Contacts of the helix formed by residues 567 - 583 (chain C) in PDB entry 6V3O
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 ARG 567 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536C MET* 4.1 28.6 - - + +
538C THR* 4.5 9.1 - - - +
566C GLU* 1.3 83.9 - - + +
568C LEU* 1.3 66.8 + - - +
569C ALA* 3.2 12.9 - - + +
570C ASP* 3.0 35.3 + - - +
571C LEU* 2.9 22.7 + - - +
603C ASP 6.0 0.4 - - - +
607C ASP* 3.4 27.8 - - + +
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Residues in contact with LEU 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C GLU 4.0 0.4 + - - -
567C ARG* 1.3 70.8 - - - +
569C ALA* 1.3 63.6 + - - +
571C LEU* 3.2 10.6 + - + +
572C GLN* 3.0 44.5 + - - +
604C SER* 4.9 4.2 - - - +
607C ASP* 2.9 18.4 + - - +
608C ALA* 3.8 25.1 - - + -
612C SER* 3.9 7.0 - - - +
613C ALA* 3.9 25.6 - - + +
616C GLN* 3.7 29.2 - - + +
725C THR* 4.5 9.4 - - + +
729C ARG* 5.2 5.6 - - - +
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Residues in contact with ALA 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C ARG* 3.2 12.4 - - + +
568C LEU* 1.3 77.2 - - - +
570C ASP* 1.3 67.8 + - - +
572C GLN* 3.5 13.0 + - - +
573C SER* 2.8 29.8 + - - -
607C ASP* 4.4 1.0 + - - -
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Residues in contact with ASP 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C MET* 5.1 5.0 - - - +
537C ALA 3.6 19.0 - - - +
538C THR* 3.4 35.0 - - - +
565C PHE* 3.9 17.8 - - + -
566C GLU* 4.3 2.6 + - - +
567C ARG* 3.0 46.6 + - - +
569C ALA* 1.3 79.3 - - - +
571C LEU* 1.3 60.9 + - - +
573C SER* 3.8 4.9 - - - +
574C ALA* 3.0 27.9 + - - +
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Residues in contact with LEU 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C PHE* 4.2 24.7 - - + +
567C ARG 2.9 13.2 + - - +
568C LEU* 3.2 11.2 + - + +
570C ASP* 1.3 75.4 - - - +
572C GLN* 1.3 65.2 + - - +
574C ALA* 3.2 19.6 + - + +
575C PRO* 3.5 5.2 - - - +
599C VAL* 4.4 9.2 - - + -
600C GLY 5.2 0.7 - - - +
604C SER* 3.8 26.9 - - - +
613C ALA 4.6 1.8 - - - +
616C GLN* 3.8 24.5 - - + -
617C LEU* 4.2 33.0 - - + +
620C ALA* 3.7 27.8 - - + +
623C GLU* 5.8 0.2 - - - +
624C MET* 6.4 0.2 - - + -
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Residues in contact with GLN 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C LEU* 3.0 37.4 + - - +
569C ALA* 3.8 12.3 - - - +
570C ASP 3.4 0.2 - - - -
571C LEU* 1.3 76.8 - - - +
573C SER* 1.3 60.5 + - - +
575C PRO* 3.5 10.6 - - - +
576C ALA* 5.2 0.7 + - - +
616C GLN* 2.9 39.4 - - - +
619C ARG* 5.2 6.3 - - - +
623C GLU* 4.9 6.4 - - - +
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Residues in contact with SER 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C THR 4.9 7.4 - - - -
569C ALA* 2.8 17.4 + - - +
570C ASP* 3.8 4.9 - - - -
571C LEU 3.2 0.4 - - - -
572C GLN* 1.3 76.4 - - - +
574C ALA* 1.3 64.8 + - - +
575C PRO* 3.4 2.2 - - - -
576C ALA* 3.1 13.5 + - - +
577C SER* 3.0 27.5 + - - -
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Residues in contact with ALA 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C PHE* 3.5 32.3 - - + -
570C ASP 3.0 15.8 + - - +
571C LEU* 3.2 17.5 + - + +
573C SER* 1.3 75.6 - - - +
575C PRO* 1.3 66.5 - - + +
577C SER* 3.2 6.9 + - - -
578C VAL* 3.0 26.3 + - - +
620C ALA* 5.0 3.4 - - + -
624C MET* 4.1 12.1 - - - -
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Residues in contact with PRO 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571C LEU 3.5 6.1 - - - +
572C GLN 3.5 15.0 - - - +
573C SER 3.5 1.1 - - - -
574C ALA* 1.3 93.4 - - + +
576C ALA* 1.3 60.4 + - - +
578C VAL* 3.2 11.8 - - + +
579C GLU* 3.0 24.9 + - - +
620C ALA* 4.2 4.9 - - - +
623C GLU* 3.5 49.4 - - + +
624C MET* 4.0 15.5 - - + +
627C VAL* 4.1 10.6 - - + +
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Residues in contact with ALA 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C GLN 5.2 0.4 + - - +
573C SER* 3.1 15.3 + - - +
575C PRO* 1.3 78.7 - - - +
577C SER* 1.3 58.0 + - - +
579C GLU* 3.4 8.4 + - - +
580C ARG* 2.9 28.6 + - - +
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Residues in contact with SER 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C THR 3.9 13.3 + - - -
539C ALA* 4.2 2.9 - - - -
540C PRO* 3.6 32.0 - - - +
565C PHE* 4.6 12.5 - - - -
573C SER* 3.0 18.0 + - - -
574C ALA* 3.2 9.2 + - - -
576C ALA* 1.3 75.1 - - - +
578C VAL* 1.3 60.3 + - - +
580C ARG* 3.1 3.7 + - - +
581C LEU* 2.9 33.9 + - - +
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Residues in contact with VAL 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C PRO* 5.4 2.5 - - + -
565C PHE* 4.6 11.2 - - + -
574C ALA 3.0 14.8 + - - +
575C PRO* 3.2 20.4 - - + +
577C SER* 1.3 76.6 - - - +
579C GLU* 1.3 57.4 + - - +
581C LEU* 3.4 12.2 + - + +
582C PHE* 2.9 51.8 + - + -
595C GLN* 5.6 3.4 - - + -
597C VAL* 4.3 23.3 - - + -
624C MET* 4.3 19.7 - - + +
627C VAL* 4.1 15.0 - - + -
635C LEU* 6.0 2.0 - - + -
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Residues in contact with GLU 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 PRO 3.0 19.2 + - - +
576C ALA* 3.7 7.4 - - - +
578C VAL* 1.3 75.2 - - - +
580C ARG* 1.3 65.5 + - - +
582C PHE* 3.2 4.2 + - - +
583C SER* 3.0 23.7 + - - -
627C VAL* 3.8 17.0 - - + +
630C ARG* 3.0 43.2 + - - -
631C TYR* 3.4 20.1 + - + +
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Residues in contact with ARG 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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487C GLN* 2.8 30.1 + - - +
491C LEU* 3.8 24.4 - - - +
540C PRO* 3.7 23.1 - - + -
576C ALA 2.9 15.7 + - - +
577C SER* 3.1 8.0 + - - +
579C GLU* 1.3 76.7 - - - +
581C LEU* 1.3 60.8 + - - +
583C SER* 2.8 37.4 + - - -
584C VAL* 3.3 23.9 - - + +
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Residues in contact with LEU 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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540C PRO* 3.7 34.8 - - + +
543C VAL* 4.0 31.9 - - + -
544C LEU* 3.9 26.0 - - + -
563C PRO* 5.8 3.8 - - + -
577C SER* 2.9 21.0 + - - +
578C VAL* 3.7 14.8 - - + +
580C ARG* 1.3 77.1 - - + +
582C PHE* 1.3 64.1 + - + +
584C VAL* 3.1 22.5 + - + +
587C TYR* 3.6 35.9 - - + +
595C GLN* 5.3 3.4 - - - +
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Residues in contact with PHE 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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578C VAL* 2.9 33.4 + - + +
579C GLU 3.2 4.4 + - - +
581C LEU* 1.3 81.3 - - + +
583C SER* 1.3 57.1 + - - +
584C VAL 3.2 0.7 - - - -
587C TYR* 4.5 2.2 - + - -
588C MET* 3.1 31.6 - - - +
591C ILE* 4.0 27.1 - - + -
595C GLN* 3.8 24.0 - - + -
627C VAL* 4.1 15.3 - - + -
628C ALA* 3.9 26.9 - - + -
631C TYR* 3.6 41.5 - - + -
633C VAL* 3.6 22.0 - - + -
635C LEU* 5.5 3.4 - - + -
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Residues in contact with SER 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579C GLU* 3.0 13.3 + - - -
580C ARG* 2.8 40.2 + - - -
582C PHE* 1.3 75.1 - - - +
584C VAL* 1.3 59.9 + - - +
585C ASP 3.9 2.1 + - - -
631C TYR* 3.9 18.4 - - - -
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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
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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