Contacts of the helix formed by residues 431 - 441 (chain E) 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 GLY 431 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428E PRO* 3.9 10.4 + - - +
429E GLU 3.6 3.8 + - - -
430E ILE* 1.3 76.1 - - - +
432E LEU* 1.3 61.2 + - - -
433E ALA 3.2 3.7 + - - -
434E GLU* 3.4 3.8 + - - -
435E GLY* 2.9 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E LEU* 5.2 11.9 - - + -
336E ASP 5.0 0.9 - - - +
337E LEU* 6.3 1.1 - - + -
342E GLU* 3.6 26.2 - - + +
343E ALA* 3.4 43.3 - - - +
344E ILE* 4.9 10.8 - - + -
427E THR* 4.7 7.2 - - - +
428E PRO* 3.6 24.6 + - + +
431E GLY* 1.3 68.7 - - - -
433E ALA* 1.3 69.4 + - - +
435E GLY 5.6 0.4 - - - -
436E ALA* 2.9 31.3 + - + +
131F ARG* 5.3 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E GLY 3.2 0.8 - - - -
432E LEU* 1.3 76.8 - - - +
434E GLU* 1.3 55.8 + - + +
436E ALA* 2.6 8.3 + - - +
437E LYS* 2.5 43.0 + - + +
148F TYR* 4.4 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E ILE* 3.3 28.0 - - + +
431E GLY* 3.4 2.9 + - - +
433E ALA* 1.3 77.3 - - + +
435E GLY* 1.3 62.7 + - - +
437E LYS* 4.1 8.3 - - - +
438E GLN* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 435 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405E TYR* 4.8 4.8 - - - -
428E PRO* 4.8 10.5 - - - -
430E ILE* 4.4 9.9 + - - +
431E GLY 2.9 17.0 + - - -
432E LEU* 3.8 2.9 - - - -
434E GLU* 1.3 76.1 - - - +
436E ALA* 1.3 58.0 + - - +
438E GLN 4.5 0.4 - - - -
439E TRP* 3.6 19.8 + - - +
473E ILE* 4.3 18.8 - - - +
474E LYS 6.1 0.7 - - - -
131F ARG* 4.9 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E LEU* 2.9 21.2 + - + +
433E ALA 2.6 10.5 + - - +
435E GLY* 1.3 73.6 - - - +
437E LYS* 1.3 58.6 + - - +
438E GLN 3.4 0.4 - - - -
439E TRP* 3.3 1.9 + - - +
440E MET* 2.9 35.3 + - + +
131F ARG* 3.7 28.1 + - - +
148F TYR* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 437 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433E ALA* 2.5 26.8 + - + +
434E GLU* 3.1 8.9 + - - +
436E ALA* 1.3 74.3 - - - +
438E GLN* 1.3 59.1 + - - +
440E MET* 3.4 19.9 + - - +
441E LYS* 3.4 10.6 + - - +
146F SER* 4.2 28.6 + - - +
147F VAL* 5.2 0.2 - - - -
148F TYR* 4.6 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 438 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E GLU 3.0 15.0 + - - +
437E LYS* 1.3 74.1 - - - +
439E TRP* 1.3 61.2 + - - +
440E MET 3.3 0.2 - - - -
441E LYS 4.7 0.7 - - - -
442E TYR* 3.4 23.0 - - - +
473E ILE* 3.5 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 439 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E ASP* 5.3 0.2 - - - -
391E ILE* 4.4 2.7 - - - -
392E THR* 3.9 24.5 - - - -
403E ILE* 4.3 17.5 - - + -
405E TYR* 3.1 47.8 - + + -
435E GLY 3.6 15.8 + - - +
436E ALA* 3.3 5.9 + - - +
437E LYS 3.3 0.4 - - - -
438E GLN* 1.3 75.6 - - - +
440E MET* 1.3 71.3 + - - +
442E TYR* 3.7 1.0 + - - -
443E GLY 2.9 27.0 + - - +
444E GLY* 3.2 26.3 + - - +
445E GLY* 3.7 14.8 + - - +
448E THR* 3.4 33.9 - - + -
473E ILE* 3.5 17.5 - - + +
131F ARG* 4.1 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 440 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E ALA* 2.9 25.0 + - + +
437E LYS* 3.4 9.2 - - - +
439E TRP* 1.3 82.3 - - - +
441E LYS* 1.3 60.9 + - + +
442E TYR 2.8 8.6 + - - -
443E GLY* 3.2 8.1 + - - -
102F HIS* 5.2 9.2 - - + -
104F ALA* 5.4 6.3 - - + -
130F ASP 5.8 0.7 - - - +
131F ARG* 4.9 17.0 - - + +
134F ALA* 3.3 33.7 - - + +
146F SER* 4.3 16.8 - - - +
148F TYR* 5.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 441 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437E LYS 3.4 10.0 + - - +
438E GLN 4.9 0.2 - - - -
440E MET* 1.3 77.2 - - + +
442E TYR* 1.3 58.0 + - - +
443E GLY 3.6 0.7 - - - -
134F ALA* 5.2 1.6 - - - -
137F ASN* 5.7 4.3 - - + -
138F SER* 3.6 22.9 - - - +
142F VAL 4.8 11.0 - - - +
144F ALA* 4.6 15.7 - - + +
146F SER* 5.2 12.6 - - - -
----------------------------------------------------------
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