Contacts of the helix formed by residues 430 - 440 (chain B) in PDB entry 2VDE
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 430 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 3.7 16.9 - - - +
423B LYS* 4.7 1.0 - - - +
428B THR 2.8 24.0 + - - +
429B LEU* 1.3 79.7 - - - +
431B GLU* 1.3 64.2 + - + +
432B GLN* 3.0 35.4 + - - +
433B ASP* 2.8 39.4 + - - +
434B LEU* 4.0 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B MET* 3.8 21.4 - - + +
29B TYR* 4.2 25.2 - - + +
30B GLN* 3.7 15.8 - - - +
33B ARG* 3.2 29.2 + - - -
128B ILE* 4.4 4.3 - - - +
430B ASN* 1.3 76.6 - - - +
432B GLN* 1.3 67.0 + - - +
433B ASP 3.4 0.2 - - - -
434B LEU* 3.7 7.6 + - + +
435B LEU 3.6 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ASN* 3.0 23.8 + - - +
431B GLU* 1.3 84.5 + - - +
433B ASP* 1.3 59.7 + - - +
435B LEU* 3.0 41.5 + - - +
436B ALA* 3.4 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU* 4.1 16.8 - - + +
423B LYS* 3.0 40.0 + - + +
429B LEU* 3.8 4.6 - - + -
430B ASN* 2.8 44.9 + - - +
432B GLN* 1.3 78.2 - - - +
434B LEU* 1.3 61.0 + - + +
436B ALA* 3.5 18.6 - - - +
437B LEU* 3.6 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.8 30.7 - - + +
26B MET* 3.7 15.7 - - - +
29B TYR* 3.6 48.0 - - + -
128B ILE* 3.6 27.4 - - + +
132B ALA* 4.7 3.8 - - + -
420B LEU* 4.0 23.8 - - + -
430B ASN 4.0 1.9 + - - +
431B GLU* 3.7 8.7 + - + +
432B GLN 3.2 0.4 - - - -
433B ASP* 1.3 79.3 - - + +
435B LEU* 1.3 59.2 + - - +
436B ALA 3.0 1.8 - - - -
437B LEU* 3.0 6.7 + - + +
438B ASN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B MET* 3.4 33.7 - - + -
431B GLU 3.6 1.7 + - - +
432B GLN* 3.0 30.9 + - - +
434B LEU* 1.3 77.5 - - - +
436B ALA* 1.3 60.0 + - - +
438B ASN* 3.8 4.5 + - + +
439B ASN* 3.0 36.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B GLN 3.4 5.4 + - - +
433B ASP* 3.5 15.7 - - - +
435B LEU* 1.3 82.1 - - - +
437B LEU* 1.3 64.5 + - + +
439B ASN* 3.1 30.5 + - - +
440B ALA* 3.9 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.1 14.1 - - + -
136B PHE* 4.0 21.5 - - + -
416B LEU* 3.6 37.8 - - + +
419B GLN* 3.6 26.9 - - - +
420B LEU* 3.8 25.8 - - + -
433B ASP 3.6 13.2 - - - +
434B LEU* 3.0 7.1 + - + +
436B ALA* 1.3 84.4 - - + +
438B ASN* 1.3 60.0 + - - +
439B ASN 3.2 0.7 - - - -
440B ALA* 3.5 15.2 + - + +
441B LEU* 3.4 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN* 2.9 49.2 - - - +
25B LEU* 3.3 4.6 + - + +
26B MET* 3.0 31.9 + - + +
216B ALA* 5.5 0.4 - - - +
434B LEU 2.9 14.8 + - - +
435B LEU* 4.1 7.9 - - + +
436B ALA 3.2 0.6 + - - -
437B LEU* 1.3 74.6 - - - +
439B ASN* 1.3 66.7 + - - +
441B LEU* 3.5 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ASN* 5.7 0.2 - - - +
222B ASN* 4.5 11.1 + - - -
435B LEU* 3.0 32.4 + - - +
436B ALA* 3.1 9.4 + - - +
438B ASN* 1.3 80.6 - - - +
440B ALA* 1.3 59.0 + - - +
441B LEU 2.9 14.0 - - - +
442B SER* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 4.1 6.6 - - + +
219B ASN* 3.0 33.3 + - - +
222B ASN* 5.0 12.0 + - - +
223B PHE* 5.3 7.9 - - + -
224B LYS* 6.6 0.2 - - + -
416B LEU* 5.0 20.6 - - + -
436B ALA 3.9 2.9 + - - +
437B LEU* 3.5 17.4 + - + +
438B ASN 3.4 0.2 - - - -
439B ASN* 1.3 77.3 - - - +
441B LEU* 1.3 59.9 + - + +
----------------------------------------------------------
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