Contacts of the helix formed by residues 411 - 431 (chain A) in PDB entry 5OQN
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 411 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLN* 1.3 79.7 + - - +
412A HIS* 1.3 70.0 + - - +
414A ASP* 3.2 10.6 + - - +
415A TYR* 2.9 43.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLN 3.3 0.6 - - - -
411A SER* 1.3 87.7 + - - +
413A PHE* 1.3 65.3 + - - +
415A TYR* 3.8 21.1 - + + +
416A ASN* 2.5 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ARG* 6.1 4.7 - - - -
410A GLN* 3.3 24.7 + - + +
411A SER 3.3 0.2 - - - -
412A HIS* 1.3 78.8 - - - +
414A ASP* 1.3 77.1 + - - +
416A ASN* 3.2 4.4 + - - +
417A THR* 2.9 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLN* 2.6 29.4 + - - +
411A SER* 3.2 10.1 + - - +
413A PHE* 1.3 88.6 - - - +
415A TYR* 1.3 64.2 + - + +
417A THR* 2.7 22.2 + - - -
418A LEU* 2.9 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ARG* 3.1 62.0 + - - +
402A HIS 5.4 0.2 + - - -
403A ASN* 4.1 20.7 + - - +
411A SER* 2.9 44.5 + - - -
412A HIS* 3.5 25.8 - + + +
414A ASP* 1.3 77.3 - - + +
416A ASN* 1.3 65.6 + - - +
418A LEU* 3.4 4.3 + - + +
419A GLU* 3.1 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A SER* 5.3 8.7 - - - +
412A HIS* 2.5 45.3 + - - +
413A PHE* 3.7 5.6 - - - +
415A TYR* 1.3 77.3 - - - +
417A THR* 1.3 59.6 + - + +
419A GLU* 3.2 14.4 + - - +
420A PHE* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A SER* 5.8 4.3 - - - +
356A VAL* 4.1 20.6 - - + +
413A PHE* 2.9 48.3 + - + +
414A ASP* 2.7 26.2 + - - -
416A ASN* 1.3 75.1 - - + +
418A LEU* 1.3 58.3 + - - +
420A PHE* 3.1 8.4 + - - +
421A ILE* 2.9 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A TYR* 3.8 32.8 - - + +
398A LEU* 3.6 39.9 - - + +
399A ARG* 3.7 26.9 - - + -
414A ASP* 2.9 31.1 + - + +
415A TYR* 3.7 4.9 - - + +
417A THR* 1.3 80.0 + - - +
419A GLU* 1.3 57.7 + - - +
421A ILE* 3.1 10.1 + - + +
422A ILE* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ARG* 2.6 42.6 + - + +
400A TYR* 3.9 10.3 + - - +
415A TYR* 3.1 19.6 + - - +
416A ASN* 3.6 13.0 - - - +
418A LEU* 1.3 74.6 - - - +
420A PHE* 1.3 57.9 + - - +
422A ILE* 4.3 2.9 - - - +
423A GLU* 2.8 32.2 + - - +
457A SER* 3.4 24.7 + - - +
459A PRO* 5.9 1.0 - - - +
460A LEU* 3.4 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 3.1 38.1 - - + -
321A SER* 3.8 21.1 - - - +
356A VAL* 3.6 44.6 - - + -
416A ASN 2.8 14.0 + - - +
417A THR* 3.3 12.1 - - - +
419A GLU* 1.3 77.2 - - - +
421A ILE* 1.3 64.1 + - - +
423A GLU* 3.0 20.9 + - - +
424A GLN* 2.9 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A PHE* 2.9 37.5 - - + +
355A THR* 4.8 1.6 - - - -
356A VAL* 4.7 9.2 - - + +
359A ALA* 3.8 28.3 - - + -
395A TYR* 4.0 42.0 - - + -
417A THR* 2.9 30.6 + - - +
418A LEU* 3.6 11.2 - - + +
420A PHE* 1.3 72.5 - - - +
422A ILE* 1.3 64.7 + - - +
424A GLN* 3.0 12.1 + - - +
425A LEU* 3.0 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 4.0 18.7 - - + +
395A TYR* 3.4 44.2 - - + +
396A ILE* 4.0 13.2 - - + +
399A ARG* 4.2 11.0 - - + -
400A TYR* 4.7 8.3 - - + -
418A LEU 2.8 28.6 + - - +
419A GLU* 3.7 7.4 - - - +
421A ILE* 1.3 72.0 - - - +
423A GLU* 1.3 57.4 + - - +
425A LEU* 3.6 2.4 + - - -
426A SER* 2.4 42.0 + - - +
450A MET* 4.3 17.3 - - - -
460A LEU* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A GLU 2.8 22.4 + - - +
420A PHE* 3.0 22.9 + - - +
422A ILE* 1.3 74.0 - - - +
424A GLN* 1.3 66.8 + - + +
426A SER* 3.1 6.1 + - - -
427A ILE* 2.9 47.5 + - + +
459A PRO* 3.9 30.8 - - - +
460A LEU* 3.9 13.0 - - + +
463A ILE* 4.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA* 3.3 25.1 - - + +
360A PHE* 3.3 35.5 - - - +
363A ARG* 2.3 52.0 + - + +
420A PHE* 2.9 56.7 + - + +
421A ILE 3.0 4.2 + - - +
423A GLU* 1.3 78.6 - - - +
425A LEU* 1.3 63.8 + - - +
427A ILE* 3.2 7.0 + - - +
428A ALA* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A TRP* 4.8 3.4 - - + -
354A PHE* 3.6 28.9 - - + -
359A ALA* 4.5 7.2 - - + +
362A PHE* 3.8 24.5 - - + -
388A LEU* 4.4 19.2 - - + +
391A HIS 4.5 1.3 - - - -
392A LEU* 4.2 35.0 - - + +
395A TYR* 4.2 14.1 - - + -
421A ILE* 3.0 30.2 + - + +
422A ILE* 4.1 3.6 - - - +
424A GLN* 1.3 76.1 - - - +
426A SER* 1.3 57.0 + - - +
428A ALA* 3.4 2.6 + - - +
429A ALA* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 3.8 17.4 - - - +
422A ILE* 2.4 32.2 + - - +
423A GLU 3.1 4.5 + - - -
425A LEU* 1.3 75.6 - - - +
427A ILE* 1.3 60.4 + - - +
429A ALA* 3.1 7.0 + - - -
430A GLU* 2.9 24.8 + - - +
450A MET* 5.0 7.2 - - - +
463A ILE* 3.6 27.9 - - - +
464A GLY* 5.4 0.7 - - - -
467A VAL* 3.2 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ARG* 3.5 45.3 - - + +
367A LEU* 4.2 18.5 - - + +
423A GLU* 2.9 42.5 + - + +
424A GLN* 3.2 2.2 + - - +
426A SER* 1.3 76.2 - - - +
428A ALA* 1.3 61.7 + - - +
430A GLU* 3.4 21.4 - - - +
431A ARG* 4.1 3.8 + - - +
462A LYS* 6.3 0.7 - - - +
463A ILE* 3.6 29.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
362A PHE* 4.1 22.0 - - + -
363A ARG* 4.2 10.5 - - - +
366A TYR* 3.6 25.6 - - + -
367A LEU* 3.7 17.0 - - + +
424A GLN 3.1 11.7 + - - +
425A LEU 3.7 6.7 - - - +
427A ILE* 1.3 76.2 - - - +
429A ALA* 1.3 63.1 + - - +
431A ARG* 3.1 20.4 + - - +
432A TYR* 3.8 4.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 4.3 5.4 - - + +
392A LEU* 4.7 3.1 - - + -
425A LEU 2.8 22.5 + - - +
426A SER* 3.1 10.3 + - - +
428A ALA* 1.3 70.6 - - - +
430A GLU* 1.3 66.4 + - - +
431A ARG 3.1 0.9 + - - -
432A TYR* 3.5 17.3 + - - -
434A TYR* 3.0 22.3 + - - +
443A MET* 3.7 30.1 - - + -
467A VAL* 4.4 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 6.0 0.2 - - - +
426A SER 2.9 11.2 + - - +
427A ILE* 3.4 21.2 - - - +
428A ALA 3.2 0.4 - - - -
429A ALA* 1.3 77.9 - - - +
431A ARG* 1.3 73.1 + - + +
432A TYR 3.8 0.5 + - - -
463A ILE* 4.3 9.6 - - + +
466A ARG* 3.7 46.2 + - - +
467A VAL* 3.7 18.6 - - + +
470A SER* 2.9 28.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
366A TYR* 3.1 18.8 + - + -
367A LEU* 4.1 28.7 - - + +
370A LEU* 3.2 37.8 + - + +
371A ASP* 3.3 30.8 + - - +
427A ILE 4.8 1.8 - - - +
428A ALA 3.1 10.4 + - - +
429A ALA 3.1 0.8 - - - -
430A GLU* 1.3 100.1 - - + +
432A TYR* 1.3 57.2 + - - +
470A SER* 5.1 0.2 - - - -
----------------------------------------------------------
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