Contacts of the helix formed by residues 438 - 449 (chain A) in PDB entry 1Q2L
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 ASP 438 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LYS* 5.3 9.4 + - - +
305A SER* 4.2 17.8 + - - +
307A THR* 4.4 0.9 - - - +
436A ARG 3.2 7.8 + - - +
437A TYR* 1.3 77.4 - - - +
439A ALA* 1.3 63.7 + - - +
440A LYS* 3.3 11.6 + - - +
441A ALA* 2.9 47.3 + - + +
442A VAL* 3.0 19.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
437A TYR* 3.8 31.5 + - + +
438A ASP* 1.3 73.2 + - - +
440A LYS* 1.3 57.0 + - - +
442A VAL* 2.8 31.1 - - - +
443A LYS* 2.9 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ASP* 3.2 8.0 + - - +
439A ALA* 1.3 77.7 - - - +
441A ALA* 1.3 57.3 + - - +
443A LYS* 3.2 9.6 + - + +
444A GLU* 2.9 67.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LYS* 5.7 9.9 - - + +
307A THR* 3.6 18.0 - - + +
438A ASP* 2.9 36.0 + - + +
440A LYS* 1.3 76.1 - - - +
442A VAL* 1.3 63.2 + - - +
444A GLU* 3.4 10.7 + - - +
445A ARG* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER 5.8 0.7 - - - +
307A THR* 3.6 30.5 - - + +
310A LEU* 4.2 22.7 - - + -
311A ILE* 4.1 8.9 - - + +
384A ILE* 5.1 18.8 - - + +
437A TYR* 4.7 9.2 - - + +
438A ASP 3.0 17.1 + - - +
439A ALA* 2.8 28.7 - - + +
441A ALA* 1.3 75.3 - - - +
443A LYS* 1.3 64.6 + - + +
445A ARG* 3.3 2.2 + - - +
446A LEU* 3.0 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ARG* 5.8 0.2 - - - +
439A ALA 2.9 14.3 + - - +
440A LYS* 3.6 12.3 - - + +
442A VAL* 1.3 80.7 - - + +
444A GLU* 1.3 61.8 + - + +
446A LEU* 3.4 9.2 + - - +
447A ALA* 2.9 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LYS* 2.9 60.4 + - + +
441A ALA* 3.9 9.0 - - - +
443A LYS* 1.3 79.3 - - + +
445A ARG* 1.3 64.7 + - - +
447A ALA* 3.5 13.9 + - - +
448A MET* 3.6 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 3.5 36.5 - - - +
297A ASP* 4.4 6.3 + - - +
299A ASN* 3.4 23.6 - - - +
307A THR* 4.5 4.8 - - + +
308A ASP* 2.6 36.0 + - - +
311A ILE* 3.5 28.0 - - + -
351A LEU* 3.8 12.3 - - + -
441A ALA 3.1 16.0 + - - +
442A VAL 3.8 0.2 - - - +
443A LYS 3.3 0.2 - - - -
444A GLU* 1.3 73.6 - - - +
446A LEU* 1.3 67.8 + - - +
448A MET* 3.0 39.7 + - - +
449A MET* 3.4 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ILE* 4.0 21.3 - - + -
376A LEU* 4.6 6.3 - - + +
379A LEU* 3.8 51.4 - - + +
380A ARG* 2.9 39.9 + - + +
383A GLY* 5.2 1.6 - - - -
384A ILE* 4.0 23.6 - - + +
442A VAL* 3.0 22.1 + - + +
443A LYS* 3.7 7.0 - - - +
445A ARG* 1.3 78.7 - - - +
447A ALA* 1.3 60.3 + - - +
449A MET* 3.2 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ARG* 4.1 12.6 - - - +
443A LYS* 2.9 20.8 + - + +
444A GLU* 3.6 10.8 - - - +
445A ARG 3.1 0.4 - - - -
446A LEU* 1.3 77.7 - - - +
448A MET* 1.3 59.6 + - - +
449A MET 3.7 0.2 + - - -
450A THR* 3.7 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PHE* 4.4 14.1 - - + -
295A ARG 3.1 28.9 - - - +
296A ILE* 4.2 11.2 - - + -
444A GLU 3.6 9.1 + - - +
445A ARG* 3.0 35.5 + - - +
447A ALA* 1.3 76.2 - - - +
449A MET* 1.3 68.8 + - - +
450A THR* 2.9 13.2 + - - -
453A ASN* 2.9 40.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PHE* 3.5 38.4 - - + -
311A ILE* 4.2 3.1 - - + -
315A ILE* 4.3 16.2 - - + -
351A LEU* 3.9 32.1 - - + -
353A ILE* 4.4 4.7 - - + -
373A PHE* 4.0 0.3 - - - -
376A LEU* 3.5 33.1 - - + +
380A ARG* 2.9 23.1 + - - +
445A ARG* 3.4 23.8 - - + +
446A LEU* 3.2 28.1 + - - +
447A ALA 3.4 0.2 - - - -
448A MET* 1.3 83.7 - - - +
450A THR* 1.3 57.2 + - - +
----------------------------------------------------------
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