Contacts of the helix formed by residues 435 - 443 (chain D) in PDB entry 2NYM
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 GLY 435 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D ALA 2.9 13.9 + - - +
432D GLY 4.2 4.7 - - - -
433D GLN 3.3 3.5 - - - -
434D LEU* 1.3 79.5 - - - +
436D VAL* 1.3 60.7 + - - -
437D GLU* 3.1 13.6 - - - +
438D PHE 3.3 2.4 + - - -
439D PHE* 2.9 26.6 + - - +
473D PHE* 4.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D GLY* 1.3 71.6 - - - -
437D GLU* 1.3 64.5 + - + +
439D PHE* 3.3 2.1 - - + +
440D ASP* 2.6 54.3 + - - +
473D PHE* 3.4 41.3 - - + -
477D TRP* 4.2 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D LEU 3.4 7.3 - - - +
435D GLY* 3.1 23.0 - - - +
436D VAL* 1.3 90.6 + - + +
438D PHE* 1.3 72.1 + - + +
440D ASP* 3.5 7.3 + - - +
441D GLU* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D SER* 3.9 16.8 - - - -
405D LEU* 4.3 17.5 - - + -
434D LEU* 3.7 52.9 - - + +
435D GLY 3.6 7.9 - - - +
437D GLU* 1.3 82.1 + - + +
439D PHE* 1.3 71.6 + - - +
441D GLU* 4.5 4.3 - - - -
442D LYS* 3.1 29.8 + - + -
443D LEU* 3.9 20.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D MSE 4.4 4.0 - - + -
431D ALA* 4.3 10.8 - - + -
434D LEU* 5.6 0.6 - - + +
435D GLY 2.9 14.1 + - - +
436D VAL* 3.3 11.2 - - - +
438D PHE* 1.3 80.6 - - - +
440D ASP* 1.3 59.8 + - - +
441D GLU 2.7 13.3 + - - -
443D LEU* 3.0 61.8 + - + -
444D ASN* 3.3 23.6 + - + -
447D CYS* 3.8 19.1 - - + -
469D LEU* 3.7 27.6 - - + -
473D PHE* 3.9 13.2 - + + -
477D TRP* 3.5 36.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D VAL* 2.6 36.1 + - - +
437D GLU* 3.8 7.4 - - - +
439D PHE* 1.3 73.8 - - - +
441D GLU* 1.3 60.4 + - - +
444D ASN* 4.0 15.4 + - - +
477D TRP* 2.8 33.8 + - - -
481D THR* 3.4 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D GLU 3.0 17.0 + - - +
438D PHE* 3.8 5.8 - - - +
439D PHE 2.7 6.0 + - - -
440D ASP* 1.3 76.2 - - - +
442D LYS* 1.3 102.3 + - + +
443D LEU 3.8 0.3 + - - -
444D ASN 5.0 1.2 + - - -
445D SER* 5.5 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D VAL* 4.8 8.0 - - - +
438D PHE* 3.1 20.8 + - + +
441D GLU* 1.3 117.7 + - + +
443D LEU* 1.3 68.5 + - - +
445D SER* 4.9 7.3 + - - -
446D LEU* 5.2 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D LEU* 3.9 27.4 - - + -
408D ILE* 6.3 0.2 - - + -
409D VAL* 4.2 12.1 - - + -
427D MSE 3.5 33.3 - - + +
430D LEU* 4.9 2.7 - - + -
431D ALA* 4.9 7.4 - - - +
434D LEU* 5.0 7.0 - - + -
438D PHE* 4.1 14.1 - - + +
439D PHE* 3.0 48.0 + - + +
441D GLU 3.6 0.4 + - - -
442D LYS* 1.3 83.0 - - - +
444D ASN* 1.3 67.0 + - - +
445D SER* 3.4 3.1 - - - -
446D LEU* 3.5 24.2 + - + +
447D CYS* 3.8 4.2 + - - -
----------------------------------------------------------
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