Contacts of the helix formed by residues 520 - 533 (chain B) in PDB entry 1XSK
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 520 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B ALA 4.0 8.3 - - - +
518B THR 3.9 5.4 - - - +
519B ALA* 1.3 91.9 - - + +
521B ALA* 1.3 67.5 + - - +
522B HIS* 3.8 26.5 - - + +
523B VAL* 3.2 17.5 + - + -
524B TYR* 3.2 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ALA 3.7 0.4 + - - -
520B PRO* 1.3 73.2 - - - +
522B HIS* 1.3 63.7 + - + +
524B TYR* 3.2 3.5 + - - +
525B LYS* 3.1 32.3 + - - +
551B TYR* 4.4 22.6 - - + +
552B ASP* 3.3 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B TYR* 2.7 32.3 + + - +
520B PRO* 3.8 19.1 - - + +
521B ALA* 1.3 76.2 - - + +
523B VAL* 1.3 89.8 + - + +
525B LYS* 3.4 2.3 + - - +
526B ARG* 3.1 28.1 + - - +
622B GLU* 3.2 44.0 + - + +
656B PHE* 3.5 33.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B ALA 4.2 10.3 - - - +
486B ASN* 4.3 12.3 - - - +
487B TYR* 3.8 26.6 - - + -
490B MET* 4.9 0.2 - - - +
519B ALA* 3.6 19.7 - - + -
520B PRO* 3.2 21.8 + - + +
522B HIS* 1.3 100.9 + - + +
524B TYR* 1.3 64.4 + - - +
526B ARG* 3.3 2.1 + - - +
527B TRP* 3.0 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B ILE* 4.8 0.2 - - + -
513B GLY* 4.0 15.7 - - - -
519B ALA* 4.1 4.2 - - + +
520B PRO 3.2 4.2 + - - +
521B ALA 3.3 8.7 - - - +
523B VAL* 1.3 80.9 - - - +
525B LYS* 1.3 64.3 + - - +
527B TRP* 3.4 6.9 + - - +
528B CYS* 3.1 44.8 + - - -
539B LEU* 3.6 18.8 - - + +
546B ARG* 2.9 28.3 + - - -
548B PRO* 3.5 19.7 - - + +
551B TYR* 3.3 58.6 - + + -
555B SER* 3.8 32.5 - - - -
559B VAL* 3.9 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ALA* 3.1 30.0 + - - +
522B HIS* 3.8 1.9 - - - +
523B VAL 3.3 0.2 - - - -
524B TYR* 1.3 79.4 - - + +
526B ARG* 1.3 65.0 + - - +
528B CYS* 2.8 24.1 + - - +
529B ALA* 3.4 4.9 + - - +
552B ASP* 3.0 18.6 + - - +
554B GLU* 2.7 32.6 + - - -
555B SER* 3.5 26.9 - - - +
558B VAL* 3.6 28.2 - - + +
656B PHE* 3.4 44.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B TYR* 3.6 20.0 - - + +
490B MET* 4.3 4.9 - - + +
522B HIS 3.1 16.0 + - - +
523B VAL 3.7 3.4 - - - +
525B LYS* 1.3 77.8 - - - +
527B TRP* 1.3 63.5 + - - +
528B CYS 3.1 0.9 + - - -
529B ALA* 3.3 14.5 + - - +
530B PHE* 3.4 11.4 + - - +
618B PRO* 5.7 0.9 - - - +
619B VAL* 3.4 42.5 + - + +
621B THR 3.3 11.0 + - - +
622B GLU 3.4 11.3 + - - -
623B ALA 4.0 1.0 - - - -
624B GLY* 3.0 20.0 - - - -
654B HIS 3.0 20.8 + - - -
655B GLY* 2.8 30.9 + - - -
656B PHE* 3.5 25.4 - - - +
658B SER 3.8 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B CYS* 3.7 19.5 - - - -
484B TYR 3.3 28.0 - - - -
486B ASN 3.6 19.1 - - - -
489B SER 4.2 1.6 - - - -
490B MET* 3.6 48.8 - - + -
493B SER* 4.3 5.6 - - - -
510B HIS* 3.0 34.0 + + - -
511B ASP 3.3 18.2 + - - -
512B ILE* 3.6 16.1 - - - +
513B GLY* 3.3 22.2 - - - +
514B GLY* 3.9 5.8 - - - -
523B VAL* 3.0 26.3 + - + +
524B TYR 3.7 3.4 - - - +
526B ARG* 1.3 76.1 - - - +
528B CYS* 1.3 56.8 + - - +
530B PHE* 3.6 2.3 + + - +
531B GLY* 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B ILE* 3.7 20.2 - - - -
524B TYR* 3.1 45.9 + - - -
525B LYS 2.8 14.3 + - - +
527B TRP* 1.3 75.3 - - - +
529B ALA* 1.3 63.0 + - - +
531B GLY* 3.2 0.7 + - - -
532B LEU* 2.8 37.9 + - + +
539B LEU* 5.0 1.3 - - - -
558B VAL* 3.6 16.8 - - + -
559B VAL* 3.7 20.4 - - + +
562B PHE* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LYS 3.4 4.0 + - - +
526B ARG* 3.3 11.0 + - - +
528B CYS* 1.3 77.4 - - - +
530B PHE* 1.3 65.6 + - - +
532B LEU* 3.3 1.2 + - - +
533B LEU* 2.9 30.4 + - - +
562B PHE* 3.5 40.9 - - + -
656B PHE 5.6 0.9 - - - +
658B SER 5.7 0.7 - - - +
659B LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B MET* 3.9 41.3 - - + -
493B SER* 5.3 0.7 - - - -
494B LEU* 3.6 43.3 - - + -
508B TRP* 4.2 6.5 - + - -
510B HIS* 3.3 28.3 - + - -
526B ARG 3.4 9.4 + - - +
527B TRP* 3.7 7.6 - + - +
529B ALA* 1.3 79.1 - - - +
531B GLY* 1.3 61.3 - - - +
533B LEU* 3.0 16.9 + - - -
534B SER* 2.9 29.2 + - - -
588B MET* 4.0 4.9 - - + -
608B TYR* 3.6 16.8 - + - -
618B PRO* 4.0 27.1 - - + -
620B PHE* 5.6 0.9 - + - -
659B LEU* 4.7 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B HIS* 3.5 18.8 + - - -
512B ILE* 3.8 13.5 - - - -
527B TRP 2.8 20.2 + - - -
528B CYS 3.2 3.3 + - - -
530B PHE* 1.3 74.6 - - - +
532B LEU* 1.3 53.5 + - - +
534B SER* 3.4 13.5 + - - -
536B HIS 4.2 0.3 - - - +
537B SER* 2.5 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 4.3 16.6 - - + +
512B ILE* 3.8 20.2 - - + -
528B CYS* 2.8 31.6 + - + +
529B ALA 4.0 0.9 - - - +
531B GLY* 1.3 71.6 - - - -
533B LEU* 1.3 61.5 + - + +
534B SER 3.2 5.1 + - - -
537B SER* 3.3 15.0 - - - +
559B VAL* 5.2 6.1 - - + +
562B PHE* 3.6 36.1 - - + +
563B THR* 3.7 31.2 - - + +
566B LYS* 3.1 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ALA 2.9 29.0 + - - +
530B PHE 3.0 8.4 + - - +
532B LEU* 1.3 81.2 - - + +
534B SER* 1.3 55.1 + - - -
562B PHE* 4.3 12.8 - - + -
565B LEU* 4.6 11.0 - - + -
566B LYS* 6.1 1.3 - - + -
569B MET* 4.4 21.1 - - + -
608B TYR* 2.8 31.1 + - - +
610B LEU* 3.7 33.2 - - + +
616B VAL* 4.2 15.7 - - + -
659B LEU* 4.1 28.9 - - + -
661B VAL* 4.5 11.7 - - + -
----------------------------------------------------------
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