Contacts of the helix formed by residues 369 - 383 (chain D) in PDB entry 2O1S
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 369 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C GLU* 3.1 43.7 - - + +
156D THR 4.7 3.1 - - - +
344D PRO* 4.1 3.7 - - - +
366D VAL* 3.6 19.9 - - + +
367D ALA 2.9 8.3 + - - -
368D ILE* 1.3 74.3 - - - +
370D GLU* 1.3 65.7 + - - +
371D GLN 3.2 2.6 + - - -
372D HIS* 3.4 5.6 + - + -
373D ALA* 2.9 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C GLU* 4.4 0.6 + - - -
344D PRO* 3.9 20.6 - - + +
368D ILE* 4.3 19.2 - - - +
369D ALA* 1.3 75.9 + - - +
371D GLN* 1.3 65.5 + - - +
373D ALA* 3.2 17.0 + - - +
374D VAL* 3.2 14.6 - - - +
389D VAL* 6.0 0.2 - - - +
391D ILE* 3.6 17.9 - - + +
395D PHE* 3.3 45.7 - - + +
398D ARG* 3.5 27.8 + - + +
399D ALA* 3.6 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C GLY* 4.4 3.8 - - - +
159C MSE 3.6 28.0 + - + +
162C GLU* 3.5 20.5 + - - +
371C GLN* 3.3 35.5 - - - +
398C ARG* 3.6 16.3 - - - +
158D GLY* 4.6 3.4 - - - -
162D GLU* 5.3 1.3 + - - +
369D ALA 3.2 0.4 - - - -
370D GLU* 1.3 76.0 - - - +
372D HIS* 1.3 60.0 + - - +
374D VAL* 2.9 22.0 - - - +
375D THR* 3.2 7.6 + - - -
398D ARG* 3.7 22.6 - - + +
399D ALA* 4.0 1.6 - - - -
402D GLN* 3.3 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C SER* 2.8 45.4 + - - +
131C ILE* 3.6 17.6 - - + +
159C MSE 4.7 1.5 - - - +
162C GLU* 2.9 34.5 + - + +
163C ALA* 3.6 12.1 - - - -
166C HIS* 2.9 45.2 - + + +
366D VAL* 3.7 14.9 + - + +
369D ALA* 3.4 4.6 + - + +
371D GLN* 1.3 70.6 - - - +
373D ALA* 1.3 59.2 + - - +
375D THR 4.5 0.2 - - - +
376D PHE* 2.6 55.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D ILE* 3.9 20.0 - - + +
344D PRO* 4.0 17.0 - - + -
366D VAL* 3.7 20.6 - - + +
369D ALA 2.9 14.7 + - - +
370D GLU 3.2 12.1 - - - +
372D HIS* 1.3 79.0 + - - +
374D VAL* 1.3 58.3 + - - +
376D PHE* 3.4 5.1 - - - +
377D ALA* 3.0 23.4 + - - +
389D VAL* 4.5 9.6 - - + +
391D ILE* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D GLU 3.2 11.0 - - - +
371D GLN 2.9 19.7 - - - +
373D ALA* 1.3 74.6 - - + +
375D THR* 1.3 57.2 - - - +
377D ALA* 3.1 8.9 + - - +
378D ALA* 3.0 23.6 + - - +
389D VAL* 4.4 8.1 - - + -
396D LEU* 5.9 0.9 - - + -
399D ALA* 3.6 15.0 - - + +
402D GLN* 3.1 32.3 - - + +
403D VAL* 3.9 6.3 - - + +
407D VAL* 3.7 25.2 - - + +
416D PHE* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 5.9 0.9 - - + -
125C THR* 3.8 15.0 - - - +
128C SER* 3.5 26.2 - - - -
129C ALA* 3.6 13.1 - - + +
159C MSE 3.4 9.4 - - + +
371D GLN 3.2 7.0 + - - -
374D VAL* 1.3 73.9 - - - +
376D PHE* 1.3 63.9 + - - +
378D ALA* 3.4 7.5 + - + +
379D GLY 3.2 15.2 + - - -
402D GLN* 2.8 17.2 - - - +
406D ASP* 2.7 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C SER* 3.7 9.8 + - - -
131C ILE* 3.6 21.8 - - + -
132C GLY* 3.3 36.7 - - - -
135C VAL* 4.0 8.1 - - + -
166C HIS* 3.9 15.5 - + - -
342D ILE* 3.6 20.9 - - + -
364D PHE* 3.8 37.0 - + + -
366D VAL* 4.4 7.2 - - + -
372D HIS* 2.6 38.5 + + + +
373D ALA* 3.4 3.8 - - - +
375D THR* 1.3 70.6 - - - +
377D ALA* 1.3 65.0 + - - +
379D GLY* 3.2 4.0 + - - -
380D LEU* 3.0 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D ILE* 3.5 26.2 - - + -
373D ALA 3.0 6.8 + - - +
374D VAL 3.1 10.1 + - - +
376D PHE* 1.3 78.2 - - - +
378D ALA* 1.3 63.0 + - - +
380D LEU* 3.0 5.8 + - - +
381D ALA* 2.9 19.6 + - - +
387D PRO* 3.2 19.1 - - + +
389D VAL* 3.6 23.1 - - + -
414D VAL* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 5.6 0.9 - - + -
129C ALA* 5.5 2.2 - - + -
374D VAL 3.0 11.6 + - - +
375D THR* 3.4 15.3 - - + +
376D PHE 3.2 0.2 - - - -
377D ALA* 1.3 75.9 - - - +
379D GLY* 1.3 62.2 + - - +
381D ALA* 3.0 5.2 + - - +
382D ILE* 2.9 27.9 + - + +
406D ASP* 3.6 17.0 - - + +
407D VAL* 4.3 4.7 - - + -
410D GLN* 5.2 2.2 - - - +
412D LEU* 3.6 23.8 - - + +
414D VAL* 4.3 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ALA* 3.6 29.8 - - - +
132C GLY 3.7 7.0 - - - -
133C ILE* 3.4 16.7 + - - +
375D THR 3.2 5.1 + - - -
376D PHE 3.2 6.9 + - - -
378D ALA* 1.3 78.6 - - - +
380D LEU* 1.3 57.1 + - - +
382D ILE* 3.3 5.0 + - - -
383D GLY* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLY* 3.1 30.7 - - - +
135C VAL* 4.0 20.6 - - + -
136C ALA* 4.5 4.9 - - + +
340D MSE 3.9 33.0 - - + -
342D ILE* 3.8 18.6 - - + -
364D PHE* 4.7 3.8 - - + -
376D PHE* 3.0 32.1 + - + +
377D ALA 3.0 12.2 + - - +
379D GLY* 1.3 77.9 - - - +
381D ALA* 1.3 58.9 + - - +
383D GLY* 3.3 7.6 + - - +
384D GLY 3.5 0.2 + - - -
385D TYR* 3.0 28.3 + - + +
387D PRO* 3.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D ALA 2.9 11.4 + - - +
378D ALA* 3.0 9.6 + - - +
380D LEU* 1.3 75.1 - - - +
382D ILE* 1.3 58.9 + - - +
384D GLY* 2.8 21.3 + - - -
385D TYR 3.5 13.2 + - - +
387D PRO* 3.9 12.7 - - + +
412D LEU* 4.2 25.8 - - + -
413D PRO* 4.7 11.9 - - + -
414D VAL* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C GLN* 4.3 8.2 - - - +
110C ARG* 4.0 29.7 + - - +
117C VAL* 3.6 28.3 - - + +
118C LEU* 3.8 25.1 - - + -
133C ILE* 4.0 25.4 - - + -
378D ALA 2.9 16.2 + - - +
379D GLY* 3.5 9.9 - - - +
381D ALA* 1.3 75.0 - - - +
383D GLY* 1.3 58.9 + - - +
384D GLY* 3.0 5.2 + - - -
412D LEU* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 383 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE* 5.1 6.5 - - - -
136C ALA* 3.7 23.0 - - - +
140C GLU* 6.2 0.7 - - - +
379D GLY 2.9 12.5 + - - -
380D LEU 3.3 4.7 + - - -
381D ALA 3.1 0.6 - - - -
382D ILE* 1.3 75.9 - - - +
384D GLY* 1.3 58.7 + - - +
385D TYR* 3.5 14.8 - - - -
----------------------------------------------------------
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