Contacts of the helix formed by residues 569 - 584 (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 MET 569 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with MET 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ALA* 3.9 9.2 - - - +
269C PHE* 3.6 42.0 - - + +
566C LYS* 3.3 13.4 + - - +
567C CYS* 3.7 11.4 - - - +
568C ARG 3.2 0.4 - - - -
569C MET* 1.3 76.7 - - - +
571C PRO* 1.3 67.7 - - + +
572C TYR 3.2 0.2 - - - -
573C LEU* 3.8 20.9 - - - -
574C TYR* 2.9 43.2 + - + +
678C PRO* 3.6 28.3 - - + +
682C TRP* 3.4 33.3 - - + +
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Residues in contact with PRO 571 (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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568C ARG 3.2 16.6 - - - +
569C MET 3.4 1.6 - - - -
570C MET* 1.3 95.4 - - + +
572C TYR* 1.3 61.1 + - - +
575C ARG* 3.7 5.7 + - - +
670C ALA* 3.6 25.4 - - + +
671C LEU 4.0 1.1 - - - -
672C GLY* 3.5 24.2 - - - +
680C TYR* 4.0 3.1 - - - +
682C TRP* 3.7 35.0 - - + +
686C THR* 5.2 0.7 - - + -
702C GLU 4.4 2.8 - - - +
703C VAL* 4.7 7.6 - - + -
704C PRO* 3.3 25.5 - - + +
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Residues in contact with TYR 572 (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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569C MET* 3.1 15.2 + - + +
571C PRO* 1.3 78.0 - - - +
573C LEU* 1.3 95.2 + - + +
575C ARG* 3.1 17.2 + - + +
576C GLU* 3.1 38.0 + - + +
610C LEU* 2.4 26.9 + - + -
611C GLY 3.3 2.3 - - - -
613C ASN* 2.9 38.0 + - + -
614C VAL* 3.1 26.0 - - + +
669C LEU* 3.2 29.4 - - + -
670C ALA* 3.6 18.4 + - - +
702C GLU 5.9 0.2 - - - -
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Residues in contact with LEU 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C PHE* 5.7 4.0 - - + -
533C LEU* 6.5 0.2 - - + -
534C SER 5.9 0.9 - - - +
535C SER* 6.5 0.2 - - - -
566C LYS* 3.7 35.9 - - + +
569C MET* 2.9 44.5 + - + +
570C MET* 3.9 14.4 - - - -
572C TYR* 1.3 101.6 - - + +
574C TYR* 1.3 59.5 + - - +
576C GLU* 3.1 8.9 + - + +
577C ALA* 2.9 22.7 + - - +
587C MET* 3.5 23.1 - - + +
610C LEU* 4.4 18.4 - - + -
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Residues in contact with TYR 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LEU* 3.7 19.2 - - + +
264C PRO 2.9 28.6 + - - -
265C PRO* 3.9 2.4 - - - +
266C ALA* 3.5 18.9 + - + -
269C PHE* 3.4 28.3 - + - -
570C MET* 2.9 32.4 + - + +
573C LEU* 1.3 70.3 - - - +
575C ARG* 1.3 63.5 - - - +
577C ALA* 3.3 4.2 + - + +
578C ALA* 3.1 19.9 + - - +
682C TRP* 3.2 30.3 - + + -
704C PRO* 4.2 9.8 - - + +
705C ALA 3.9 6.7 - - - -
706C ALA 3.1 28.4 + - - -
708C GLY* 4.1 10.8 - - - -
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Residues in contact with ARG 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571C PRO 3.7 14.4 + - - +
572C TYR* 3.1 12.0 + - + +
574C TYR* 1.3 78.7 - - - +
576C GLU* 1.3 74.3 + - - +
578C ALA* 3.1 17.8 + - - +
579C ARG* 2.8 49.7 + - - +
702C GLU* 3.2 58.0 + - + +
704C PRO* 4.0 15.0 - - + +
708C GLY 5.1 2.9 + - - -
710C VAL* 4.0 14.4 - - - +
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Residues in contact with GLU 576 (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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572C TYR* 3.5 33.2 - - + +
573C LEU* 3.1 7.8 + - + +
575C ARG* 1.3 82.9 - - - +
577C ALA* 1.3 59.2 + - - +
579C ARG* 2.9 45.2 + - - +
580C ALA* 3.2 7.4 + - - +
585C THR 4.7 1.2 - - - +
587C MET* 4.3 14.8 - - + +
589C ARG* 3.2 7.8 + - - +
611C GLY* 3.2 20.8 - - - -
612C ASP* 2.5 43.3 + - - +
613C ASN* 5.8 0.2 + - - -
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Residues in contact with ALA 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LEU* 4.0 10.0 - - + +
269C PHE* 3.9 15.0 - - + -
507C PHE* 3.6 29.0 - - + -
573C LEU 2.9 12.8 + - - +
574C TYR* 3.5 12.6 - - + +
575C ARG 3.1 0.2 - - - -
576C GLU* 1.3 73.1 - - - +
578C ALA* 1.3 66.4 + - - +
579C ARG 3.0 1.6 - - - -
580C ALA* 2.9 16.0 + - - +
581C ASN* 3.2 9.0 + - - +
587C MET* 3.7 14.6 - - - -
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Residues in contact with ALA 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LEU* 4.0 13.4 - - + +
574C TYR 3.1 13.1 + - - +
575C ARG* 3.1 19.5 + - - +
577C ALA* 1.3 75.4 - - - +
579C ARG* 1.3 57.8 + - - +
581C ASN* 3.2 8.8 + - - +
582C ALA* 3.0 29.5 + - - +
708C GLY* 3.7 32.8 - - - +
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Residues in contact with ARG 579 (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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575C ARG* 2.8 51.1 + - - +
576C GLU* 2.9 27.5 + - - +
577C ALA 3.0 0.2 - - - -
578C ALA* 1.3 76.5 - - - +
580C ALA* 1.3 57.3 + - - +
582C ALA* 4.7 3.6 - - - -
583C ARG* 2.8 38.8 + - + +
584C GLY 3.6 2.3 + - - -
585C THR* 3.8 17.1 + - - +
589C ARG* 3.2 26.7 - - - +
612C ASP* 2.7 29.0 + - - -
702C GLU* 5.0 2.6 + - - -
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Residues in contact with ALA 580 (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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261C PRO* 3.3 13.7 - - - +
506C GLY* 4.1 17.3 - - - +
507C PHE* 3.8 20.6 - - + -
576C GLU 3.2 5.2 + - - +
577C ALA* 2.9 10.6 + - - +
579C ARG* 1.3 78.8 - - - +
581C ASN* 1.3 58.5 + - - +
584C GLY* 3.0 23.4 + - - -
585C THR 2.9 28.4 + - - +
586C PRO* 4.5 0.4 - - + -
587C MET 4.7 1.8 - - - +
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Residues in contact with ASN 581 (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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260C ARG* 3.6 23.7 - - - +
261C PRO 2.7 28.7 + - - +
262C ALA* 3.7 13.4 - - - +
263C LEU* 3.7 27.2 - - + +
507C PHE* 5.1 0.2 - - - -
577C ALA 3.2 9.0 + - - +
578C ALA* 3.5 11.5 - - - +
579C ARG 3.1 0.4 - - - -
580C ALA* 1.3 80.0 - - - +
582C ALA* 1.3 62.1 + - - +
584C GLY 4.6 0.4 - - - -
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Residues in contact with ALA 582 (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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260C ARG* 3.2 25.7 + - - +
578C ALA 3.0 15.7 + - - +
579C ARG* 4.1 3.4 - - - +
581C ASN* 1.3 81.9 - - - +
583C ARG* 1.3 65.6 + - + +
584C GLY 3.7 0.4 - - - -
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Residues in contact with ARG 583 (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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248C LYS* 3.6 35.6 + - - +
249C ALA* 3.6 12.7 - - - +
252C ASP* 3.1 47.5 + - - +
260C ARG* 3.7 11.0 - - - +
579C ARG* 2.8 19.0 + - + +
582C ALA* 1.3 80.4 - - + +
584C GLY* 1.3 62.0 + - - +
585C THR* 3.0 20.5 + - - +
3007C SO4 2.9 33.1 + - - -
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Residues in contact with GLY 584 (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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251C LEU* 4.0 14.6 - - - +
255C THR* 3.5 27.4 + - - +
260C ARG* 4.1 0.8 - - - +
261C PRO* 4.1 7.7 - - - +
501C GLY 5.0 0.9 - - - +
504C GLY 5.2 4.9 - - - +
506C GLY* 5.6 1.3 - - - -
580C ALA* 3.0 21.2 + - - -
581C ASN 4.6 0.2 - - - -
582C ALA 3.7 1.0 - - - -
583C ARG* 1.3 78.3 - - - +
585C THR* 1.3 62.3 + - - +
586C PRO* 3.3 9.4 - - - +
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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
------------------------------------------------------------
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