Contacts of the helix formed by residues 256 - 276 (chain A) in PDB entry 4EG8
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 256 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ALA* 6.1 2.7 - - + -
254A ALA 4.1 8.3 - - - +
255A PRO* 1.3 74.3 - - - +
257A ILE* 1.3 69.6 + - + +
258A GLY* 3.1 23.3 + - - -
259A HIS* 3.1 40.2 + + - +
260A VAL* 3.1 25.8 + - - +
555A ILE* 6.2 3.1 - - + -
563A PHE 5.5 2.0 - - - +
565A PRO* 4.5 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A HIS* 1.3 80.5 - - + +
258A GLY* 1.3 61.8 + - - +
260A VAL* 3.1 4.5 + - + +
261A TYR* 2.7 29.6 + - + +
548A TRP* 4.7 22.4 - - + -
555A ILE* 3.7 32.8 - - + -
563A PHE* 3.4 45.6 + - + +
565A PRO* 3.7 26.2 - - + +
581A LEU* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 4.8 1.1 - - - -
256A HIS* 3.1 17.1 + - - -
257A ILE* 1.3 81.3 - - - +
259A HIS* 1.3 58.3 + - - +
261A TYR* 3.8 6.9 - - - +
262A SER* 3.1 31.5 + - - -
545A HIS* 4.8 3.5 - - - -
548A TRP* 5.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 3.2 48.0 + + + +
250A TYR 4.9 4.2 + - - -
253A ALA* 5.1 1.3 - - + -
254A ALA 4.0 2.7 - - - -
255A PRO* 3.3 9.3 - - + +
256A HIS* 3.1 58.8 + + - +
257A ILE 3.2 0.4 - - - -
258A GLY* 1.3 73.4 - - - +
260A VAL* 1.3 67.2 + - - +
262A SER 3.4 0.5 + - - -
263A THR* 3.0 25.3 + - - -
315A PHE* 3.6 32.4 - + + -
319A PHE* 4.3 6.7 - - + -
815A MET* 5.7 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PRO* 5.7 0.2 - - + -
256A HIS* 3.1 12.5 + - - +
257A ILE* 3.1 13.1 + - + +
259A HIS* 1.3 79.9 - - + +
261A TYR* 1.3 57.6 + - - +
264A LEU* 2.8 19.7 + - + +
318A CYS* 3.8 27.8 - - - -
319A PHE* 4.4 7.2 - - + -
322A MET* 4.1 17.5 - - + -
324A TYR* 2.5 35.3 + - - +
565A PRO* 3.8 34.5 - - + -
581A LEU* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 2.7 25.6 + - + +
258A GLY* 3.8 5.4 - - - +
260A VAL* 1.3 72.1 - - - +
262A SER* 1.3 66.9 + - - +
264A LEU* 3.1 7.8 + - + +
265A ILE* 3.1 43.0 + - + +
545A HIS* 3.4 45.0 - + + +
546A GLY 4.2 4.0 + - - -
548A TRP* 3.6 35.7 - + + +
581A LEU* 3.6 42.3 + - + -
582A LEU* 4.6 6.9 - - + -
585A SER* 4.3 12.5 + - - -
586A GLY 5.0 2.1 + - - -
587A PHE* 3.9 15.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
246A SER* 4.6 0.2 - - - -
247A PRO* 3.9 20.2 - - - +
249A TYR* 3.1 20.7 - - - -
258A GLY 3.1 12.9 + - - -
261A TYR* 1.3 79.0 - - - +
263A THR* 1.3 61.2 - - - +
265A ILE* 3.2 5.1 + - - +
266A THR* 3.1 24.3 + - - -
514A VAL* 3.7 6.1 - - - +
516A GLY 4.5 1.2 + - - -
545A HIS* 2.7 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 4.3 6.5 - - - -
249A TYR* 2.6 25.2 + - - -
259A HIS 3.0 13.2 + - - -
260A VAL 4.1 0.2 - - - -
262A SER* 1.3 73.1 - - - +
264A LEU* 1.3 60.6 + - - +
266A THR* 3.3 1.6 + - - -
267A ASP* 2.8 27.7 + - - +
284A THR* 3.2 16.7 + - - +
319A PHE* 3.3 14.7 - - + -
324A TYR* 3.4 34.1 - - + -
326A ILE* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 2.8 21.7 + - + +
261A TYR* 3.1 8.3 + - + +
263A THR* 1.3 77.0 - - - +
265A ILE* 1.3 57.3 + - - +
267A ASP* 3.1 5.3 + - + +
268A VAL* 2.8 48.2 + - + +
322A MET* 6.2 0.9 - - + -
324A TYR* 3.6 24.6 + - + +
578A LYS* 3.9 42.4 - - + +
581A LEU* 4.5 17.5 - - + -
582A LEU* 3.9 32.1 - - + -
716A ILE 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 3.1 41.4 + - + +
262A SER 3.7 6.5 - - - +
264A LEU* 1.3 71.4 - - - +
266A THR* 1.3 66.0 + - - +
268A VAL* 3.3 1.6 + - - +
269A ILE* 3.1 29.5 + - + +
514A VAL* 3.6 22.0 - - + -
543A VAL* 5.1 2.2 - - + -
545A HIS* 3.7 17.5 - - + -
582A LEU* 4.1 16.6 - - + -
587A PHE* 3.3 43.5 - - + -
661A ILE* 3.9 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 3.9 21.7 - - + +
245A THR* 3.0 35.6 + - - +
246A SER* 3.2 20.3 - - - +
262A SER 3.1 8.4 + - - -
263A THR* 3.5 8.1 - - - -
265A ILE* 1.3 79.4 - - - +
267A ASP* 1.3 63.5 + - - +
269A ILE* 3.4 2.4 + - - +
270A GLY* 3.1 19.1 + - - -
282A ALA* 4.3 2.5 - - + +
283A LEU 3.9 9.4 - - - +
326A ILE* 4.3 12.6 - - + -
514A VAL* 3.4 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A THR 2.8 20.4 + - - +
264A LEU* 3.4 9.9 - - + +
266A THR* 1.3 73.0 - - - +
268A VAL* 1.3 58.1 + - - +
270A GLY* 3.3 2.0 + - - -
271A ARG* 2.7 57.4 + - - +
274A ARG* 5.0 0.3 + - - -
282A ALA* 5.5 1.5 - - - +
323A ASP 4.5 0.3 - - - +
324A TYR* 3.5 27.9 - - + -
325A SER* 2.6 40.4 + - - +
326A ILE* 3.8 11.7 + - + +
578A LYS* 4.9 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 2.8 29.8 + - + +
265A ILE 3.9 3.6 - - - +
266A THR 3.3 0.2 - - - -
267A ASP* 1.3 74.8 - - - +
269A ILE* 1.3 66.7 + - - +
271A ARG* 3.2 3.8 + - - +
272A TYR* 2.9 22.5 + - - +
582A LEU* 3.7 25.1 - - + -
656A TYR* 4.1 15.7 - - + -
661A ILE* 3.7 28.5 - - + -
715A PRO* 3.6 27.6 - - + +
716A ILE* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 3.7 18.6 - - + -
244A VAL* 4.1 7.2 - - + -
265A ILE* 3.1 24.1 + - + +
266A THR 3.8 3.1 - - - +
268A VAL* 1.3 76.3 - - - +
270A GLY* 1.3 65.0 + - - +
272A TYR* 3.2 5.0 + - - +
273A HIS* 3.1 45.8 + - + +
512A VAL* 4.0 11.7 - - + -
514A VAL* 3.9 21.8 - - + -
656A TYR* 4.9 9.4 - - + +
659A PRO* 3.8 32.8 - - + -
661A ILE* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 5.3 0.2 - - - -
244A VAL* 4.1 8.9 - - - +
266A THR 3.1 13.6 + - - -
267A ASP 3.7 3.1 - - - -
269A ILE* 1.3 78.8 - - - +
271A ARG* 1.3 55.2 + - - +
273A HIS* 3.2 3.6 + - - -
274A ARG* 2.9 41.5 + - - +
280A VAL* 3.7 24.6 - - - +
282A ALA* 5.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP* 2.7 39.7 + - - +
268A VAL 3.2 5.1 + - - +
270A GLY* 1.3 75.9 - - - +
272A TYR* 1.3 62.4 - - - +
274A ARG* 3.1 21.6 + - - +
275A VAL* 3.0 28.1 + - - +
323A ASP* 3.2 29.3 + - - -
324A TYR 3.6 4.6 + - - -
325A SER* 3.5 23.1 + - - -
578A LYS* 5.5 0.4 - - - +
715A PRO* 3.6 31.6 - - + -
718A PRO* 3.5 27.7 - - - +
803A GOL 3.3 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL 2.9 12.4 + - - +
269A ILE* 3.2 8.0 + - - +
271A ARG* 1.3 73.7 - - - +
273A HIS* 1.3 73.5 + + - +
275A VAL* 3.1 30.6 - - + +
276A LYS* 3.1 22.7 + - + +
653A ASP* 2.6 44.2 + - - +
656A TYR* 3.5 62.4 - + + -
657A LEU* 4.9 3.8 - - + -
712A LEU* 4.1 14.8 - - + +
715A PRO* 3.7 14.5 - - + +
741A PHE* 3.7 23.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 3.2 45.0 - + + -
269A ILE* 3.1 30.4 + - + +
270A GLY 3.7 2.5 - - - +
272A TYR* 1.3 84.5 - + - +
274A ARG* 1.3 62.7 + - - +
276A LYS* 3.4 9.7 + - + +
277A GLY 3.4 3.8 + - - -
278A GLU* 2.6 55.1 + - - +
280A VAL* 3.6 18.8 - - + -
656A TYR 4.9 2.4 + - - -
657A LEU* 3.2 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP* 5.0 1.0 + - - -
270A GLY* 2.9 8.6 + - - +
271A ARG* 3.1 33.8 + - - +
273A HIS* 1.3 78.6 - - - +
275A VAL* 1.3 57.8 + - + +
277A GLY* 2.9 15.2 + - - -
278A GLU 4.0 9.6 - - - +
280A VAL* 3.6 36.7 + - + +
282A ALA* 4.2 5.9 - - - +
325A SER* 3.0 42.2 + - - -
327A ASP* 3.0 31.8 + - - -
736A LYS* 3.1 27.3 + - - +
803A GOL 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG 3.0 21.5 + - - +
272A TYR* 3.1 36.2 + - + +
274A ARG* 1.3 72.4 - - + +
276A LYS* 1.3 55.9 + - - +
277A GLY 3.1 4.9 - - - -
711A LEU* 4.9 11.2 - - + +
712A LEU* 6.2 0.4 - - - -
714A SER* 3.8 21.8 - - - +
715A PRO* 4.5 6.5 - - + -
735A ARG 5.3 3.6 - - - +
736A LYS* 3.9 12.7 - - + +
737A GLY* 2.6 34.6 + - - +
741A PHE* 4.6 13.2 - - + -
803A GOL 4.3 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 3.1 44.6 + - + +
273A HIS* 3.6 13.2 - - - +
274A ARG 3.2 0.4 - - - -
275A VAL* 1.3 75.6 - - - +
277A GLY* 1.3 60.4 + - - +
278A GLU* 3.4 27.6 + - - +
653A ASP* 2.6 30.8 + - - +
657A LEU* 4.1 14.3 - - - +
737A GLY* 4.4 2.6 - - - -
738A ILE* 3.7 34.6 + - + +
741A PHE* 4.1 7.9 - - + -
807A GOL 3.4 22.3 + - - -
----------------------------------------------------------
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