Contacts of the helix formed by residues 428 - 441 (chain A) in PDB entry 5HVO
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 ASN 428 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ASN* 2.8 29.6 + - + +
426A PRO 4.2 1.1 - - - -
427A TRP* 1.3 75.8 - - - +
429A THR* 1.3 63.2 + - - +
430A GLU* 3.9 6.2 + - - +
431A GLU* 3.2 38.5 + - + +
432A LEU* 3.0 19.1 + - - +
117B PHE* 5.1 2.2 - - - -
119B GLU* 4.7 6.2 - - - +
192B PRO* 3.8 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN 5.0 1.6 - - - +
299A HIS* 3.8 10.3 - - + +
300A ALA* 3.7 29.3 - - + +
303A VAL* 3.7 20.6 - - + -
426A PRO 4.7 3.6 + - - -
427A TRP 3.2 5.7 + - - -
428A ASN* 1.3 72.0 + - - +
430A GLU* 1.3 61.0 + - - +
432A LEU* 3.1 8.0 + - - +
433A ALA* 2.9 27.6 + - - +
115B ILE 3.7 3.8 + - - -
116B VAL* 3.5 18.8 - - + -
117B PHE* 3.4 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 3.3 22.0 - - + +
307A ASN* 3.3 26.5 + - - +
428A ASN* 3.4 3.9 + - - +
429A THR* 1.3 77.8 - - - +
431A GLU* 1.3 58.0 + - - +
433A ALA* 3.3 5.1 + - - +
434A ARG* 2.9 46.6 + - - +
117B PHE* 5.9 1.3 - - - +
119B GLU* 3.7 36.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLU* 4.9 0.7 - - - +
423A VAL 4.6 2.1 - - - +
424A VAL* 3.1 16.3 - - + +
425A ASN* 2.7 36.8 + - - +
428A ASN* 3.2 35.9 + - - +
430A GLU* 1.3 79.2 - - - +
432A LEU* 1.3 56.2 + - - +
434A ARG* 3.2 23.8 + - - +
435A ALA* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN 3.8 14.6 - - - +
297A LYS* 4.0 0.7 - - + -
300A ALA* 3.3 26.0 - - + -
380A VAL* 4.7 3.8 - - + -
382A SER* 3.8 20.6 - - - +
407A ILE* 4.0 13.7 - - + -
424A VAL* 3.8 29.1 - - + +
425A ASN 4.9 1.1 - - - +
426A PRO* 4.3 15.9 - - + +
428A ASN 3.0 12.9 + - - +
429A THR* 3.1 4.5 + - - +
431A GLU* 1.3 76.0 - - - +
433A ALA* 1.3 62.4 + - - +
435A ALA* 3.2 3.0 + - + +
436A TYR* 3.0 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 3.5 25.7 - - - +
303A VAL* 3.6 13.7 - - + -
304A PHE* 3.6 24.6 - - - +
307A ASN* 4.7 4.9 - - - +
429A THR 2.9 12.9 + - - +
430A GLU 3.5 8.1 - - - +
432A LEU* 1.3 76.2 - - - +
434A ARG* 1.3 60.6 + - - +
436A TYR* 3.2 11.5 + - - +
437A HIS* 3.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ASN* 5.7 0.2 + - - -
430A GLU* 2.9 41.1 + - - +
431A GLU* 3.2 30.8 + - - +
433A ALA* 1.3 74.7 - - - +
435A ALA* 1.3 59.0 + - - +
437A HIS* 3.3 10.4 + - + +
438A GLU* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ILE* 3.6 30.2 - - + +
422A LEU* 4.1 12.4 - - + +
424A VAL* 4.8 7.2 - - + -
431A GLU 2.9 13.7 + - - +
432A LEU* 3.2 12.1 + - + +
434A ARG* 1.3 72.6 - - - +
436A TYR* 1.3 59.7 + - - +
438A GLU* 3.7 11.2 - - - +
439A ALA* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A MET* 3.5 25.4 - - + -
297A LYS* 2.8 37.6 + - - +
300A ALA* 3.5 6.7 - - + -
301A LEU* 3.3 36.1 - - + -
304A PHE* 3.8 35.7 - + + -
317A LEU* 5.3 3.0 - - + +
380A VAL* 3.9 27.1 - - + +
407A ILE* 4.0 4.9 - - + -
432A LEU* 3.0 33.7 + - + +
433A ALA* 3.2 7.1 + - - +
435A ALA* 1.3 75.9 - - - +
437A HIS* 1.3 62.3 + - - +
439A ALA* 3.2 3.1 + - - +
440A VAL* 3.1 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 3.6 19.0 - + + -
308A HIS* 3.4 42.7 + + - +
310A GLU* 4.8 1.4 + - - -
311A TRP* 3.7 24.5 + - - -
433A ALA 3.2 7.1 + - - +
434A ARG* 3.7 13.4 - - + +
435A ALA 3.3 0.2 - - - -
436A TYR* 1.3 79.2 - - - +
438A GLU* 1.3 57.5 + - - +
440A VAL* 3.1 13.7 - - - +
441A SER* 2.7 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 3.6 28.1 - - + +
434A ARG* 2.9 23.0 + - + +
435A ALA* 3.7 9.5 - - - +
437A HIS* 1.3 79.7 + - - +
439A ALA* 1.3 62.0 + - - +
441A SER* 3.5 4.5 + - - -
442A MET* 3.1 40.5 + - + +
446A GLN* 5.3 5.1 + - - +
450A LYS* 5.2 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LYS* 5.2 0.3 - - - +
282A MET* 4.6 1.3 - - + -
377A ASP* 5.3 2.4 - - - +
378A ALA* 4.1 13.9 - - + -
405A VAL* 3.8 41.8 - - + +
407A ILE* 3.8 13.7 - - + -
422A LEU* 4.5 0.2 - - - +
435A ALA 2.9 17.7 + - - +
436A TYR* 3.6 4.5 - - - +
438A GLU* 1.3 79.9 - - - +
440A VAL* 1.3 61.3 + - - +
441A SER 3.4 0.5 + - - -
442A MET* 3.6 12.4 + - - +
447A ARG* 4.7 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LYS* 3.0 51.7 + - + -
282A MET* 4.4 22.4 - - + -
304A PHE* 4.5 4.9 - - + -
311A TRP* 3.5 41.6 - - + +
315A VAL* 4.5 7.6 - - + -
378A ALA* 5.6 1.6 - - + -
436A TYR 3.3 14.4 - - - +
437A HIS* 3.1 22.4 - - - +
439A ALA* 1.3 79.5 - - + +
441A SER* 1.3 58.0 + - - +
442A MET 3.5 0.8 + - - +
447A ARG* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TRP* 4.8 7.4 - - - -
437A HIS* 2.7 39.5 + - - -
438A GLU* 3.8 5.1 + - - -
440A VAL* 1.3 82.5 - - - +
442A MET* 1.3 62.5 + - - +
443A SER* 3.6 1.7 + - - -
----------------------------------------------------------
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