Contacts of the helix formed by residues 520 - 533 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D ALA 4.1 6.7 - - - +
518D THR 3.8 6.3 - - - +
519D ALA* 1.3 89.6 - - + +
521D ALA* 1.3 66.6 + - - +
522D HIS* 3.7 23.3 - - + +
523D VAL* 3.1 29.1 + - + -
524D TYR* 3.1 16.6 + - - +
551D TYR* 3.8 0.4 - - + -
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Residues in contact with ALA 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D PRO* 1.3 72.3 - - - +
522D HIS* 1.3 59.3 + - + +
524D TYR* 3.2 4.0 + - - +
525D LYS* 2.8 38.6 + - - +
551D TYR* 3.4 31.6 - - + +
552D ASP* 3.7 23.3 - - - +
555D SER* 4.6 0.7 - - - +
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Residues in contact with HIS 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D TYR* 2.8 27.4 + + - +
520D PRO* 3.7 21.4 - - + +
521D ALA* 1.3 78.8 - - + +
523D VAL* 1.3 85.5 + - + +
525D LYS* 3.2 3.8 + - - +
526D ARG* 3.0 27.5 + - - +
622D GLU* 3.2 47.7 + - + +
656D PHE* 3.5 32.5 - - + -
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Residues in contact with VAL 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D ALA 4.0 22.4 - - - +
486D ASN* 4.1 9.9 - - - +
487D TYR* 3.5 29.5 - - + -
490D MET* 4.9 0.2 - - - +
519D ALA* 4.1 7.0 - - + -
520D PRO* 3.1 27.8 + - + +
522D HIS* 1.3 98.2 + - + +
524D TYR* 1.3 63.7 + - - +
526D ARG* 3.4 2.1 + - - +
527D TRP* 3.1 43.7 + - + +
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Residues in contact with TYR 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D ILE* 4.2 17.3 - - + -
513D GLY* 4.0 18.4 - - - -
519D ALA* 4.6 2.4 - - + +
520D PRO 3.1 7.4 + - - +
521D ALA 3.3 7.6 - - - +
523D VAL* 1.3 79.5 - - - +
525D LYS* 1.3 63.2 + - - +
527D TRP* 3.5 6.5 + - - +
528D CYS* 3.1 45.1 + - - -
539D LEU* 3.3 22.8 - - + +
546D ARG* 5.8 11.6 - - - -
547D VAL 5.1 0.6 - - - -
548D PRO* 3.6 23.1 - - + +
551D TYR* 3.5 49.4 - + + +
555D SER* 3.9 25.6 - - - -
559D VAL* 4.2 4.1 - - + +
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Residues in contact with LYS 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D ALA* 2.8 28.3 + - - +
522D HIS 3.2 1.0 + - - +
524D TYR* 1.3 74.1 - - - +
526D ARG* 1.3 65.5 + - - +
528D CYS* 3.1 23.3 + - - +
529D ALA* 3.5 5.4 + - - +
552D ASP* 2.9 23.0 + - - -
554D GLU* 3.2 17.2 + - + -
555D SER* 3.3 33.7 - - - +
558D VAL* 3.6 32.5 - - + +
656D PHE* 3.3 49.5 - - + +
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Residues in contact with ARG 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D TYR* 3.5 20.9 - - + +
490D MET* 4.3 5.0 - - + +
522D HIS 3.0 20.0 + - - +
523D VAL 3.8 4.3 - - - +
525D LYS* 1.3 76.2 - - - +
527D TRP* 1.3 61.8 + - - +
529D ALA* 3.4 8.3 + - - +
530D PHE* 3.4 19.4 + - - +
618D PRO* 5.4 2.1 - - - +
619D VAL* 3.5 45.7 + - - +
621D THR 3.6 10.6 + - - +
622D GLU 3.8 7.1 + - - -
623D ALA 4.4 0.6 - - - -
624D GLY* 3.2 17.4 - - - +
654D HIS 2.8 24.0 + - - -
655D GLY* 3.0 29.1 + - - -
656D PHE* 3.6 26.8 - - - +
658D SER 3.7 10.5 + - - -
659D LEU* 5.8 0.4 - - - +
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Residues in contact with TRP 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D CYS* 3.5 28.3 - - + -
484D TYR 3.3 26.9 - - - -
486D ASN 3.6 19.5 - - - -
489D SER 4.0 2.9 - - - -
490D MET* 3.5 42.8 - - + -
493D SER* 4.6 7.2 - - - -
510D HIS* 3.6 19.8 + + - -
511D ASP 3.4 14.5 + - - -
512D ILE* 4.0 5.6 - - - +
513D GLY* 3.6 33.2 - - - +
514D GLY* 4.5 1.1 - - - -
523D VAL* 3.1 29.2 + - + +
524D TYR 3.7 4.9 - - - +
525D LYS 3.2 0.2 - - - -
526D ARG* 1.3 74.1 - - - +
528D CYS* 1.3 60.5 + - - +
530D PHE* 3.4 13.4 + + - -
531D GLY* 2.8 26.7 + - - -
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Residues in contact with CYS 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D ILE* 3.4 25.1 - - + -
524D TYR* 3.1 39.5 + - - -
525D LYS* 3.1 12.6 + - - +
527D TRP* 1.3 75.5 - - - +
529D ALA* 1.3 61.9 + - - +
531D GLY* 3.4 0.3 + - - -
532D LEU* 3.1 33.3 + - + +
539D LEU* 4.7 0.2 - - - -
555D SER 5.1 0.4 - - - -
558D VAL* 3.7 15.5 - - + +
559D VAL* 3.5 32.3 - - + +
562D PHE* 4.8 1.3 - - - -
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Residues in contact with ALA 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D LYS 3.5 4.1 + - - +
526D ARG* 3.4 11.1 + - - +
527D TRP 3.3 0.8 - - - -
528D CYS* 1.3 77.5 - - - +
530D PHE* 1.3 65.1 + - - +
532D LEU* 3.2 2.9 + - - +
533D LEU* 3.0 30.0 + - - +
562D PHE* 3.7 43.4 - - + -
656D PHE 5.7 0.4 - - - +
658D SER 5.9 0.4 - - - +
659D LEU* 4.1 19.3 - - + -
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Residues in contact with PHE 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D MET* 3.8 39.0 - - + -
493D SER* 4.7 2.2 - - - -
494D LEU* 3.8 44.2 - - + -
508D TRP* 4.2 8.5 - + - -
510D HIS* 3.3 33.0 - + - -
526D ARG 3.4 9.7 + - - +
527D TRP* 3.4 13.8 + + - +
529D ALA* 1.3 79.4 - - - +
531D GLY* 1.3 59.7 + - - +
533D LEU* 3.5 9.0 + - - +
534D SER* 2.8 25.6 + - - -
588D MET* 4.7 0.9 - - + -
608D TYR* 3.8 16.8 - + - -
618D PRO* 3.9 29.8 - - + -
620D PHE* 5.7 0.9 - + - -
659D LEU* 4.9 2.1 - - - +
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Residues in contact with GLY 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D HIS* 3.4 19.9 + - - -
512D ILE* 4.2 12.6 - - - -
527D TRP 2.8 19.9 + - - -
528D CYS 3.8 1.6 - - - -
529D ALA 3.2 0.2 - - - -
530D PHE* 1.3 74.9 - - - +
532D LEU* 1.3 53.6 + - - +
534D SER* 3.3 12.6 - - - -
537D SER* 2.4 33.4 + - - -
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Residues in contact with LEU 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D GLY 6.0 0.2 - - - -
271D LEU* 4.6 14.1 - - + +
512D ILE* 3.5 22.2 - - + -
528D CYS* 3.1 32.0 + - + +
529D ALA 4.0 1.1 - - - +
531D GLY* 1.3 71.9 - - - +
533D LEU* 1.3 61.0 + - + +
534D SER 3.0 10.9 + - - +
537D SER* 3.4 13.2 - - - +
559D VAL* 5.1 6.3 - - + +
562D PHE* 3.5 43.7 - - + +
563D THR* 3.9 23.8 - - + +
566D LYS* 3.0 42.2 - - + +
573D LEU* 5.8 0.2 - - - +
610D LEU* 5.5 0.2 - - - +
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Residues in contact with LEU 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529D ALA 3.0 20.5 + - - +
530D PHE 3.6 0.4 - - - +
531D GLY 3.3 0.4 - - - -
532D LEU* 1.3 81.6 - - + +
534D SER* 1.3 58.0 + - - +
562D PHE* 4.5 10.3 - - + +
565D LEU* 4.4 9.4 - - + -
566D LYS* 5.5 0.4 - - + -
569D MET* 3.6 32.3 - - + -
608D TYR* 2.5 43.5 + - - +
610D LEU* 3.7 22.8 - - + +
616D VAL* 4.3 9.9 - - + -
659D LEU* 4.0 33.7 - - + -
661D VAL* 4.1 17.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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