Contacts of the helix formed by residues 421 - 433 (chain A) in PDB entry 3ECP
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 SER 421 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER 5.7 1.8 - - - -
391A GLN* 3.2 17.0 - - - -
392A SER* 3.8 2.2 - - - +
393A ALA* 3.3 4.8 - - - +
418A LYS* 2.9 43.4 + - - +
419A ALA 3.3 1.4 - - - -
420A GLY* 1.3 79.4 - - - +
422A LEU* 1.3 58.7 + - - +
423A GLN* 3.4 11.7 + - - +
424A TRP* 3.0 21.2 + - - +
425A ALA 2.8 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A SER 4.5 0.9 - - - +
370A PHE* 3.6 30.5 - - + +
372A PRO* 4.6 23.6 - - + -
390A SER 4.9 11.9 - - - +
391A GLN* 2.7 26.8 + - - +
392A SER 3.9 10.5 - - - +
393A ALA* 3.2 10.6 - - - +
395A THR* 4.3 11.2 - - - +
396A VAL* 3.5 31.2 - - + -
421A SER* 1.3 68.8 - - - +
423A GLN* 1.3 59.9 + - - +
425A ALA* 3.6 4.4 - - + +
426A TYR* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE 5.6 0.9 - - - -
371A THR 6.0 1.8 - - - -
372A PRO 5.9 5.6 - - - +
390A SER 5.3 9.3 - - - +
391A GLN 4.4 0.4 + - - -
416A LYS* 4.4 21.8 + - - +
417A GLU* 4.4 18.8 - - + -
418A LYS* 5.0 1.6 - - + +
421A SER* 3.2 10.8 + - - +
422A LEU* 1.3 77.3 - - - +
424A TRP* 1.3 67.3 - - - +
426A TYR* 3.2 13.3 + - - +
427A MET* 3.2 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ALA* 4.1 16.2 - - + -
397A LEU* 5.5 0.9 - - + -
402A CYS* 4.2 8.1 - - + -
405A LEU* 3.9 20.9 - - + -
406A GLY* 3.7 36.8 - - - -
409A ASP* 2.8 24.3 + - + +
413A ARG* 3.6 23.2 - - + +
417A GLU* 3.5 31.6 - - + -
418A LYS 3.4 20.9 - - - +
420A GLY* 3.8 20.4 - - - -
421A SER* 3.0 18.1 + - - +
423A GLN* 1.3 77.0 - - - +
425A ALA* 1.3 68.9 + - - +
427A MET* 3.3 1.6 + - - +
428A ALA* 2.8 39.6 + - + +
431A ARG* 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 5.2 2.7 - - + -
393A ALA* 3.8 20.2 - - + -
396A VAL* 6.3 0.2 - - + -
397A LEU* 4.2 20.0 - - + -
405A LEU* 4.2 4.9 - - + -
421A SER 2.8 12.3 + - - +
422A LEU* 3.6 15.3 - - + +
423A GLN 3.2 0.2 - - - -
424A TRP* 1.3 85.2 - - + +
426A TYR* 1.3 61.6 + - - +
429A ILE* 3.1 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ARG* 4.3 12.2 - - + -
370A PHE* 3.8 34.9 - - + +
371A THR* 4.5 16.2 - - + +
422A LEU 3.0 13.9 + - - +
423A GLN* 3.4 15.5 - - - +
424A TRP 3.2 0.4 - - - -
425A ALA* 1.3 78.0 - - - +
427A MET* 1.3 80.6 + - + +
429A ILE* 3.5 3.8 + - - +
430A ALA* 3.0 21.6 + - + +
442A GLY 3.5 19.3 - - - -
443A ILE* 3.6 9.4 - - - +
444A ALA* 2.8 40.5 + - + +
449A LEU* 4.0 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LYS* 5.1 8.5 - - + -
417A GLU* 3.3 31.9 - - + +
423A GLN* 3.2 19.6 + - - +
424A TRP 3.8 3.4 - - - +
426A TYR* 1.3 101.1 - - + +
428A ALA* 1.3 57.9 + - - +
430A ALA* 2.9 4.9 + - - +
431A ARG* 2.8 59.8 + - + +
435A PHE* 4.2 22.9 - - + -
437A ASP* 5.2 5.4 - - + +
442A GLY* 4.1 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 3.8 28.7 - - + -
409A ASP* 3.7 25.1 - - - +
424A TRP* 2.8 29.9 + - + +
425A ALA 3.9 0.4 - - - +
426A TYR 3.3 0.2 - - - -
427A MET* 1.3 71.3 - - - +
429A ILE* 1.3 62.6 + - - +
431A ARG* 3.2 14.8 + - - +
432A LEU* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 3.5 42.6 - - + -
397A LEU* 4.5 10.5 - - + -
405A LEU* 4.0 20.2 - - + +
425A ALA 3.1 18.5 + - - +
426A TYR* 3.8 3.8 - - - +
428A ALA* 1.3 73.3 - - - +
430A ALA* 1.3 63.6 + - - +
432A LEU* 3.2 6.6 + - - +
433A GLY 3.0 16.5 + - - -
448A ALA 4.5 0.3 - - - +
449A LEU* 3.7 19.5 - - + +
452A GLY* 3.3 9.1 - - - +
453A TRP* 3.3 36.3 - - + +
456A LEU* 4.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A TYR* 3.0 17.5 + - + +
427A MET* 2.9 12.2 + - - +
429A ILE* 1.3 75.6 - - - +
431A ARG* 1.3 57.8 + - - +
433A GLY* 3.0 12.9 + - - +
434A GLY 3.2 0.3 + - - -
435A PHE* 3.0 51.0 + - + +
444A ALA* 4.0 15.0 - - + -
448A ALA* 4.6 4.2 - - - +
449A LEU* 4.2 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ASP* 2.8 40.4 + - - +
412A LYS* 3.6 41.8 + - + +
413A ARG* 4.0 2.8 - - - +
414A LYS* 4.3 11.1 - - - +
417A GLU* 3.1 38.4 + - - -
424A TRP* 4.0 1.4 - - - +
427A MET* 2.8 31.2 + - + +
428A ALA* 3.2 17.5 + - - +
430A ALA* 1.3 79.5 - - + +
432A LEU* 1.3 55.4 + - - +
433A GLY 3.0 0.2 - - - -
434A GLY* 3.1 18.0 + - - -
435A PHE* 4.0 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 4.1 13.5 - - + -
408A LEU* 3.9 36.1 - - + +
412A LYS* 5.4 10.1 - - - +
428A ALA 3.1 13.1 + - - +
429A ILE* 3.2 10.1 + - - +
431A ARG* 1.3 74.8 - - - +
433A GLY* 1.3 59.5 + - - +
434A GLY 3.3 0.6 + - - -
451A GLU* 4.8 0.7 - - - +
452A GLY* 3.9 10.1 - - - +
455A ALA* 4.2 11.6 - - + +
456A LEU* 3.9 32.1 - - + +
459A LYS* 4.2 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE 3.0 4.9 + - - -
430A ALA 3.0 11.1 + - - -
432A LEU* 1.3 78.9 - - - +
434A GLY* 1.3 56.5 + - - +
435A PHE 3.5 1.0 + - - -
448A ALA* 3.5 17.9 - - - +
451A GLU* 4.0 16.3 - - - +
452A GLY 3.5 22.0 - - - -
----------------------------------------------------------
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