
272A ARG* 3.1 20.8 + - - +
285A VAL* 4.6 5.6 - - + -
287A LEU* 4.3 17.7 - - + -
297A LEU* 3.9 24.2 - - + -
300A ALA* 3.8 24.5 - - + -
301A CYS* 4.3 11.7 - - - +
304A LEU* 3.7 26.5 - - + +
311A LEU* 4.2 13.5 - - + -
118P LEU* 3.5 13.5 - - + +
----------------------------------------------------------
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 LEU 2.9 14.1 + - - +
266A ILE* 3.1 11.0 + - - +
268A LEU* 1.3 75.6 - - - +
270A PHE* 1.3 64.0 + - - +
272A ARG* 3.2 6.6 + - + +
273A LYS* 3.0 24.3 + - + +
113P HIS* 2.8 32.6 + - - -
114P VAL 4.0 0.7 - - - +
115P PHE* 3.2 22.5 - - - +
116P HIS* 3.3 30.3 + - - +
117P GLY* 4.1 9.3 + - - +
118P LEU* 3.7 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 5.2 3.1 - + - -
203A THR* 4.2 32.1 - - + -
204A ASP* 4.5 13.0 - - - -
205A PHE* 3.8 31.6 - + + -
250A LEU* 3.6 20.9 - - + -
266A ILE 2.8 13.5 + - - +
267A GLY 3.3 9.2 - - - +
269A GLU* 1.3 76.4 - - - +
271A ILE* 1.3 63.4 + - + +
273A LYS* 3.5 12.1 + - + +
274A SER* 3.2 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 3.8 29.6 - - + -
185A LEU* 3.4 32.8 - - + -
250A LEU* 4.3 7.0 - - + -
267A GLY 3.1 13.0 + - - +
268A LEU* 3.4 14.6 - - + +
269A GLU 3.2 0.4 - - - -
270A PHE* 1.3 74.8 - - - +
272A ARG* 1.3 60.1 + - - +
274A SER* 3.2 9.8 + - - -
275A GLN* 2.9 26.9 + - + +
283A LEU* 4.4 17.4 - - + +
285A VAL* 3.8 32.1 - - + -
304A LEU* 4.9 9.4 - - + -
309A VAL* 5.4 0.4 - - + -
----------------------------------------------------------
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 LEU 3.1 6.6 + - - +
269A GLU* 3.2 9.4 + - + +
271A ILE* 1.3 77.6 - - - +
273A LYS* 1.3 63.1 + - - +
275A GLN* 2.8 37.9 + - - +
276A LEU* 3.1 60.6 + - + +
303A ARG* 3.2 31.1 - - - +
304A LEU* 3.8 24.2 - - + +
307A ALA* 3.7 14.4 - - - +
117P GLY* 4.0 23.9 + - - +
118P LEU* 4.0 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 3.0 13.7 + - + +
270A PHE* 3.6 15.5 - - + +
271A ILE 3.3 0.2 - - - -
272A ARG* 1.3 77.7 - - - +
274A SER* 1.3 58.2 + - - +
276A LEU* 3.3 9.7 + - - +
277A VAL* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 3.1 30.5 + - - -
248A ARG* 6.2 1.1 - - - -
270A PHE* 3.2 18.9 + - - -
271A ILE* 3.2 12.9 + - - -
273A LYS* 1.3 76.5 - - - +
275A GLN* 1.3 65.6 + - - +
277A VAL* 3.9 12.1 - - - -
278A GLN* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ILE* 2.9 13.4 + - + +
272A ARG* 2.8 43.5 + - - +
274A SER* 1.3 81.1 + - - +
276A LEU* 1.3 60.8 + - + +
278A GLN 5.2 0.7 - - - -
279A PRO* 3.5 26.8 - - + +
281A GLY 5.4 4.6 + - - +
283A LEU* 3.6 25.5 - - + +
304A LEU* 4.8 0.2 - - - +
307A ALA* 3.3 29.1 + - - +
308A GLY 5.0 0.6 - - - -
309A VAL* 3.6 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.1 53.3 + - + +
273A LYS* 3.7 9.6 - - - +
275A GLN* 1.3 78.8 - - + +
277A VAL* 1.3 63.6 + - - +
279A PRO* 3.7 8.9 - - - +
116P HIS* 6.3 3.8 - - + -
117P GLY* 6.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LYS* 3.0 27.1 + - + +
274A SER* 4.3 10.1 - - - -
275A GLN 3.4 0.2 - - - -
276A LEU* 1.3 79.0 - - - +
278A GLN* 1.3 71.2 + - + +
279A PRO* 3.2 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A SER* 3.1 18.3 + - - +
275A GLN* 5.1 0.5 - - - -
277A VAL* 1.3 91.6 - - + +
279A PRO* 1.4 59.8 - - - +
280A VAL* 3.2 15.1 - - - +
----------------------------------------------------------
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