Contacts of the helix formed by residues 608 - 618 (chain G) 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 ASP 608 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587G PHE* 3.7 8.7 - - - +
588G ALA 3.4 2.9 - - - +
589G GLN 3.5 19.7 - - - +
590G PRO* 3.2 36.5 - - + +
606G PRO* 6.1 0.2 - - - +
607G MET* 1.3 79.7 + - - +
609G PHE* 1.3 64.2 + - - +
610G ALA* 2.8 11.4 + - - -
611G THR* 2.5 42.5 + - - -
612G MET* 3.0 22.7 + - - +
634G ILE* 3.7 15.3 - - - -
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Residues in contact with PHE 609 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575G LEU* 3.5 23.7 - - + +
578G LEU* 3.8 35.7 - - + -
579G GLN* 3.5 39.7 - - + +
582G ASP* 4.0 22.0 - - + -
587G PHE* 2.9 44.3 + - + +
588G ALA* 4.1 1.3 - - - -
608G ASP* 1.3 72.6 - - - +
610G ALA* 1.3 59.1 + - - +
612G MET* 3.3 7.2 + - - +
613G ARG* 2.9 26.5 + - - +
631G PHE* 4.1 11.0 - + - -
634G ILE* 3.8 17.5 - - + +
655G LEU* 4.0 19.1 - - + -
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Residues in contact with ALA 610 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579G GLN* 5.7 1.1 - - - +
588G ALA 3.0 20.0 + - - +
589G GLN* 3.7 24.5 - - - +
590G PRO* 5.0 0.9 - - + -
608G ASP* 2.8 9.4 + - - +
609G PHE* 1.3 72.9 - - - +
611G THR* 1.3 59.3 + - - +
613G ARG* 3.2 11.8 + - - +
614G LYS* 3.0 40.4 + - - +
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Residues in contact with THR 611 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600C LEU* 5.7 0.8 - - + +
590G PRO* 4.2 7.8 - - - +
606G PRO 5.6 0.4 - - - +
607G MET* 3.8 24.9 - - + -
608G ASP* 2.5 35.6 + - - -
609G PHE 3.3 0.2 - - - -
610G ALA* 1.3 73.6 - - - +
612G MET* 1.3 65.6 + - - +
614G LYS* 3.3 17.6 + - + +
615G ARG* 3.1 22.4 + - + +
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Residues in contact with MET 612 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575G LEU* 4.1 9.9 - - + -
578G LEU* 5.3 0.2 - - + -
607G MET* 3.9 13.9 - - - -
608G ASP 3.0 19.0 + - - +
609G PHE* 3.3 15.7 + - - +
611G THR* 1.3 75.7 - - - +
613G ARG* 1.3 53.0 + - - +
615G ARG* 3.2 1.9 + - - -
616G LEU* 2.7 35.3 + - - +
621G TYR* 3.5 26.3 - - + +
627G PHE* 3.6 56.1 - - + +
630G ASP* 3.8 1.3 - - + -
631G PHE* 3.8 22.4 - - + +
634G ILE* 3.8 20.2 - - - -
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Residues in contact with ARG 613 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C LYS* 5.1 12.4 - - - +
572G ARG* 4.0 20.2 + - - +
575G LEU* 3.6 30.6 - - + +
576G ASP* 2.5 33.3 + - - +
579G GLN* 2.8 33.7 + - - +
609G PHE 2.9 13.0 + - - +
610G ALA* 3.2 15.0 - - - +
612G MET* 1.3 76.8 - - - +
614G LYS* 1.3 56.9 + - + +
616G LEU* 3.2 6.8 + - + +
617G GLU* 2.8 44.0 + - + +
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Residues in contact with LYS 614 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590C PRO* 5.7 0.2 - - - +
600C LEU* 4.3 10.0 - - + +
604C LYS 3.5 22.8 + - - -
605C HIS* 4.6 10.6 + - - +
606C PRO* 3.9 35.1 - - + +
610G ALA* 3.0 31.2 + - - +
611G THR* 3.3 18.8 + - + +
613G ARG* 1.3 75.6 - - + +
615G ARG* 1.3 63.6 + - - +
617G GLU* 3.2 6.9 + - - +
618G ALA* 2.9 25.3 + - - +
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Residues in contact with ARG 615 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593C LEU* 4.5 12.1 - - + +
600C LEU* 3.7 17.4 - - + +
611G THR* 3.1 14.8 + - + +
612G MET* 3.6 7.0 - - - +
614G LYS* 1.3 76.4 - - - +
616G LEU* 1.3 61.8 + - - +
618G ALA* 3.4 5.4 + - - +
620G GLY* 2.6 59.5 + - - +
621G TYR* 3.5 19.4 - - + +
626G GLU* 3.4 32.3 + - - +
630G ASP* 3.3 31.4 + - - +
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Residues in contact with LEU 616 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568G THR* 4.4 22.5 + - + +
571G LEU* 3.7 31.0 - - + +
572G ARG* 3.5 42.4 - - + +
575G LEU* 4.4 14.4 - - + -
612G MET 2.7 20.4 + - - +
613G ARG* 3.4 9.4 - - + +
614G LYS 3.2 0.2 - - - -
615G ARG* 1.3 73.0 - - - +
617G GLU* 1.3 62.5 + - + +
619G GLN* 2.9 22.4 + - - +
620G GLY 4.8 0.4 - - - +
621G TYR* 3.7 21.5 - - + +
627G PHE* 4.8 1.1 - - + -
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Residues in contact with GLU 617 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589C GLN* 5.7 0.5 - - - +
590C PRO* 3.9 36.9 - - + +
614C LYS* 5.6 9.3 + - - +
572G ARG* 2.9 44.1 + - - +
613G ARG* 2.8 30.0 + - + +
614G LYS* 3.7 6.7 - - - +
616G LEU* 1.3 80.4 - - + +
618G ALA* 1.3 55.8 + - - +
619G GLN* 3.2 10.4 + - - +
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Residues in contact with ALA 618 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590C PRO* 4.5 4.7 - - + +
591C VAL 3.1 24.0 - - - +
592C SER* 3.3 2.1 - - - +
593C LEU* 2.8 47.4 + - + -
599C TYR* 6.2 0.2 - - + -
600C LEU* 4.3 9.0 - - + -
614G LYS 2.9 17.2 + - - +
615G ARG 3.7 6.3 - - - +
616G LEU 3.1 0.6 - - - -
617G GLU* 1.3 73.1 - - - +
619G GLN* 1.3 67.0 + - - +
620G GLY 3.2 1.4 + - - -
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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