Contacts of the helix formed by residues 565 - 581 (chain C) in PDB entry 3RCW
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 THR 565 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566C PRO* 1.3 72.8 - - - +
567C LEU* 3.4 8.6 + - - +
568C THR* 2.7 33.9 + - - +
569C VAL* 3.6 24.1 + - - +
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Residues in contact with PRO 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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565C THR* 1.3 86.9 - - - +
567C LEU* 1.3 66.1 + - - +
569C VAL* 3.4 7.0 + - + +
570C LEU* 3.0 23.6 + - - +
673C ILE* 4.7 28.7 - - + +
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Residues in contact with LEU 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C THR* 3.4 8.2 + - - +
566C PRO* 1.3 78.5 - - - +
568C THR* 1.3 54.4 + - - +
570C LEU* 3.1 9.5 + - + +
571C LEU* 2.7 55.2 + - + +
621C TYR 3.3 26.5 - - - +
622C LYS 3.6 20.0 - - - +
623C ASN* 3.9 4.7 - - - -
624C LEU* 4.3 18.6 - - + +
670C VAL* 5.2 11.4 - - + -
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Residues in contact with THR 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C THR* 2.7 30.0 + - - +
566C PRO 3.2 0.6 - - - -
567C LEU* 1.3 76.1 - - - +
569C VAL* 1.3 66.7 + - - +
571C LEU* 4.4 0.8 - - - +
572C ARG* 3.1 44.7 + - - +
616C LEU* 4.2 32.7 - - + +
617C GLU* 5.6 0.2 - - - +
619C GLN* 5.8 6.7 - - + +
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Residues in contact with VAL 569 (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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565C THR 3.6 15.0 + - - +
566C PRO* 3.4 8.3 + - + +
568C THR* 1.3 77.7 - - - +
570C LEU* 1.3 65.0 + - - +
572C ARG* 3.8 14.5 - - + +
573C SER* 3.5 21.6 + - - +
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Residues in contact with LEU 570 (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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566C PRO 3.0 14.4 + - - +
567C LEU* 3.3 13.5 - - + +
569C VAL* 1.3 77.9 - - - +
571C LEU* 1.3 68.3 + - + +
573C SER* 3.1 8.5 + - - -
574C VAL* 3.1 36.9 + - + +
624C LEU* 6.1 1.1 - - + -
666C ALA* 4.3 8.7 - - + +
669C GLU* 4.2 27.8 - - + -
670C VAL* 3.7 29.4 - - + -
673C ILE* 4.3 15.3 - - + -
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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
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567C LEU* 2.7 41.5 + - + +
568C THR* 5.5 0.2 - - - -
570C LEU* 1.3 77.9 - - + +
572C ARG* 1.3 57.0 + - - +
574C VAL* 3.6 8.3 - - + +
575C LEU* 2.8 31.5 + - - +
616C LEU* 3.6 25.4 - - + +
621C TYR* 3.8 29.6 - - + -
623C ASN 4.6 1.8 - - - +
624C LEU* 4.1 19.5 - - + -
627C PHE* 3.6 44.7 - - + -
666C ALA* 6.1 0.2 - - + -
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Residues in contact with ARG 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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568C THR* 3.1 35.6 + - - +
569C VAL* 3.8 14.5 - - - +
570C LEU 3.2 0.2 - - - -
571C LEU* 1.3 77.2 - - - +
573C SER* 1.3 60.3 + - - +
575C LEU* 3.9 1.9 - - - +
576C ASP* 3.0 33.8 + - - +
613C ARG* 4.1 7.4 + - - +
616C LEU* 3.6 19.9 - - + +
617C GLU* 2.6 37.1 + - - +
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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
----------------------------------------------------------
569C VAL* 3.5 11.6 + - - +
570C LEU* 3.1 11.0 + - - -
572C ARG* 1.3 77.1 - - - +
574C VAL* 1.3 67.7 + - - +
576C ASP* 3.1 12.6 + - - +
577C GLN* 2.9 36.4 + - - +
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Residues in contact with VAL 574 (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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570C LEU* 3.1 26.4 + - + +
571C LEU* 3.6 14.1 - - + +
573C SER* 1.3 76.3 - - - +
575C LEU* 1.3 56.2 + - - +
577C GLN* 3.1 7.4 + - - +
578C LEU* 2.9 28.6 + - + +
624C LEU* 5.6 0.2 - - + -
627C PHE* 3.4 26.5 - - + -
662C VAL* 4.0 17.4 - - + +
663C LEU* 3.7 19.7 - - + -
666C ALA* 3.6 27.8 - - + -
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Residues in contact with LEU 575 (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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571C LEU 2.8 18.4 + - - +
572C ARG 3.9 3.8 - - - +
574C VAL* 1.3 71.8 - - - +
576C ASP* 1.3 67.5 + - - +
578C LEU* 3.1 5.0 + - + +
579C GLN* 3.1 24.8 + - + +
609C PHE* 3.8 33.9 - - + +
612C MET* 4.2 14.4 - - + -
613C ARG* 3.6 60.1 - - + +
616C LEU* 4.2 9.9 - - + -
627C PHE* 3.8 22.0 - - + -
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Residues in contact with ASP 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 ARG* 3.0 21.9 + - - +
573C SER* 3.4 13.4 + - - +
575C LEU* 1.3 75.7 - - - +
577C GLN* 1.3 60.2 + - + +
579C GLN* 3.2 5.8 + - - +
580C ASP* 3.0 34.7 + - - +
613C ARG* 3.2 31.5 + - - +
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Residues in contact with GLN 577 (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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573C SER* 2.9 23.6 + - - +
574C VAL* 3.6 9.7 - - - +
576C ASP* 1.3 76.7 - - + +
578C LEU* 1.3 64.9 + - - +
580C ASP* 3.5 11.6 + - - +
581C LYS* 3.0 41.1 + - - +
662C VAL* 3.5 27.4 - - + +
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Residues in contact with LEU 578 (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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574C VAL* 2.9 21.9 + - + +
575C LEU* 3.1 7.1 + - + +
577C GLN* 1.3 72.6 - - - +
579C GLN* 1.3 63.6 + - - +
581C LYS* 3.1 20.9 + - - +
582C ASP 3.7 2.6 + - - -
609C PHE* 3.9 22.0 - - + -
612C MET* 4.8 1.1 - - + -
627C PHE* 4.0 31.0 - - + -
631C PHE* 3.6 32.3 - - + -
655C LEU* 3.8 8.2 - - - +
659C GLY* 3.8 34.8 - - - +
662C VAL* 4.0 16.4 - - + -
663C LEU* 4.5 7.4 - - + -
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Residues in contact with GLN 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 LEU* 3.1 17.9 + - + +
576C ASP* 3.5 8.1 - - - +
578C LEU* 1.3 74.8 - - - +
580C ASP* 1.3 58.2 + - - +
582C ASP* 2.8 35.1 + - - +
583C PRO* 3.9 0.9 - - - +
585C ARG* 3.8 34.9 + - - +
588C ALA* 3.9 10.1 + - - +
609C PHE* 3.5 50.5 + - + +
610C ALA* 5.3 1.4 - - - +
613C ARG* 3.1 30.3 - - - +
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Residues in contact with ASP 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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576C ASP* 3.0 21.6 + - - +
577C GLN* 3.7 19.1 + - - +
578C LEU 3.3 0.2 - - - -
579C GLN* 1.3 76.0 - - - +
581C LYS* 1.3 71.1 + - - +
582C ASP 3.2 1.6 + - - -
583C PRO* 3.7 13.8 - - - +
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Residues in contact with LYS 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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577C GLN* 3.0 42.2 + - - +
578C LEU* 3.1 10.9 + - - +
579C GLN 3.0 1.8 - - - -
580C ASP* 1.3 89.5 + - + +
582C ASP* 1.3 57.9 + - - +
583C PRO* 3.4 8.5 - - - +
655C LEU* 3.6 21.6 - - + +
658C GLN* 3.7 52.2 + - + +
659C GLY* 4.9 0.7 - - - +
662C VAL* 4.4 14.3 - - + +
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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