Contacts of the helix formed by residues 371 - 384 (chain C) in PDB entry 2I2X
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 ALA 371 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LEU* 3.8 12.3 - - + +
305C GLN* 3.7 7.2 - - - -
357C MET* 3.5 22.4 - - + -
361C ARG* 3.7 13.7 - - + +
367C ALA 3.1 5.3 + - - -
368C TYR 3.4 14.6 - - - +
369C MET 3.3 0.2 - - - -
370C LEU* 1.3 75.2 - - - +
372C TYR* 1.3 60.1 + - - +
373C ASP* 3.3 11.4 - - - +
374C ASN* 2.9 23.0 + - - +
375C ALA 2.9 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA* 3.3 39.0 - - + +
15C ASP* 4.3 5.1 + - + -
17C MET* 4.8 6.4 - - + +
274C ILE* 4.0 6.7 - - + -
305C GLN* 3.0 30.7 + - - +
306C CYS* 3.9 19.1 - - - -
353C ARG* 3.1 35.1 + - + -
354C ASP* 2.5 31.4 + - - -
357C MET* 4.1 15.5 - - + -
370C LEU 3.3 4.4 + - - -
371C ALA* 1.3 69.7 - - - +
373C ASP* 1.3 62.4 + - - +
375C ALA* 3.8 5.3 - - - +
376C TYR* 3.1 24.3 + - - +
1D MET* 3.4 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA* 3.6 17.1 - - + +
361C ARG* 2.6 41.5 + - - -
371C ALA* 3.4 7.6 - - - +
372C TYR* 1.3 78.8 + - - +
374C ASN* 1.3 67.0 + - - +
376C TYR* 3.5 4.2 + - - +
377C ARG* 3.1 24.1 + - - +
1D MET* 3.3 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ARG* 3.4 21.6 + - - +
368C TYR* 3.0 41.2 + - - +
369C MET 3.5 15.9 - - - +
371C ALA 2.9 3.5 + - - +
373C ASP* 1.3 87.0 + - - +
375C ALA* 1.3 60.5 + - - +
377C ARG* 3.2 16.0 + - - +
378C VAL* 2.9 30.8 + - - +
403C ILE* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ILE* 3.6 33.9 - - + +
275C ILE* 3.6 29.9 - - + +
278C ALA* 5.0 0.4 - - + -
369C MET 3.3 7.9 + - - +
370C LEU 3.8 5.6 - - - +
371C ALA 2.9 12.8 + - - +
372C TYR 3.8 2.7 - - - +
373C ASP 3.3 0.2 - - - -
374C ASN* 1.3 73.9 - - - +
376C TYR* 1.3 54.6 + - - +
378C VAL* 3.2 5.9 + - - +
379C GLY* 2.8 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C MET* 3.5 25.8 - - + +
11C TYR* 2.3 39.2 + - + -
12C ALA* 3.0 14.7 + - - -
13C ASN* 3.6 22.4 - - + -
14C ALA* 3.6 22.7 - - + -
17C MET* 4.3 4.0 - - - -
278C ALA* 4.0 21.4 - - + +
372C TYR 3.1 18.2 + - - +
373C ASP 3.5 6.1 - - - +
375C ALA* 1.3 71.4 - - - +
377C ARG* 1.3 61.0 + - - +
379C GLY* 3.1 2.4 + - - -
380C GLN* 2.8 57.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C ASP 3.1 10.4 + - - +
374C ASN* 3.3 19.6 + - - +
375C ALA 3.2 0.2 - - - -
376C TYR* 1.3 77.4 - - - +
378C VAL* 1.3 67.4 + - - +
380C GLN* 3.1 29.4 + - - +
381C SER* 3.1 12.6 + - - -
399C GLU* 2.6 29.9 + - + +
402C ASN* 3.9 18.2 - - - +
403C ILE* 3.7 22.5 - - + +
406C GLU* 2.8 44.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ALA* 4.6 5.6 - - + +
275C ILE* 4.1 16.8 - - + -
369C MET* 3.8 24.2 - - + -
374C ASN 2.9 18.5 + - - +
375C ALA 3.2 6.7 + - - +
377C ARG* 1.3 74.1 - - - +
379C GLY* 1.3 64.5 + - - +
381C SER* 2.8 25.3 + - - -
382C ILE* 3.2 23.2 + - + +
396C ALA* 4.0 20.6 - - + +
399C GLU* 4.4 3.8 - - + -
400C CYS* 4.7 9.6 - - + +
403C ILE* 3.6 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C MET* 3.6 10.5 - - - -
275C ILE* 3.9 6.2 - - - +
279C ILE* 3.9 24.0 - - - -
375C ALA 2.8 14.6 + - - -
376C TYR 3.1 4.9 + - - -
378C VAL* 1.3 76.7 - - - +
380C GLN* 1.3 60.9 + - - +
382C ILE* 3.0 14.4 + - - +
383C VAL* 3.1 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C MET* 3.7 16.0 - - + +
376C TYR* 2.8 47.2 + - + +
377C ARG* 3.1 24.8 + - + +
379C GLY* 1.3 72.7 - - - +
381C SER* 1.3 60.7 + - - +
383C VAL* 3.5 6.3 - - - +
384C LYS* 3.4 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ARG 3.1 3.9 + - - -
378C VAL 2.8 15.2 + - - -
380C GLN* 1.3 75.3 - - - +
382C ILE* 1.3 62.1 + - - +
384C LYS* 3.6 18.0 - - - +
395C ASN* 3.0 37.8 + - - +
396C ALA* 3.4 23.6 - - - -
399C GLU* 3.6 34.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR 5.8 0.4 - - - +
251C ALA* 4.2 0.9 - - + -
252C PRO* 3.8 29.8 - - + -
255C LEU* 4.2 9.0 - - + -
275C ILE* 3.9 17.9 - - + -
279C ILE* 4.1 17.9 - - + -
378C VAL* 3.6 28.0 - - + +
379C GLY 3.0 5.3 + - - +
381C SER* 1.3 78.4 - - - +
383C VAL* 1.3 67.5 + - + +
385C ASP 3.1 11.8 + - - -
386C GLY* 3.3 3.4 + - - -
392C ARG* 3.2 50.0 - - + +
396C ALA* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 4.0 15.9 - - + +
7C THR* 3.4 30.0 - - - +
8C SER* 3.7 30.1 - - - +
9C MET* 3.9 15.3 - - + -
279C ILE* 3.7 27.8 - - + -
379C GLY 3.1 11.9 + - - +
380C GLN* 3.5 13.9 - - - +
382C ILE* 1.3 78.1 - - + +
384C LYS* 1.3 67.4 + - + +
385C ASP 3.1 3.3 + - - -
386C GLY* 3.2 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C THR 5.3 0.9 - - - -
380C GLN 3.4 12.5 + - - +
381C SER* 3.6 23.3 - - - +
383C VAL* 1.3 82.2 - - + +
385C ASP* 1.3 71.1 + - - +
386C GLY 3.7 0.2 - - - -
395C ASN* 3.7 22.8 - - - +
399C GLU* 4.9 7.3 + - - -
----------------------------------------------------------
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