Contacts of the helix formed by residues 360 - 374 (chain B) in PDB entry 2DOU
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 PRO 360 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 4.1 11.2 - - - +
292B ARG* 3.8 11.6 - - - +
359B ARG* 1.3 111.9 - - + +
361B LEU* 1.3 68.1 + - - +
362B GLU* 3.1 20.1 + - + +
363B GLU* 3.1 22.3 + - + +
364B LEU 3.1 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU* 4.3 32.9 + - + +
292B ARG* 4.4 13.3 - - - +
295B GLY* 4.1 18.4 - - - -
296B MET 4.2 4.9 - - - +
359B ARG 3.6 0.8 + - - -
360B PRO* 1.3 71.3 - - - +
362B GLU* 1.3 74.7 + - - +
364B LEU* 3.0 13.8 + - + +
365B LEU* 2.7 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PRO* 3.1 12.2 + - + +
361B LEU* 1.3 84.4 + - - +
363B GLU* 1.3 60.9 + - + +
365B LEU* 2.7 34.6 + - - +
366B GLU* 2.9 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.4 24.7 - - + +
359B ARG* 3.4 47.7 + - + +
360B PRO* 3.1 24.2 + - + +
362B GLU* 1.3 81.6 - - + +
364B LEU* 1.3 51.7 + - - +
366B GLU* 3.1 9.8 + - - +
367B ALA* 2.6 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.6 39.5 - - + -
292B ARG* 3.5 35.9 - - + +
296B MET* 3.7 27.1 - - + +
356B ALA 4.6 0.2 - - - +
357B LEU* 4.1 21.5 - - + -
359B ARG* 3.0 29.4 - - + +
360B PRO 3.1 6.6 + - - +
361B LEU* 3.0 11.2 + - + +
363B GLU* 1.3 73.1 - - - +
365B LEU* 1.3 61.8 + - - +
367B ALA* 3.6 5.0 - - - +
368B ALA* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLY* 4.0 23.3 - - - +
296B MET* 4.5 1.6 - - - +
299B ALA* 4.2 15.6 - - + +
361B LEU* 2.7 40.9 + - + +
362B GLU* 2.7 18.0 + - - +
364B LEU* 1.3 72.9 - - - +
366B GLU* 1.3 55.7 + - - +
368B ALA* 3.2 5.7 + - - +
369B LYS* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.8 7.4 - - + -
362B GLU 2.9 10.3 + - - +
363B GLU* 3.4 10.8 - - - +
365B LEU* 1.3 77.1 - - - +
367B ALA* 1.3 57.7 + - - +
369B LYS* 2.8 34.1 + - - +
370B ARG* 2.7 55.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.8 11.4 - - + +
30B LEU* 3.7 29.4 - - + -
296B MET* 5.3 0.9 - - + -
337B VAL* 3.7 25.4 - - + +
363B GLU 2.6 20.5 + - - +
364B LEU* 3.7 4.3 - - - +
366B GLU* 1.3 73.7 - - - +
368B ALA* 1.3 58.7 + - - +
370B ARG* 3.7 1.2 + - - +
371B ILE* 3.0 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B MET* 3.9 9.6 - - + -
299B ALA* 3.9 25.6 - - + +
300B LEU* 3.6 31.4 - - + +
364B LEU 2.8 17.5 + - - +
365B LEU* 3.6 5.6 - - - +
366B GLU 3.1 0.2 - - - -
367B ALA* 1.3 76.0 - - - +
369B LYS* 1.3 65.9 + - - +
371B ILE* 3.8 3.5 - - - +
372B ARG* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU 2.9 12.6 + - - +
366B GLU* 2.8 26.4 + - - +
368B ALA* 1.3 76.6 - - - +
370B ARG* 1.3 59.8 + - - +
372B ARG* 3.1 17.2 + - - +
373B GLU* 3.1 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY* 3.2 19.3 + - - -
28B ILE* 3.7 15.7 - - - +
332B LEU* 4.5 3.8 - - + -
335B ARG* 3.5 25.1 - - + +
336B GLY* 2.8 30.7 + - - -
337B VAL* 3.7 17.5 - - + -
366B GLU* 2.7 47.8 + - - +
367B ALA* 3.9 4.9 - - - +
369B LYS* 1.3 74.1 - - + +
371B ILE* 1.3 55.2 + - - +
373B GLU* 2.9 11.3 + - - +
374B ALA* 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 5.9 0.2 - - + -
296B MET* 4.3 10.8 - - + -
300B LEU* 4.4 10.5 - - + -
303B VAL* 3.9 19.0 - - + +
304B LEU* 4.7 11.4 - - + -
328B PHE* 4.2 17.2 - - + -
332B LEU* 3.9 24.9 - - + +
337B VAL* 4.4 3.8 - - + -
339B LEU* 4.1 27.6 - - + -
355B ILE* 4.1 18.8 - - + -
367B ALA* 3.0 24.6 + - + +
368B ALA* 3.8 6.1 - - - +
369B LYS 3.4 0.2 - - - -
370B ARG* 1.3 76.8 - - - +
372B ARG* 1.3 63.4 + - - +
374B ALA* 3.3 13.2 + - - +
375B LEU* 3.6 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ALA 5.3 2.5 - - - +
303B VAL* 3.9 26.0 - - + +
368B ALA 3.1 12.8 + - - +
369B LYS* 3.1 13.0 - - - +
370B ARG 3.1 0.2 - - - -
371B ILE* 1.3 75.1 - - - +
373B GLU* 1.3 67.0 + - - +
375B LEU* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ARG* 4.4 20.7 + - - +
369B LYS 3.1 8.1 + - - +
370B ARG* 2.9 13.6 + - - +
372B ARG* 1.3 73.8 - - - +
374B ALA* 1.3 53.8 + - - +
375B LEU* 2.7 20.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 3.0 33.2 - - + -
331B ARG* 4.7 11.2 + - - +
332B LEU* 3.8 13.7 - - + -
335B ARG* 3.6 30.9 - - - +
370B ARG 2.8 17.7 + - - +
371B ILE 3.6 8.1 - - - +
372B ARG 3.2 0.6 - - - -
373B GLU* 1.3 70.5 - - - +
375B LEU* 1.3 57.3 + - - +
----------------------------------------------------------
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