Contacts of the helix formed by residues 486 - 503 (chain A) in PDB entry 2GQ3
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 GLN 486 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A VAL* 4.1 20.3 - - + +
482A THR* 3.2 31.4 + - - +
483A MET* 3.0 22.6 + - - +
484A LYS 3.4 0.2 - - - -
485A SER* 1.3 95.7 + - - +
487A PRO* 1.3 79.6 - - + +
488A TRP* 3.7 19.5 - - + -
489A ILE* 3.0 20.3 + - - +
490A LEU* 3.3 5.6 + - - +
582A PRO* 4.0 21.6 - - + +
583A LEU 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A SER 3.9 3.8 - - - +
486A GLN* 1.3 95.0 - - + +
488A TRP* 1.3 64.4 + - - +
489A ILE 3.0 0.5 + - - -
490A LEU* 3.2 9.1 + - + -
491A ALA* 2.9 26.0 + - - +
577A GLN* 4.0 15.0 - - + +
580A THR* 4.3 27.4 - - + +
582A PRO* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ARG* 3.5 41.7 - - + -
464A THR* 3.7 43.7 - - + -
467A GLU* 3.7 16.4 - - + +
483A MET* 3.7 22.9 + - + -
486A GLN* 3.2 23.4 + - + +
487A PRO* 1.3 78.5 - - - +
489A ILE* 1.3 93.6 + - + +
491A ALA* 4.1 0.7 - - - +
492A TYR* 2.9 34.1 + + + +
577A GLN 3.5 13.2 + - - +
578A LEU* 3.9 16.7 - - - +
580A THR 3.2 20.4 + - - +
582A PRO* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A PHE* 4.4 22.4 - - + -
464A THR* 4.1 9.9 - - - +
483A MET* 3.3 23.8 - - + +
484A LYS* 3.5 24.7 - - - +
486A GLN 3.0 15.3 + - - +
488A TRP* 1.3 115.8 - - + +
490A LEU* 1.3 68.9 + - + +
492A TYR* 3.5 10.2 - - + +
493A GLU* 3.1 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LYS 3.8 17.7 - - - +
485A SER* 4.0 22.4 - - - +
486A GLN 3.7 9.0 - - - +
487A PRO* 3.2 9.1 + - + +
489A ILE* 1.3 78.0 - - + +
491A ALA* 1.3 63.5 + - - +
493A GLU* 3.6 5.2 + - + +
494A ASP* 3.3 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A PRO 2.9 20.0 + - - +
488A TRP 4.1 1.1 - - - +
490A LEU* 1.3 69.1 - - - +
492A TYR* 1.3 56.0 + - - +
494A ASP* 3.2 3.5 + - - -
495A HIS* 2.7 36.6 + - - +
573A ALA* 3.4 16.6 - - + +
577A GLN* 3.5 34.8 - - + +
578A LEU* 3.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASP* 2.5 49.1 + - - +
439A THR* 3.3 23.3 - - + -
458A THR* 3.1 20.1 - - + -
459A GLY 3.0 24.4 + - - -
460A PHE* 4.0 12.1 - - + -
463A ARG* 3.5 20.1 - - + +
488A TRP* 2.9 33.8 + + + +
489A ILE* 3.5 21.5 - - + +
491A ALA* 1.3 72.5 - - - +
493A GLU* 1.3 79.2 + - + +
495A HIS* 3.7 2.7 - - - +
496A ASN* 3.2 24.4 + - - +
578A LEU* 3.4 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A THR* 3.0 32.7 + - - +
460A PHE* 4.0 14.4 - - - +
489A ILE* 3.1 21.7 + - + +
490A LEU* 4.0 7.0 - - + +
491A ALA 3.3 0.4 - - - -
492A TYR* 1.3 88.2 - - + +
494A ASP* 1.3 70.5 + - - +
496A ASN* 3.6 1.2 + - - +
497A VAL* 3.4 11.4 + - - +
513A LYS* 2.8 58.1 + - - +
514A GLY 5.3 2.1 + - - -
532A GLN* 6.0 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A LEU* 3.3 16.4 + - - +
491A ALA* 3.2 4.8 + - - +
493A GLU* 1.3 78.6 - - - +
495A HIS* 1.3 57.2 + - - +
497A VAL* 3.3 2.6 + - - -
498A ASP* 2.9 27.9 + - - -
535A ALA* 5.6 5.2 - - - +
572A ARG* 3.2 56.1 + - + +
573A ALA* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 5.5 6.7 - - - -
433A ASP* 5.3 0.2 - - - -
439A THR* 3.0 32.0 + - + -
440A VAL* 5.6 2.0 - - - -
442A LEU* 3.7 22.4 + - + +
443A LYS* 5.8 2.9 - - + -
491A ALA 2.7 22.6 + - - +
492A TYR 3.7 3.1 - - - +
494A ASP* 1.3 73.0 - - - +
496A ASN* 1.3 56.9 + - - +
498A ASP* 3.4 9.3 + - - +
499A ALA* 3.0 33.7 + - + +
571A ARG* 6.1 1.2 - - - -
573A ALA* 3.7 22.0 + - + +
575A ILE* 6.2 1.6 - - + -
578A LEU* 3.7 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASP* 3.0 36.9 + - - +
442A LEU* 3.5 14.9 - - - +
456A ILE* 3.3 37.0 - - - +
457A ASN 4.1 3.2 - - - +
458A THR* 3.5 30.3 - - + +
492A TYR 3.2 11.2 + - - +
493A GLU 3.8 2.7 - - - +
494A ASP 3.3 0.2 - - - -
495A HIS* 1.3 71.6 - - - +
497A VAL* 1.3 63.6 + - - +
499A ALA* 3.3 2.1 + - - +
500A GLY 2.9 25.3 + - - -
511A VAL* 3.9 11.1 - - - +
512A GLY 4.2 6.9 - - - +
513A LYS* 5.0 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLU 3.4 2.7 + - - +
494A ASP* 3.3 7.5 + - - +
496A ASN* 1.3 79.0 - - - +
498A ASP* 1.4 64.2 + - - +
500A GLY* 3.8 0.2 - - - -
501A LEU* 2.9 45.9 + - + +
511A VAL* 3.7 24.6 - - + +
513A LYS* 3.3 36.3 - - - +
535A ALA* 3.7 22.4 - - + +
536A GLY* 4.6 5.6 - - - +
567A LEU* 4.3 3.1 - - + -
572A ARG* 3.7 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ASP 2.9 20.2 + - - +
495A HIS* 3.4 14.1 + - - +
497A VAL* 1.4 71.0 - - - +
499A ALA* 1.3 57.8 + - - +
501A LEU* 3.8 4.1 - - - +
502A ALA* 2.9 32.3 + - - +
567A LEU* 5.2 3.4 - - - +
569A GLY 5.5 1.4 + - - -
570A LYS 3.2 19.6 - - - +
571A ARG* 3.6 8.0 - - + +
572A ARG* 2.6 57.1 + - - +
573A ALA 3.6 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU* 3.8 26.5 - - + -
443A LYS* 4.8 12.5 - - + +
446A ILE* 3.8 13.8 - - + +
495A HIS* 3.0 23.5 + - + +
498A ASP* 1.3 73.2 - - - +
500A GLY* 1.3 65.9 + - - +
502A ALA* 3.4 5.4 + - - +
503A ALA* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE* 4.5 0.2 - - - -
456A ILE* 3.7 22.0 - - - +
496A ASN 2.9 11.9 + - - -
497A VAL 3.8 1.8 - - - -
499A ALA* 1.3 76.1 - - - +
501A LEU* 1.3 62.7 + - - +
503A ALA 3.1 5.5 + - - -
505A PHE* 3.1 46.3 + - - -
511A VAL* 4.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A VAL* 2.9 37.5 + - + +
498A ASP* 4.1 3.6 - - - +
500A GLY* 1.3 72.6 - - - +
502A ALA* 1.3 56.9 + - - +
504A GLY* 3.1 17.2 + - - -
505A PHE 4.5 1.1 - - - +
506A SER* 4.0 21.5 + - - +
511A VAL* 4.2 9.9 - - + -
564A GLN* 3.5 61.0 - - + +
567A LEU* 3.8 21.3 - - + -
568A ALA* 3.9 25.6 - - + +
569A GLY 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 5.5 9.2 - - - +
98A PHE 3.5 9.9 + - - +
99A THR* 5.2 1.2 + - - -
443A LYS* 5.9 5.2 - - - -
498A ASP 2.9 20.3 + - - +
499A ALA* 4.0 5.4 - - - +
501A LEU* 1.3 76.7 - - - +
503A ALA* 1.3 59.5 + - - +
504A GLY 3.2 1.4 + - - -
569A GLY* 4.9 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.5 25.6 - - + -
99A THR* 3.4 4.8 - - - -
100A ILE* 3.2 26.0 + - + +
443A LYS* 6.4 0.4 - - + -
446A ILE* 3.9 17.0 - - + -
499A ALA 3.1 17.6 + - - +
500A GLY 3.1 4.2 + - - +
502A ALA* 1.3 74.8 - - - +
504A GLY* 1.4 61.6 + - - +
505A PHE* 3.5 19.1 - - + -
----------------------------------------------------------
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