Contacts of the helix formed by residues 358 - 376 (chain A) in PDB entry 1ECX
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 THR 358 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.4 0.2 - - - +
264A HIS* 4.7 4.0 - - - -
268A LEU* 3.6 7.7 - - - +
356A TYR 3.7 9.9 - - - +
357A ASN* 1.3 80.7 - - - +
359A GLU* 1.3 62.6 + - - +
360A GLU* 3.2 13.8 + - - +
361A GLU* 2.8 38.8 + - - +
362A VAL* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS* 5.2 1.2 + - - -
267A LYS* 3.5 25.6 + - - +
268A LEU* 3.4 18.5 - - + +
271A LYS* 2.6 46.0 + - + +
358A THR* 1.3 71.1 - - - +
360A GLU* 1.3 66.5 + - - +
361A GLU 3.0 1.8 - - - -
362A VAL* 3.0 3.1 + - - +
363A ASP* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 27.7 - - + +
358A THR* 3.2 11.6 + - - +
359A GLU* 1.3 78.5 - - - +
361A GLU* 1.3 60.3 + - - +
363A ASP* 3.6 8.8 + - + +
364A TYR* 3.3 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.1 23.8 - - + -
2A ARG 4.1 11.8 - - - +
3A VAL* 3.9 24.1 - - + +
4A TYR 5.1 0.9 + - - -
5A PHE* 4.3 6.2 - - + -
356A TYR 4.7 2.4 - - - +
357A ASN* 2.8 33.1 + - - +
358A THR* 2.8 39.8 + - + +
359A GLU 3.0 0.2 - - - -
360A GLU* 1.3 76.1 - - - +
362A VAL* 1.3 58.9 + - - +
364A TYR* 3.2 3.1 + - - +
365A PHE* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 4.5 10.8 - - + -
268A LEU* 3.4 38.8 - - + +
271A LYS* 4.2 20.9 - - + -
272A LEU* 3.6 30.5 - - + -
353A LEU* 5.6 0.7 - - + -
358A THR 3.1 14.9 + - - +
359A GLU* 3.0 8.6 + - - +
361A GLU* 1.3 77.7 - - - +
363A ASP* 1.3 61.2 - - - +
365A PHE* 3.3 7.0 + - - +
366A LEU* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS* 2.8 36.5 + - - -
359A GLU* 3.0 20.6 + - - +
360A GLU* 3.8 8.4 - - - +
362A VAL* 1.3 76.2 - - - +
364A TYR* 1.3 54.2 + - - +
366A LEU* 3.4 6.8 + - - +
367A LYS* 2.8 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.6 52.0 + - + -
3A VAL* 3.7 16.4 - - + -
314A TYR 3.0 18.8 + - - -
316A ILE* 3.6 23.3 - - + -
360A GLU 3.3 5.5 + - - +
361A GLU 3.2 8.4 + - - +
363A ASP* 1.3 79.1 - - - +
365A PHE* 1.3 53.6 + - - +
367A LYS* 3.2 7.5 + - + +
368A LYS* 2.7 68.0 + - + +
288B GLU* 3.1 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 5.1 1.6 - - + -
5A PHE* 3.6 25.8 - + + -
272A LEU* 3.7 20.2 - - + -
276A LEU* 3.9 24.2 - - + -
311A LEU* 4.3 9.6 - - + -
316A ILE* 3.5 43.3 - - + +
318A VAL* 4.0 15.5 - - + -
349A ILE* 4.9 2.0 - - + -
351A ILE* 3.8 21.1 - - + -
361A GLU 2.9 13.3 + - - +
362A VAL* 3.5 8.1 - - - +
364A TYR* 1.3 76.0 - - - +
366A LEU* 1.3 60.2 + - + +
368A LYS* 3.7 0.7 - - - +
369A ILE* 2.8 59.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS* 3.9 27.1 - - + +
272A LEU* 4.3 5.2 - - + +
275A GLY* 3.7 27.1 - - - +
276A LEU* 3.7 32.3 - - + +
279A LEU* 4.5 8.0 - - + +
362A VAL* 3.0 30.0 + - + +
363A ASP* 3.8 8.1 - - - +
365A PHE* 1.3 81.5 - - + +
367A LYS* 1.3 65.1 + - - +
369A ILE* 3.2 17.6 - - - +
370A GLU* 3.2 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ASP 2.8 23.5 + - - +
364A TYR* 3.7 7.2 - - + +
366A LEU* 1.3 77.0 - - - +
368A LYS* 1.3 76.8 + - + +
370A GLU* 3.5 9.2 + - - +
371A GLU* 3.4 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A TYR* 3.9 24.1 - - + -
316A ILE* 4.0 13.7 - - + -
364A TYR* 2.7 67.2 + - + +
365A PHE 4.0 1.8 - - - +
367A LYS* 1.3 86.9 - - - +
369A ILE* 1.3 64.0 + - - +
370A GLU 3.1 2.0 - - - -
371A GLU* 3.4 31.4 + - - +
372A ILE* 3.1 30.4 + - + +
288B GLU* 4.5 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU* 4.4 4.7 - - + -
279A LEU* 3.9 17.9 - - + -
299A PHE* 4.3 15.7 - - + -
307A LEU* 4.2 33.0 - - + -
311A LEU* 4.2 18.8 - - + +
349A ILE* 4.8 2.5 - - + -
365A PHE* 2.8 48.9 + - + +
366A LEU* 3.2 18.8 - - - +
368A LYS* 1.3 74.5 - - - +
370A GLU* 1.3 61.8 + - - +
372A ILE* 3.6 5.8 + - - +
373A LEU* 3.1 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 4.0 27.4 - - + +
366A LEU 3.2 9.1 + - - +
367A LYS* 3.6 12.7 - - - +
368A LYS 3.1 0.4 - - - -
369A ILE* 1.3 81.1 - - - +
371A GLU* 1.3 67.6 + - + +
373A LEU* 2.8 21.8 + - + +
374A SER* 3.1 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A TYR* 4.2 18.1 + - + +
367A LYS* 3.4 25.6 + - + +
368A LYS* 3.4 33.9 + - - +
370A GLU* 1.3 76.4 - - + +
372A ILE* 1.3 62.1 - - - +
374A SER* 2.6 29.6 + - - -
375A PHE* 3.2 23.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 4.2 12.8 - - + -
310A LEU* 3.6 26.0 - - + -
311A LEU* 3.7 38.4 - - + +
314A TYR* 3.6 43.1 - - + +
368A LYS 3.1 18.7 + - - +
369A ILE* 3.7 5.4 - - - +
371A GLU* 1.3 77.8 - - - +
373A LEU* 1.3 62.6 + - - +
375A PHE* 3.3 17.6 + - + +
376A LEU* 3.3 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 4.3 24.2 - - + +
299A PHE* 3.6 37.7 - - + -
302A ILE* 3.2 34.0 - - + +
307A LEU* 5.0 11.0 - - + -
369A ILE* 3.1 26.3 + - + +
370A GLU* 2.8 11.9 + - + +
372A ILE* 1.3 76.7 - - - +
374A SER* 1.3 62.2 + - - +
376A LEU* 3.3 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLU 3.1 7.9 + - - -
371A GLU* 2.6 23.8 + - - -
373A LEU* 1.3 79.1 - - - +
375A PHE* 1.3 76.8 + - - +
376A LEU 3.5 3.3 + - - -
267B LYS* 5.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 6.1 1.8 - - + -
314A TYR* 3.5 24.5 - + - -
371A GLU* 3.2 35.0 - - + -
372A ILE* 3.3 13.6 + - + +
374A SER* 1.3 86.8 - - - +
376A LEU* 1.3 62.8 + - + +
263B LYS* 5.1 4.3 - - + -
266B GLU* 3.3 41.1 - - + -
267B LYS* 4.3 36.7 - - + +
270B SER* 3.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASN 5.5 0.9 - - - +
302A ILE* 3.6 49.7 - - + +
306A THR* 4.3 20.6 - - + -
307A LEU* 5.0 4.7 - - + -
310A LEU* 4.5 13.2 - - + -
372A ILE* 3.3 29.4 - - + +
373A LEU* 3.3 19.4 + - + +
374A SER 3.2 4.4 - - - -
375A PHE* 1.3 86.9 - - + +
270B SER* 4.8 8.7 - - - +
----------------------------------------------------------
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