Contacts of the helix formed by residues 493 - 509 (chain B) in PDB entry 4CCN
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 PRO 493 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 3.9 7.4 - - + +
438B LEU* 3.5 35.4 - - + +
439B ALA* 4.0 15.9 - - + +
442B ALA* 5.8 0.4 - - + -
491B PHE 3.4 8.7 - - - +
492B ALA* 1.3 80.0 - - + +
494B VAL* 1.3 64.8 + - - +
495B ASP 3.2 2.9 - - - -
496B ALA* 3.1 22.4 + - + -
497B VAL* 3.2 13.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A MET* 3.2 29.4 - - + -
477A PHE* 3.7 4.3 - - + -
478A MET* 3.4 25.1 - - + -
481A VAL* 4.1 14.1 - - + -
431B PHE* 3.4 24.2 - - + -
435B ILE* 3.6 12.8 - - + +
492B ALA* 2.9 26.2 + - + +
493B PRO* 1.3 72.8 - - - +
495B ASP* 1.3 57.5 + - - +
497B VAL 3.4 0.9 + - - -
498B ALA* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A MET* 4.2 5.1 - - - +
463A GLY* 2.9 44.0 + - - +
464A ALA* 3.8 7.2 - - + +
467A SER* 4.2 6.9 + - - +
474A ARG* 2.8 35.9 + - - -
478A MET* 5.5 2.6 - - - +
493B PRO 3.2 1.2 - - - -
494B VAL* 1.3 76.9 - - - +
496B ALA* 1.3 63.2 + - - +
498B ALA* 3.1 3.6 + - - +
499B ASP* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU* 5.2 6.5 - - + -
493B PRO* 3.1 22.1 + - + +
495B ASP* 1.3 78.8 - - - +
497B VAL* 1.3 58.0 + - + +
499B ASP* 3.1 11.0 + - - +
500B GLN* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PHE* 3.7 29.8 - - + +
434B ALA* 3.7 23.6 - - + -
435B ILE* 3.4 37.0 - - + +
438B LEU* 4.1 19.1 - - + -
493B PRO* 3.2 6.4 + - + +
494B VAL 3.8 6.3 - - - +
496B ALA* 1.3 73.3 - - - +
498B ALA* 1.3 60.6 + - - +
500B GLN* 3.2 9.4 + - + +
501B ARG* 2.8 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A PHE* 4.1 16.5 - - + -
459A MET* 5.1 0.6 - - - +
462A MET* 3.9 37.9 - - + +
463A GLY 4.1 0.4 - - - +
431B PHE* 4.1 10.0 - - + -
494B VAL 2.9 14.7 + - - +
495B ASP 3.4 8.5 - - - +
497B VAL* 1.3 75.2 - - - +
499B ASP* 1.3 59.1 + - - +
501B ARG* 3.2 2.9 + - - +
502B ALA* 2.8 31.4 + - - +
557B ARG* 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A GLY* 3.6 4.2 - - - -
464A ALA* 3.1 30.4 + - - +
465A GLN* 5.4 1.6 + - - +
495B ASP 2.9 15.2 + - - +
496B ALA* 3.1 11.0 + - - +
498B ALA* 1.3 77.3 - - - +
500B GLN* 1.3 56.4 + - - +
502B ALA* 3.3 6.6 + - - +
503B LYS* 2.8 30.0 + - - +
557B ARG* 3.2 27.9 + - - +
558B LEU 4.0 14.0 - - - +
559B VAL* 3.8 23.9 - - + +
560B GLY 4.8 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU* 6.5 0.7 - - + -
496B ALA* 3.0 22.3 + - + +
497B VAL* 3.6 11.0 - - + +
499B ASP* 1.3 73.2 - - - +
501B ARG* 1.3 62.0 + - + +
503B LYS* 3.2 23.7 + - - +
504B ASP* 2.9 38.4 + - - +
559B VAL* 3.5 29.1 - - - +
560B GLY 4.3 4.8 + - - -
561B GLU* 3.5 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU* 3.6 14.6 - - - +
458A PHE* 4.2 14.7 - - + -
459A MET* 5.0 1.1 - - - -
424B GLN 5.4 0.2 + - - -
425B ARG 3.4 20.6 + - - -
426B ASN* 2.7 30.5 + - - +
430B ASP* 4.0 26.9 + - - +
431B PHE* 3.5 31.6 - - - +
434B ALA* 6.1 2.2 - - + +
497B VAL* 2.8 25.0 + - + +
498B ALA 3.6 4.5 - - - +
500B GLN* 1.3 76.7 - - + +
502B ALA* 1.3 52.9 - - - +
504B ASP* 3.0 12.4 + - - +
505B PHE* 2.8 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A MET* 3.6 28.1 - - + -
498B ALA 2.8 16.4 + - - +
499B ASP 3.4 5.6 - - - +
501B ARG* 1.3 75.0 - - - +
503B LYS* 1.3 57.9 + - - +
505B PHE* 3.1 5.0 + - - +
506B ILE* 2.9 34.2 + - + +
557B ARG* 3.5 35.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ASP 2.8 17.7 + - - +
500B GLN* 3.2 30.2 + - - +
501B ARG 3.1 0.2 - - - -
502B ALA* 1.3 78.0 - - - +
504B ASP* 1.3 75.4 + - - +
506B ILE* 3.1 10.9 + - - +
507B HIS* 3.0 21.3 + - - +
557B ARG* 4.8 1.1 - - - +
559B VAL* 4.2 12.1 - - + -
561B GLU* 3.4 14.8 + - - +
568B TYR* 3.3 56.2 + - + +
582B PRO* 5.6 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B GLN* 2.9 23.4 + - - +
501B ARG* 3.0 12.5 + - - +
503B LYS* 1.3 92.0 + - - +
505B PHE* 1.3 57.9 + - - +
507B HIS* 3.3 9.0 + - - +
508B ASP* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A MET* 3.7 27.8 - - + -
316B GLN* 3.9 28.0 - - + -
317B GLU* 4.9 4.3 - - - -
320B GLY* 3.9 7.0 - - - +
321B SER* 3.5 33.0 - - - -
322B MET* 3.7 16.4 - - - -
501B ARG 2.8 13.2 + - - +
502B ALA* 3.1 12.5 + - - +
504B ASP* 1.3 74.1 - - - +
506B ILE* 1.3 67.1 + - + +
508B ASP* 4.0 8.5 - - + -
509B SER* 2.5 56.1 + - - -
554B GLY* 5.2 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B ALA 2.9 18.8 + - - +
503B LYS* 3.1 11.0 + - - +
505B PHE* 1.3 88.7 - - + +
507B HIS* 1.3 59.6 + - - +
508B ASP 3.5 0.2 + - - -
509B SER* 3.6 1.3 + - - +
554B GLY 4.1 13.9 - - - +
555B ILE 4.4 7.9 - - - +
556B ALA 4.5 6.5 - - - +
557B ARG* 4.0 20.9 - - + -
568B TYR* 4.0 9.2 - - + +
569B TYR 3.2 37.2 - - - +
570B THR* 3.3 25.3 - - + +
573B ASN* 2.9 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LYS 3.0 12.3 + - - +
504B ASP* 3.6 11.8 + - - +
506B ILE* 1.3 80.0 - - - +
508B ASP* 1.3 57.6 + - - +
509B SER 3.9 0.3 - - - +
573B ASN* 3.1 21.3 + - - +
578B HIS* 3.4 46.1 + + + -
580B GLU 2.9 28.3 + - - -
581B GLU* 3.9 4.0 - - - -
582B PRO* 3.5 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B MET* 4.0 39.0 - - + +
504B ASP* 2.9 21.2 + - - +
505B PHE* 3.7 11.1 - - + +
507B HIS* 1.3 75.0 - - - +
509B SER* 1.3 68.7 + - - +
510B LEU* 3.7 3.8 + - - +
577B TYR* 3.2 29.0 + - - -
578B HIS* 2.8 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLN* 3.5 19.3 + - - -
322B MET* 5.6 2.5 - - - -
505B PHE* 2.5 51.2 + - - -
506B ILE* 3.8 9.8 - - - -
507B HIS 3.5 1.5 - - - +
508B ASP* 1.3 80.3 - - - +
510B LEU* 1.3 63.5 + - - +
554B GLY 5.2 1.0 + - - -
570B THR* 3.9 15.5 - - - +
573B ASN* 2.8 26.0 + - - +
574B SER 4.6 2.3 - - - +
----------------------------------------------------------
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