Contacts of the helix formed by residues 520 - 533 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C ALA 4.3 5.2 - - - +
518C THR 3.8 4.7 - - - +
519C ALA* 1.3 91.8 - - + +
521C ALA* 1.3 65.8 + - - +
522C HIS* 3.2 32.6 + - + +
523C VAL* 3.3 17.1 + - + -
524C TYR* 3.2 14.2 + - - +
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Residues in contact with ALA 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C ALA 3.6 1.2 + - - -
520C PRO* 1.3 72.0 - - - +
522C HIS* 1.3 58.6 + - - +
524C TYR* 3.3 1.4 + - - +
525C LYS* 2.8 40.0 + - - +
551C TYR* 4.1 26.8 - - + +
552C ASP* 3.5 30.7 - - + +
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Residues in contact with HIS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C TYR* 2.8 29.8 + + - +
520C PRO* 3.3 29.0 - - + +
521C ALA* 1.3 77.6 - - - +
523C VAL* 1.3 79.8 + - + +
525C LYS* 3.0 5.0 + - - +
526C ARG* 2.9 26.9 + - - +
622C GLU* 3.2 49.4 + - + +
656C PHE* 3.6 26.9 - - + -
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Residues in contact with VAL 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C ALA 4.0 9.6 - - - +
486C ASN* 4.2 12.3 - - - -
487C TYR* 3.5 41.4 - - + -
490C MET* 4.7 0.3 - - - +
519C ALA* 3.6 18.8 - - + -
520C PRO* 3.3 19.2 + - + +
522C HIS* 1.3 89.4 - - + +
524C TYR* 1.3 65.5 + - - +
526C ARG* 3.3 1.4 + - - +
527C TRP* 2.9 45.4 + - + +
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Residues in contact with TYR 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C ILE 4.5 1.3 - - - -
513C GLY* 4.1 16.8 - - - -
519C ALA* 4.6 2.2 - - + -
520C PRO 3.2 4.8 + - - +
521C ALA 3.3 6.5 + - - +
523C VAL* 1.3 80.3 - - - +
525C LYS* 1.3 59.5 + - - +
527C TRP* 3.8 5.8 - - - +
528C CYS* 3.0 53.5 + - - -
539C LEU* 3.6 18.2 - - + +
546C ARG* 3.1 29.1 + - - -
548C PRO* 3.4 20.3 - - + +
551C TYR* 3.3 57.2 - + + -
555C SER* 3.8 33.4 - - - -
559C VAL* 3.9 4.5 - - + +
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Residues in contact with LYS 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C ALA* 2.8 32.8 + - - +
522C HIS* 3.2 10.5 - - - +
524C TYR* 1.3 77.1 - - + +
526C ARG* 1.3 68.5 + - - +
528C CYS* 3.1 16.8 + - - +
529C ALA* 3.4 5.4 + - - +
552C ASP* 3.3 17.3 + - - -
554C GLU* 2.9 33.7 + - - +
555C SER* 3.0 38.1 - - - +
558C VAL* 3.3 35.4 - - + +
656C PHE* 3.2 28.4 - - + +
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Residues in contact with ARG 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C TYR* 3.5 21.3 - - + +
490C MET* 4.2 5.2 - - + +
522C HIS 2.9 15.3 + - - +
523C VAL 3.9 2.9 - - - +
525C LYS* 1.3 74.7 - - - +
527C TRP* 1.3 62.9 + - - +
529C ALA* 3.2 17.0 + - - +
530C PHE* 3.2 12.1 + - - +
618C PRO* 5.6 0.7 - - - +
619C VAL* 3.3 45.6 + - - +
621C THR 3.3 10.0 + - - +
622C GLU 3.2 12.7 + - - -
623C ALA 4.1 0.6 - - - -
624C GLY* 2.9 29.3 - - - -
654C HIS 3.0 11.9 + - - -
655C GLY* 3.3 28.9 + - - -
656C PHE* 3.6 26.7 - - - +
658C SER 3.9 9.5 + - - -
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Residues in contact with TRP 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C CYS* 3.7 22.7 - - - -
484C TYR 3.3 26.7 - - - -
485C ALA* 4.1 0.9 - - - -
486C ASN 3.6 19.3 - - - -
489C SER 4.2 1.6 - - - -
490C MET* 3.6 46.6 - - + -
493C SER* 4.4 7.4 - - - -
510C HIS* 3.4 24.2 + + + -
511C ASP 3.5 12.9 + - - -
512C ILE* 3.7 7.7 - - - +
513C GLY* 3.4 27.1 - - - +
514C GLY* 3.9 11.0 - - - -
523C VAL* 2.9 31.6 + - + +
524C TYR 3.8 2.7 - - - +
526C ARG* 1.3 77.8 - - - +
528C CYS* 1.3 56.4 + - - +
530C PHE* 3.5 11.9 - + - +
531C GLY* 2.8 25.5 + - - -
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Residues in contact with CYS 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C ILE* 3.6 17.9 - - - -
524C TYR* 3.0 54.9 + - - -
525C LYS* 3.1 10.2 + - - +
527C TRP* 1.3 72.9 - - - +
529C ALA* 1.3 60.9 - - - +
531C GLY* 3.4 0.3 + - - -
532C LEU* 2.9 41.0 + - + +
539C LEU* 4.7 1.1 - - - -
558C VAL* 3.8 15.7 - - + -
559C VAL* 3.7 20.9 - - + +
562C PHE* 4.8 1.8 - - + -
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Residues in contact with ALA 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C LYS 3.4 4.3 + - - +
526C ARG* 3.2 11.1 + - - +
528C CYS* 1.3 79.6 - - - +
530C PHE* 1.3 62.4 + - - +
532C LEU* 3.2 2.8 + - - +
533C LEU* 3.0 31.1 + - - +
562C PHE* 3.6 41.6 - - + -
656C PHE 5.7 0.2 - - - +
658C SER 5.9 0.9 - - - +
659C LEU* 4.0 20.2 - - + -
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Residues in contact with PHE 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490C MET* 3.7 42.0 - - + -
493C SER* 5.1 2.0 - - - -
494C LEU* 3.5 44.6 - - + -
508C TRP* 4.3 5.2 - + - -
510C HIS* 3.4 31.4 - + - -
526C ARG 3.2 9.2 + - - +
527C TRP* 3.5 11.2 - + - +
529C ALA* 1.3 78.1 - - - +
531C GLY* 1.3 59.9 + - - +
533C LEU* 3.1 14.2 + - - +
534C SER* 2.9 21.3 + - - -
588C MET* 4.7 3.4 - - - -
608C TYR* 3.7 21.1 - + - -
618C PRO* 3.8 27.8 - - + -
620C PHE* 5.5 0.7 - + - -
659C LEU* 4.9 2.4 - - - +
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Residues in contact with GLY 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510C HIS* 3.7 18.6 - - - -
512C ILE* 4.0 14.4 - - - -
527C TRP 2.8 19.7 + - - -
528C CYS 3.8 1.1 - - - -
530C PHE* 1.3 76.5 - - - +
532C LEU* 1.3 54.5 + - - +
534C SER* 3.4 12.3 - - - -
536C HIS 4.0 0.2 - - - +
537C SER* 2.5 31.9 + - - -
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Residues in contact with LEU 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C GLY 6.0 0.7 - - - +
271C LEU* 4.3 16.6 - - + +
512C ILE* 3.9 19.7 - - + -
528C CYS* 2.9 31.9 + - + +
529C ALA 3.9 2.0 - - - +
531C GLY* 1.3 74.2 - - - +
533C LEU* 1.3 59.9 + - + +
534C SER 3.2 4.9 + - - +
537C SER* 3.6 8.7 - - - +
559C VAL* 5.2 5.8 - - + +
562C PHE* 3.6 35.9 - - + +
563C THR* 3.7 30.3 - - + +
566C LYS* 2.9 51.3 - - + +
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Residues in contact with LEU 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C ALA 3.0 21.7 + - - +
530C PHE 3.1 5.8 + - - +
532C LEU* 1.3 82.7 - - + +
534C SER* 1.3 55.0 + - - +
562C PHE* 4.3 11.4 - - + +
565C LEU* 4.3 12.1 - - + -
566C LYS* 5.5 3.4 - - + +
569C MET* 4.2 23.6 - - + -
608C TYR* 2.6 35.5 + - - +
610C LEU* 3.4 34.1 - - + +
616C VAL* 4.4 10.5 - - + -
659C LEU* 4.0 33.2 - - + -
661C VAL* 4.4 13.9 - - + -
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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