Contacts of the helix formed by residues 371 - 385 (chain A) in PDB entry 1OY6
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE 2.9 16.6 + - - +
368A PRO 3.5 7.1 + - - +
370A ILE* 1.3 78.6 - - - +
372A VAL* 1.3 65.3 + - + +
374A VAL* 3.2 17.7 + - - +
375A VAL* 3.4 15.4 + - + +
409A ALA* 3.8 16.8 - - + -
484A VAL* 4.0 6.8 - - + +
488A LEU* 4.2 9.9 - - + -
489A THR* 3.8 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ILE* 5.0 14.4 - - + -
351A VAL* 5.9 2.2 - - + -
368A PRO 3.7 8.7 + - - +
369A THR* 4.9 1.6 - - - +
371A ALA* 1.3 76.4 - - + +
373A PRO* 1.3 76.6 - - + +
374A VAL 3.2 1.8 - - - -
375A VAL* 3.6 8.6 - - + +
376A LEU* 3.1 31.3 + - + +
402A ILE* 5.0 6.5 - - + +
405A LEU* 3.4 23.6 - - + +
406A VAL* 3.2 53.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 5.3 6.1 - - + -
348A ILE* 5.4 11.2 - - + -
369A THR 3.2 28.3 - - - +
370A ILE* 3.5 19.7 - - + +
371A ALA 3.5 0.4 - - - -
372A VAL* 1.3 98.6 - - + +
374A VAL* 1.3 61.3 + - + +
376A LEU* 3.6 9.5 + - + +
377A LEU* 3.2 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 3.8 41.1 - - + +
19A ILE* 3.1 25.2 - - + +
20A MET* 4.0 21.8 - - + -
370A ILE* 4.0 17.7 - - + +
371A ALA 3.2 8.6 + - - +
372A VAL 3.2 0.6 - - - -
373A PRO* 1.3 74.2 - - + +
375A VAL* 1.3 60.5 + - - +
377A LEU* 3.5 5.4 + - - -
378A GLY* 3.1 22.3 + - - -
484A VAL* 4.2 12.3 - - + -
488A LEU* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA* 3.4 16.6 - - + +
372A VAL* 3.2 15.3 + - + +
374A VAL* 1.3 74.6 - - - +
376A LEU* 1.3 65.2 + - - +
378A GLY* 3.4 1.1 + - - -
379A THR* 3.3 21.1 + - - -
405A LEU* 3.3 19.7 - - + +
477A ALA* 3.2 28.0 - - - +
480A LEU* 3.6 13.0 - - + +
481A SER* 3.3 22.4 - - - +
484A VAL* 3.9 23.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
344A LEU* 3.2 36.1 - - + -
348A ILE* 5.4 1.8 - - + -
372A VAL* 3.1 24.5 + - + +
373A PRO* 3.9 9.0 - - + +
375A VAL* 1.3 74.8 - - - +
377A LEU* 1.3 68.3 + - + +
379A THR* 3.0 10.3 + - - +
380A PHE* 3.2 7.1 + - + -
398A MET* 3.0 71.4 - - + +
401A ALA* 5.6 0.2 - - + -
402A ILE* 4.2 4.7 - - + -
405A LEU* 3.6 18.6 - - + -
477A ALA* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.3 14.1 - - - +
20A MET* 3.6 51.4 - - + +
23A GLY* 2.9 27.0 - - - -
24A GLY* 4.4 12.3 - - - +
373A PRO* 3.2 16.5 + - + +
374A VAL* 3.8 5.6 - - - +
375A VAL 3.4 0.2 - - - -
376A LEU* 1.3 79.9 - - + +
378A GLY* 1.3 61.9 + - - +
380A PHE* 3.3 20.1 + - + -
381A ALA* 3.1 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.2 19.6 - - - +
374A VAL 3.1 11.1 + - - -
375A VAL 3.7 4.9 - - - -
376A LEU 3.1 0.4 - - - -
377A LEU* 1.3 77.0 - - - +
379A THR* 1.3 54.6 + - - +
381A ALA* 3.1 7.4 + - - +
382A VAL* 2.9 32.6 + - - +
480A LEU* 3.3 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL 3.3 5.4 + - - -
376A LEU* 3.0 11.1 + - - +
378A GLY* 1.3 73.0 - - - +
380A PHE* 1.3 60.0 + - - +
382A VAL* 4.2 3.4 - - - -
383A LEU* 3.0 42.7 + - + +
398A MET* 3.5 24.9 - - - -
473A THR* 3.4 20.4 - - + +
476A SER* 3.4 6.9 + - - +
477A ALA* 3.4 20.3 - - + +
480A LEU* 3.1 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.6 14.8 - - - +
24A GLY* 6.0 0.2 - - - -
26A ALA* 3.4 7.5 - - + +
27A ILE* 3.4 34.5 - - + -
30A LEU* 5.1 8.2 - - + +
376A LEU* 3.2 14.5 + - + -
377A LEU* 3.3 26.7 + - + +
379A THR* 1.3 76.6 - - + +
381A ALA* 1.3 59.4 + - - +
383A LEU* 5.0 5.8 - - + -
384A ALA* 3.2 27.7 + - - +
390A ILE* 4.8 7.6 - - + -
394A THR* 5.1 1.8 - - - -
395A MET* 4.0 24.5 - - + -
398A MET* 3.4 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 5.5 1.3 - - + +
22A ALA* 3.3 44.0 - - + +
23A GLY* 3.8 0.6 - - - +
26A ALA* 4.3 2.7 - - - -
377A LEU 3.1 9.1 + - - +
378A GLY* 3.1 12.5 + - - +
380A PHE* 1.3 75.5 - - - +
382A VAL* 1.3 60.2 + - + +
384A ALA* 4.2 2.1 - - - +
385A ALA* 3.4 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLY 2.9 21.1 + - - +
379A THR* 3.9 6.3 - - - +
380A PHE 3.3 0.2 - - - -
381A ALA* 1.3 78.9 - - + +
383A LEU* 1.3 62.7 + - + +
384A ALA 3.3 0.4 - - - -
385A ALA* 3.2 7.0 + - - +
386A PHE* 3.1 50.3 + - + -
476A SER* 3.6 24.5 - - - -
480A LEU* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 6.2 1.8 - - + -
379A THR* 3.0 28.1 + - + +
380A PHE* 4.7 6.1 - - + +
382A VAL* 1.3 77.7 - - + +
384A ALA* 1.3 60.0 + - - +
385A ALA 3.3 0.2 - - - -
386A PHE* 3.4 4.8 + - + +
387A GLY 3.1 6.6 + - - -
388A PHE* 2.8 58.6 + - + +
389A SER 5.1 2.7 - - - +
394A THR* 3.8 19.7 - - + +
398A MET* 5.1 1.6 - - - -
472A ILE* 4.2 15.9 - - + -
473A THR* 3.2 48.7 - - + +
476A SER* 4.3 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.7 15.7 - - + -
29A LYS* 5.1 7.9 - - - +
30A LEU* 3.4 29.1 - - + +
380A PHE 3.2 21.1 + - - +
381A ALA 4.3 3.6 - - - +
382A VAL 3.3 0.2 - - - -
383A LEU* 1.3 79.9 - - - +
385A ALA* 1.3 59.3 + - - +
386A PHE 3.4 0.7 + - - -
387A GLY* 3.5 10.0 + - - -
388A PHE 3.9 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA 3.4 18.8 + - - +
382A VAL* 3.2 8.6 + - - +
384A ALA* 1.3 78.9 - - - +
386A PHE* 1.3 67.0 + - + +
387A GLY 3.6 0.2 - - - -
----------------------------------------------------------
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