Contacts of the helix formed by residues 552 - 569 (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 ASP 552 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C ALA* 3.5 13.7 - - + +
525C LYS* 3.3 18.4 + - - -
548C PRO 3.5 10.8 + - - +
549C TRP* 4.1 12.5 + - - -
551C TYR* 1.3 84.3 - - - +
553C ASP* 1.3 67.2 + - - +
554C GLU* 3.1 7.8 + - - +
555C SER* 2.6 47.4 + - - -
556C CYS* 3.9 2.4 + - - -
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Residues in contact with ASP 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552C ASP* 1.3 76.1 - - - +
554C GLU* 1.3 65.1 + - - +
556C CYS* 3.1 24.6 + - - +
557C ASP* 3.7 8.2 + - - +
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Residues in contact with GLU 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C LYS* 2.9 26.8 + - - +
552C ASP* 3.1 5.5 + - - +
553C ASP* 1.3 75.9 - - - +
555C SER* 1.3 58.6 + - - +
557C ASP* 2.6 39.4 + - + +
558C VAL* 2.8 21.3 + - + +
656C PHE* 3.4 30.5 + - - +
657C LEU* 5.2 5.0 - - + +
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Residues in contact with SER 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C TYR* 3.8 16.6 - - - -
525C LYS* 3.0 28.3 - - - +
548C PRO* 3.5 22.9 - - - -
551C TYR* 3.6 12.0 - - - +
552C ASP* 2.6 30.4 + - - -
553C ASP 3.2 0.4 - - - -
554C GLU* 1.3 71.9 - - - +
556C CYS* 1.3 56.0 + - - +
558C VAL* 3.3 2.7 + - - +
559C VAL* 3.0 34.3 + - - +
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Residues in contact with CYS 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ARG* 3.8 26.0 - - - -
298C LEU* 3.5 14.4 - - + +
548C PRO* 3.8 10.3 - - - -
549C TRP* 3.6 35.7 - - - -
552C ASP 4.2 2.2 - - - -
553C ASP* 3.1 14.4 + - - +
554C GLU 3.0 0.4 - - - -
555C SER* 1.3 79.7 - - - +
557C ASP* 1.3 63.1 + - - +
559C VAL* 4.0 1.0 - - - +
560C ARG* 3.1 34.9 + - - +
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Residues in contact with ASP 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C ASP* 4.1 7.0 - - - +
554C GLU* 2.6 27.8 + - + +
556C CYS* 1.3 71.3 - - - +
558C VAL* 1.3 58.7 + - - +
560C ARG* 2.6 35.1 + - - +
561C PHE* 2.9 32.9 + - - +
657C LEU* 4.2 15.7 - - + +
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Residues in contact with VAL 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C LYS* 3.3 47.3 - - + +
528C CYS* 3.8 11.4 - - + -
554C GLU* 2.8 16.0 + - + +
555C SER* 3.6 7.4 - - - +
557C ASP* 1.3 78.0 - - - +
559C VAL* 1.3 63.7 + - - +
561C PHE* 3.4 0.3 + - - +
562C PHE* 3.1 47.2 + - + -
656C PHE* 3.2 27.1 - - + +
657C LEU* 3.8 14.6 - - + -
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Residues in contact with VAL 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 4.3 17.3 - - + -
293C MET* 5.0 1.6 - - + -
298C LEU* 4.9 12.3 - - + -
524C TYR* 3.9 4.7 - - - +
528C CYS* 3.7 29.4 - - + -
532C LEU* 5.0 4.9 - - + +
539C LEU* 5.1 5.4 - - + -
548C PRO* 3.8 27.8 - - + -
555C SER 3.0 21.3 + - - +
556C CYS 4.0 3.8 - - - +
558C VAL* 1.3 76.1 - - - +
560C ARG* 1.3 57.7 + - - +
562C PHE* 4.5 2.1 - - - +
563C THR* 2.5 47.7 + - - +
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Residues in contact with ARG 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ARG* 2.4 35.5 + - - +
297C ASN* 3.1 29.5 - - - +
298C LEU* 3.2 22.0 - - + +
299C PRO* 4.6 3.4 - - + -
556C CYS* 3.1 21.6 + - - +
557C ASP* 2.6 40.9 + - - +
558C VAL 3.2 0.2 - - - -
559C VAL* 1.3 76.0 - - - +
561C PHE* 1.3 65.6 + - - +
563C THR* 3.4 3.2 + - - -
564C GLN* 3.0 51.1 + - - +
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Residues in contact with PHE 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C ASP 2.9 17.5 + - - +
558C VAL 3.7 2.5 - - - +
560C ARG* 1.3 78.1 - - - +
562C PHE* 1.3 86.1 + + - +
564C GLN* 3.7 12.6 + - - +
565C LEU* 3.0 32.2 + - + +
639C TRP* 3.6 38.8 - + - -
657C LEU* 3.2 46.2 - - + -
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Residues in contact with PHE 562 (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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528C CYS* 4.8 0.7 - - + -
529C ALA* 3.6 33.4 - - + -
532C LEU* 3.6 25.1 - - + +
533C LEU* 4.3 7.7 - - + +
558C VAL* 3.1 42.3 + - + +
559C VAL* 4.5 0.7 - - - +
561C PHE* 1.3 97.2 - + - +
563C THR* 1.3 68.2 + - - +
565C LEU* 3.6 15.3 - - + +
566C LYS* 3.0 25.1 + - - +
639C TRP* 3.9 7.2 - + - -
656C PHE 3.9 10.1 - - - -
657C LEU* 3.5 20.6 - - - -
658C SER 4.4 1.1 - - - -
659C LEU* 3.6 25.4 - - + -
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Residues in contact with THR 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 3.9 15.7 - - + +
299C PRO* 3.8 42.1 + - + +
301C HIS* 4.3 12.8 - - + -
532C LEU* 3.7 17.5 - - + +
559C VAL* 2.5 36.3 + - - +
560C ARG 3.9 2.7 - - - -
562C PHE* 1.3 76.1 - - - +
564C GLN* 1.3 64.6 + - - +
566C LYS* 3.5 2.3 + - - +
567C CYS* 3.1 24.7 + - - -
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Residues in contact with GLN 564 (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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297C ASN 4.8 0.5 - - - +
299C PRO* 4.8 5.6 - - + +
560C ARG* 3.0 43.4 + - + +
561C PHE* 3.7 12.7 + - - +
563C THR* 1.3 75.1 - - - +
565C LEU* 1.3 65.5 + - - +
567C CYS* 3.3 3.8 + - - +
568C ARG* 3.0 27.2 + - - +
675C ASP* 3.3 47.1 + - + +
676C GLN* 4.2 11.4 + - - +
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Residues in contact with LEU 565 (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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533C LEU* 4.3 11.9 - - + -
561C PHE* 3.0 25.2 + - + +
562C PHE* 3.3 19.5 + - + +
564C GLN* 1.3 75.2 - - - +
566C LYS* 1.3 59.6 + - - +
568C ARG* 2.8 28.8 + - + +
569C MET* 2.8 41.2 + - + +
638C LEU* 4.1 14.6 - - + -
639C TRP* 3.4 38.8 - - + -
661C VAL* 5.8 0.2 - - + -
671C LEU* 6.2 4.0 - - + -
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Residues in contact with LYS 566 (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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269C PHE* 3.2 32.8 + - - +
270C GLY 4.5 1.3 + - - +
532C LEU* 2.9 35.9 - - + +
533C LEU* 5.5 2.0 - - + +
534C SER 2.9 23.5 + - - -
535C SER* 3.3 16.2 + - - +
536C HIS* 3.8 0.4 - - - +
537C SER* 2.8 26.1 + - - +
562C PHE 3.0 13.9 + - - +
563C THR 3.9 3.6 - - - +
565C LEU* 1.3 79.6 - - - +
567C CYS* 1.3 64.7 + - - +
569C MET* 3.0 23.2 + - - +
570C MET* 3.3 15.6 + - - +
573C LEU* 3.7 20.5 - - + +
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Residues in contact with CYS 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C GLY* 5.7 2.5 - - - -
301C HIS* 4.2 15.3 - - - -
563C THR* 3.1 23.0 + - - +
564C GLN 3.5 9.0 - - - +
565C LEU 3.1 0.2 - - - -
566C LYS* 1.3 78.7 - - - +
568C ARG* 1.3 58.9 + - - +
570C MET* 3.6 13.6 + - - +
674C ASN 3.4 9.6 - - - +
675C ASP 3.8 9.2 - - - -
676C GLN 4.0 4.0 - - - -
677C ARG* 3.6 39.3 - - - +
678C PRO* 3.9 5.4 - - - -
680C TYR* 2.9 24.8 + - - -
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Residues in contact with ARG 568 (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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564C GLN 3.0 17.4 + - - +
565C LEU* 2.8 15.3 + - + +
567C CYS* 1.3 77.1 - - - +
569C MET* 1.3 58.4 + - + +
570C MET 3.2 1.3 - - - -
571C PRO* 3.2 5.2 - - - +
671C LEU* 3.3 39.0 - - + +
672C GLY 2.7 53.4 + - - +
673C ASN* 4.9 4.8 - - - +
674C ASN 4.1 1.3 - - - +
675C ASP* 3.7 22.0 - - + +
680C TYR* 3.9 6.5 - - - -
687C ALA* 4.2 15.4 - - - +
689C HIS* 5.4 1.8 + - - -
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Residues in contact with MET 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C LEU* 4.2 13.5 - - + -
565C LEU* 2.8 46.1 + - + +
566C LYS* 3.0 12.2 + - - +
568C ARG* 1.3 77.5 - - + +
570C MET* 1.3 58.2 + - - +
571C PRO* 3.3 3.1 - - - -
572C TYR* 3.1 18.5 + - + +
573C LEU* 2.9 50.7 + - + +
610C LEU* 4.7 10.5 - - + -
614C VAL* 4.6 15.5 - - + -
638C LEU* 3.9 23.1 - - + -
661C VAL* 5.4 0.9 - - + -
669C LEU* 5.9 2.7 - - + -
670C ALA 4.9 3.8 - - - -
671C LEU* 5.2 8.5 - - + +
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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
------------------------------------------------------------
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