Contacts of the helix formed by residues 432 - 441 (chain D) in PDB entry 4LQL
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 LEU 432 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D LEU* 4.9 15.9 - - + -
336D ASP 4.7 14.8 - - - +
337D LEU* 4.8 14.8 - - + -
342D GLU* 4.2 29.2 - - + +
343D ALA 4.6 12.3 - - - +
344D ILE* 4.6 20.9 - - + +
426D TRP* 6.0 0.2 - - - +
427D THR* 6.4 0.2 - - - -
428D PRO* 4.1 20.5 + - + -
431D GLY* 1.3 66.8 - - - -
433D ALA* 1.3 69.4 + - - +
435D GLY 2.8 12.5 + - - -
436D ALA* 2.9 18.4 + - + +
131E ARG* 6.3 1.3 - - - +
148E TYR* 4.7 9.0 - - + -
149E GLY* 6.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D GLY 3.5 0.2 - - - -
432D LEU* 1.3 78.8 - - - +
434D GLU* 1.3 62.7 + - + +
436D ALA* 3.5 1.0 + - - +
437D LYS* 3.0 36.8 + - + +
148E TYR* 3.6 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D ILE* 3.1 40.8 - - + +
431D GLY* 3.3 4.7 + - - -
432D LEU 3.1 0.8 - - - -
433D ALA* 1.3 80.7 - - + +
435D GLY* 1.3 57.7 + - - +
436D ALA 3.4 0.4 - - - -
437D LYS* 4.2 11.0 - - + -
438D GLN* 4.3 14.2 + - - +
473D ILE* 5.1 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 435 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D TYR* 4.5 7.7 - - - -
428D PRO* 4.4 9.9 - - - +
430D ILE* 3.5 12.6 - - - -
431D GLY 2.6 21.1 + - - -
432D LEU 3.5 1.6 - - - -
434D GLU* 1.3 74.6 - - - +
436D ALA* 1.3 59.6 + - - +
438D GLN 5.0 0.4 - - - -
439D TRP* 3.0 27.6 - - - +
473D ILE* 5.3 2.6 - - - +
131E ARG* 4.6 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D LEU* 2.9 15.7 + - + +
433D ALA 4.1 2.5 - - - +
435D GLY* 1.3 80.4 - - - +
437D LYS* 1.3 59.2 + - - +
439D TRP* 3.6 5.4 - - - -
440D MET* 2.5 51.3 + - + +
131E ARG* 4.7 10.5 - - - +
148E TYR* 4.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D ALA* 3.0 26.1 + - + +
434D GLU* 4.3 8.1 - - + -
436D ALA* 1.3 78.9 - - - +
438D GLN* 1.3 54.6 + - + +
439D TRP 2.5 13.9 + - - -
440D MET* 3.8 0.8 - - - -
441D LYS* 3.0 31.1 + - + +
146E SER* 4.8 20.0 - - - +
148E TYR* 5.4 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D ILE* 4.8 2.8 - - - +
434D GLU 4.3 9.1 + - - +
435D GLY 5.2 0.2 - - - -
437D LYS* 1.3 76.9 - - - +
439D TRP* 1.3 56.1 + - - +
441D LYS* 4.3 11.2 - - - -
442D TYR* 4.2 12.0 - - - +
471D ILE* 5.7 1.0 - - - +
473D ILE* 3.1 42.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D ASP* 5.8 2.2 - - - -
390D ASP* 4.9 7.2 - - + -
391D ILE 5.1 0.9 - - - -
392D THR* 4.6 7.9 - - - -
403D ILE* 3.9 29.4 - - + -
405D TYR* 4.1 31.9 - + + -
435D GLY 3.0 28.3 - - - +
436D ALA* 3.5 2.7 - - - +
437D LYS 2.5 7.5 + - - -
438D GLN* 1.3 75.6 - - - +
440D MET* 1.3 64.8 + - + +
441D LYS 3.0 3.6 - - - -
442D TYR 2.5 31.9 + - - +
443D GLY 4.3 2.3 - - - +
444D GLY* 3.6 24.3 - - - -
445D GLY 3.6 17.3 - - - -
448D THR* 4.4 18.8 - - + -
473D ILE* 4.7 7.2 - - + -
131E ARG* 2.8 43.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D ALA* 2.5 37.1 + - + +
437D LYS* 3.8 1.3 - - - +
439D TRP* 1.3 81.7 - - + +
441D LYS* 1.3 58.0 + - - +
442D TYR 5.1 0.7 - - - -
443D GLY 5.6 1.1 - - - -
444D GLY 6.0 0.2 - - - -
102E HIS* 5.9 4.0 - - + -
104E ALA* 5.4 9.9 - - + -
130E ASP 4.3 15.9 - - - +
131E ARG* 4.5 10.3 - - + +
134E ALA* 3.9 25.9 - - + +
137E ASN* 6.1 0.2 - - - +
138E SER* 4.7 5.7 + - - -
146E SER* 4.6 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D LYS* 3.0 30.4 + - + +
438D GLN* 4.3 7.9 - - - +
439D TRP 3.0 0.6 - - - -
440D MET* 1.3 80.1 - - - +
442D TYR* 1.3 61.4 + - + +
138E SER* 3.1 18.5 - - - -
146E SER* 4.9 13.7 - - - +
----------------------------------------------------------
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