Contacts of the helix formed by residues 520 - 533 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A ALA 4.3 6.7 - - - +
518A THR 3.8 4.0 - - - +
519A ALA* 1.3 90.8 - - + +
521A ALA* 1.3 67.0 + - - +
522A HIS* 3.7 23.6 - - + +
523A VAL* 3.1 34.3 + - + -
524A TYR* 3.2 7.4 + - - +
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Residues in contact with ALA 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A ALA 3.6 1.2 + - - -
520A PRO* 1.3 72.2 - - - +
522A HIS* 1.3 64.5 + - + +
524A TYR* 3.2 3.3 + - - +
525A LYS* 2.9 32.4 + - - +
551A TYR* 4.2 24.7 - - + +
552A ASP* 3.5 28.7 - - + +
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Residues in contact with HIS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A TYR* 2.8 28.5 + + - +
520A PRO* 3.7 21.2 - - + +
521A ALA* 1.3 78.1 - - - +
523A VAL* 1.3 85.7 + - + +
525A LYS* 3.2 5.7 + - - +
526A ARG* 3.0 27.5 + - - +
622A GLU* 3.2 46.2 + - + +
656A PHE* 3.7 31.8 - - + -
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Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASN* 4.3 18.2 - - - +
487A TYR* 3.5 41.6 - - + +
490A MET* 5.0 0.2 - - - +
519A ALA* 3.8 15.9 - - + -
520A PRO* 3.1 22.7 + - + +
522A HIS* 1.3 90.9 + - + +
524A TYR* 1.3 66.3 + - - +
525A LYS 3.1 0.3 + - - -
526A ARG* 3.2 3.3 + - - +
527A TRP* 3.0 43.0 + - + +
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Residues in contact with TYR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A ILE* 4.6 0.4 - - + +
513A GLY* 4.1 15.3 - - - -
519A ALA* 4.2 4.2 - - + +
520A PRO 3.2 4.3 + - - +
521A ALA 3.4 6.7 - - - +
523A VAL* 1.3 81.2 - - - +
525A LYS* 1.3 58.3 + - - +
527A TRP* 3.4 6.3 + - - +
528A CYS* 3.0 53.5 + - - -
539A LEU* 3.6 13.7 - - + +
546A ARG* 2.7 29.7 + - - -
548A PRO* 3.2 23.2 - - + +
551A TYR* 3.3 58.8 - + + -
555A SER* 3.7 36.1 - - - -
559A VAL* 3.9 2.3 - - + +
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Residues in contact with LYS 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ALA* 2.9 33.8 + - - +
522A HIS* 3.3 9.5 - - - +
524A TYR* 1.3 76.9 - - - +
526A ARG* 1.3 67.3 + - - +
528A CYS* 3.1 17.7 + - - +
529A ALA* 3.5 5.2 + - - +
552A ASP* 3.6 15.1 + - - -
554A GLU* 3.3 23.8 + - - -
555A SER* 3.2 40.2 - - - +
558A VAL* 3.4 34.9 - - + +
656A PHE* 3.5 37.6 - - + +
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Residues in contact with ARG 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A TYR* 3.5 18.8 - - + +
490A MET* 4.4 4.2 - - + +
522A HIS 3.0 15.5 + - - +
523A VAL 3.8 3.4 - - - +
525A LYS* 1.3 75.2 - - - +
527A TRP* 1.3 62.0 + - - +
529A ALA* 3.2 17.6 + - - +
530A PHE* 3.3 12.0 + - - +
618A PRO* 5.4 2.4 - - - +
619A VAL* 3.4 48.6 + - - +
621A THR 3.7 4.2 + - - +
622A GLU 4.0 3.6 + - - -
623A ALA 4.2 1.0 + - - -
624A GLY* 3.0 21.2 - - - +
654A HIS 2.7 22.8 + - - -
655A GLY* 2.9 30.3 + - - -
656A PHE* 3.5 31.5 - - - +
658A SER 3.8 10.3 + - - -
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Residues in contact with TRP 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A CYS* 3.8 16.6 - - - -
484A TYR 3.5 26.2 - - - -
486A ASN 3.6 11.2 - - - -
489A SER 4.3 1.3 - - - -
490A MET* 3.6 54.2 - - + -
493A SER* 4.4 5.6 - - - -
510A HIS* 3.3 29.0 + + + -
511A ASP 3.3 22.4 + - - -
512A ILE* 3.4 15.7 - - + +
513A GLY* 3.3 21.1 - - - +
514A GLY* 3.7 11.0 - - - -
523A VAL* 3.0 27.0 + - + +
524A TYR 3.7 4.5 - - - +
526A ARG* 1.3 76.2 - - - +
528A CYS* 1.3 54.0 + - - +
530A PHE* 3.3 4.5 + + - +
531A GLY* 2.7 32.1 + - - -
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Residues in contact with CYS 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A ILE* 3.6 21.5 - - - -
524A TYR* 3.0 50.6 + - - -
525A LYS* 3.1 10.0 + - - +
527A TRP* 1.3 78.1 - - - +
529A ALA* 1.3 60.6 + - - +
531A GLY 3.4 0.2 + - - -
532A LEU* 3.0 36.4 + - + +
539A LEU* 4.7 2.0 - - - -
558A VAL* 4.0 15.0 - - + +
559A VAL* 3.7 21.1 - - + +
562A PHE* 4.6 2.2 - - + +
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Residues in contact with ALA 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A LYS 3.5 4.7 + - - +
526A ARG* 3.2 11.9 + - - +
528A CYS* 1.3 74.2 - - - +
530A PHE* 1.3 67.0 + - - +
532A LEU* 3.3 2.3 + - - +
533A LEU* 3.1 30.1 + - - +
562A PHE* 3.6 41.8 - - + -
656A PHE 5.8 0.2 - - - +
658A SER 5.5 1.1 - - - +
659A LEU* 4.0 21.3 - - + -
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Residues in contact with PHE 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A MET* 3.8 38.4 - - + -
493A SER* 5.1 2.2 - - - -
494A LEU* 3.7 43.3 - - + -
508A TRP* 4.1 7.6 - + - -
510A HIS* 3.2 28.5 - + - -
526A ARG 3.3 8.5 + - - +
527A TRP* 3.3 11.8 + + - +
529A ALA* 1.3 77.1 - - - +
531A GLY* 1.3 63.2 + - - +
533A LEU* 3.1 14.3 + - - +
534A SER* 3.0 27.1 + - - -
588A MET* 4.6 2.5 - - + -
608A TYR* 3.7 18.4 - + - -
616A VAL* 5.8 0.2 - - - -
618A PRO* 3.8 28.3 - - + -
620A PHE* 5.8 0.7 - + - -
659A LEU* 4.8 3.2 - - - +
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Residues in contact with GLY 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A HIS* 3.7 19.3 - - - -
512A ILE* 3.8 14.6 - - - -
527A TRP 2.7 20.2 + - - -
528A CYS 3.8 1.3 - - - -
530A PHE* 1.3 74.4 - - - +
532A LEU* 1.3 61.3 + - - +
534A SER* 3.4 14.6 - - - -
537A SER* 2.8 23.1 + - - -
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Residues in contact with LEU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLY 5.9 0.2 - - - -
271A LEU* 4.2 15.9 - - + -
512A ILE* 4.1 15.0 - - + -
528A CYS* 3.0 37.0 + - + +
529A ALA 4.1 1.1 - - - +
531A GLY* 1.3 77.6 - - - +
533A LEU* 1.3 61.9 + - + +
534A SER 3.2 3.5 + - - -
537A SER* 3.6 17.0 - - - +
539A LEU* 6.4 0.2 - - + -
559A VAL* 5.2 6.1 - - + +
562A PHE* 3.7 36.6 - - + +
563A THR* 3.8 28.3 - - + +
566A LYS* 3.1 43.0 - - + +
573A LEU* 5.8 0.3 - - - +
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Residues in contact with LEU 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A ALA 3.1 19.9 + - - +
530A PHE 3.1 6.3 + - - +
532A LEU* 1.3 83.8 - - + +
534A SER* 1.3 53.3 + - - -
562A PHE* 4.2 14.6 - - + +
565A LEU* 4.6 11.0 - - + -
566A LYS* 5.7 3.8 - - + +
569A MET* 4.3 23.3 - - + -
573A LEU* 6.2 0.7 - - + -
608A TYR* 2.6 33.8 + - - +
610A LEU* 3.4 33.0 - - + +
616A VAL* 4.5 12.3 - - + -
659A LEU* 4.1 28.5 - - + -
661A VAL* 4.4 16.6 - - + -
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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