Contacts of the helix formed by residues 565 - 581 (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 THR 565 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564G LEU* 1.3 83.5 - - + +
566G PRO* 1.3 73.4 - - - +
567G LEU* 3.5 8.9 + - - +
568G THR* 3.2 27.6 + - - +
569G VAL* 3.1 27.3 + - - +
619G GLN* 5.0 12.1 - - - +
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Residues in contact with PRO 566 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B ALA* 3.5 27.1 - - + +
564G LEU 4.4 2.2 - - - +
565G THR* 1.3 89.2 - - - +
567G LEU* 1.3 62.4 - - - +
568G THR 3.3 0.2 + - - -
569G VAL* 3.3 4.8 + - + +
570G LEU* 3.1 17.5 + - - +
673G ILE* 4.4 26.0 - - + -
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Residues in contact with LEU 567 (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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1G EDO 5.1 2.7 - - - +
565G THR* 3.4 7.9 + - - +
566G PRO* 1.3 78.3 - - - +
568G THR* 1.3 60.2 + - - +
570G LEU* 3.3 14.7 + - + +
571G LEU* 2.9 59.9 + - + +
621G TYR 3.4 25.8 - - - +
622G LYS 4.1 15.0 - - - +
623G ASN* 4.3 5.4 - - - +
624G LEU* 4.7 10.5 - - - +
670G VAL* 5.0 9.2 - - + -
673G ILE* 6.3 0.4 - - - -
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Residues in contact with THR 568 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564G LEU 4.2 14.7 + - - +
565G THR* 3.2 29.0 + - - +
566G PRO 3.2 0.2 - - - -
567G LEU* 1.3 78.1 - - - +
569G VAL* 1.3 68.6 + - + +
571G LEU* 3.1 1.9 + - - +
572G ARG* 3.0 56.7 + - + +
616G LEU* 4.4 23.0 + - + +
617G GLU* 5.6 0.2 - - - +
619G GLN* 5.3 11.8 + - - +
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Residues in contact with VAL 569 (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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677B GLU* 3.2 38.6 - - + +
678B ALA* 4.4 9.0 - - + +
564G LEU* 5.3 4.7 - - - +
565G THR 3.1 17.7 + - - +
566G PRO* 3.7 7.9 - - + +
568G THR* 1.3 78.9 - - + +
570G LEU* 1.3 63.4 + - - +
572G ARG* 3.4 16.1 - - + +
573G SER* 3.3 23.2 + - - +
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Residues in contact with LEU 570 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B LEU* 3.5 37.5 - - + +
678B ALA* 3.8 13.4 - - + +
566G PRO 3.1 13.2 + - - +
567G LEU* 3.4 17.7 - - + +
568G THR 3.1 0.2 - - - -
569G VAL* 1.3 78.4 - - - +
571G LEU* 1.3 65.2 + - + +
573G SER* 3.1 6.1 + - - -
574G VAL* 3.0 29.6 + - + +
624G LEU* 5.3 0.7 - - + -
666G ALA* 3.9 18.2 - - + +
669G GLU* 4.1 17.3 - - + -
670G VAL* 3.8 28.9 - - + +
673G ILE* 5.0 6.1 - - + -
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Residues in contact with LEU 571 (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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567G LEU* 2.9 51.8 + - + +
568G THR 3.1 0.4 + - - -
570G LEU* 1.3 77.9 - - + +
572G ARG* 1.3 57.4 + - - +
574G VAL* 3.7 5.1 - - + +
575G LEU* 2.7 38.1 + - - +
616G LEU* 3.7 22.9 - - + -
621G TYR* 3.8 23.8 - - + -
623G ASN 4.7 1.8 - - - +
624G LEU* 3.6 31.9 - - + -
627G PHE* 3.7 29.9 - - + -
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Residues in contact with ARG 572 (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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564G LEU 5.6 4.0 - - - +
568G THR* 3.0 40.7 + - + +
569G VAL* 3.4 19.0 - - + +
571G LEU* 1.3 77.3 - - - +
573G SER* 1.3 58.0 + - - +
575G LEU* 3.8 2.4 - - - +
576G ASP* 2.9 38.7 + - - +
613G ARG* 4.9 9.6 - - - +
616G LEU* 3.5 16.0 - - + +
617G GLU* 2.9 37.5 + - - +
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Residues in contact with SER 573 (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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674B GLY 3.7 16.7 + - - -
675B LEU* 3.7 20.4 - - - -
677B GLU* 4.7 10.6 - - - +
569G VAL* 3.3 11.6 + - - +
570G LEU* 3.1 11.0 + - - -
572G ARG* 1.3 74.4 - - - +
574G VAL* 1.3 60.7 + - - +
576G ASP* 3.3 9.2 + - - +
577G GLN* 2.9 34.8 + - - +
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Residues in contact with VAL 574 (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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675B LEU* 3.9 18.8 - - + -
570G LEU* 3.0 24.9 + - + +
571G LEU* 3.7 10.5 - - + +
573G SER* 1.3 75.6 - - - +
575G LEU* 1.3 57.6 + - - +
577G GLN* 2.9 4.5 + - - +
578G LEU* 2.8 33.9 + - + +
627G PHE* 3.5 26.0 - - + -
662G VAL* 4.0 12.6 - - + -
663G LEU* 3.7 19.3 - - + -
666G ALA* 3.6 27.8 - - + -
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Residues in contact with LEU 575 (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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571G LEU 2.7 21.8 + - - +
572G ARG* 3.9 2.9 - - - +
574G VAL* 1.3 74.1 - - - +
576G ASP* 1.3 63.5 + - - +
578G LEU* 3.2 4.6 + - + +
579G GLN* 2.9 29.6 + - + +
609G PHE* 3.5 38.1 - - + +
612G MET* 4.1 15.3 - - + -
613G ARG* 3.6 59.5 - - + +
616G LEU* 4.4 10.5 - - + -
627G PHE* 3.7 21.1 - - + -
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Residues in contact with ASP 576 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572G ARG* 2.9 18.7 + - - +
573G SER* 3.4 11.8 - - - +
575G LEU* 1.3 75.5 - - - +
577G GLN* 1.3 59.2 + - + +
579G GLN* 3.3 4.9 + - - +
580G ASP* 2.8 37.3 + - - +
613G ARG* 2.5 38.0 + - - +
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Residues in contact with GLN 577 (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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671B ASP* 2.8 58.6 + - - +
674B GLY* 3.8 12.9 - - - -
675B LEU* 3.4 25.4 - - - +
573G SER* 2.9 19.5 + - - +
574G VAL 3.4 6.5 - - - +
576G ASP* 1.3 71.8 - - + +
578G LEU* 1.3 67.1 + - - +
580G ASP* 3.0 20.3 + - - +
581G LYS* 3.1 21.8 + - - +
662G VAL* 3.8 21.2 - - + +
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Residues in contact with LEU 578 (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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574G VAL* 2.8 25.3 + - + +
575G LEU* 3.6 5.8 - - + +
577G GLN* 1.3 72.6 - - - +
579G GLN* 1.3 58.4 + - - +
581G LYS* 3.0 27.5 + - - +
582G ASP 3.6 2.9 + - - -
609G PHE* 3.8 19.0 - - + -
612G MET* 5.3 0.2 - - + -
627G PHE* 3.7 32.8 - - + -
631G PHE* 3.6 30.3 - - + -
655G LEU* 3.7 9.5 - - + +
659G GLY* 3.6 38.1 - - - +
662G VAL* 4.1 11.7 - - + -
663G LEU* 4.6 5.2 - - + -
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Residues in contact with GLN 579 (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* 2.9 20.8 + - + +
576G ASP* 3.6 4.9 - - - +
578G LEU* 1.3 72.4 - - - +
580G ASP* 1.3 61.8 + - - +
581G LYS 3.1 1.8 - - - -
582G ASP* 2.9 29.0 + - - +
583G PRO* 4.0 0.5 - - - +
585G ARG* 3.6 37.8 + - - +
588G ALA* 3.9 14.5 + - - +
609G PHE* 3.5 48.0 - - + +
610G ALA* 5.4 0.5 + - - +
613G ARG* 2.8 31.4 + - - -
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Residues in contact with ASP 580 (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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576G ASP* 2.8 25.0 + - - +
577G GLN* 3.0 17.3 + - - +
579G GLN* 1.3 76.9 - - - +
581G LYS* 1.3 66.3 + - + +
582G ASP 3.2 0.7 + - - -
583G PRO* 3.5 13.4 - - - +
585G ARG* 5.2 5.2 + - - +
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Residues in contact with LYS 581 (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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597A PRO 5.6 0.5 - - - +
667B ARG* 5.0 12.3 - - - +
668B ARG* 6.4 0.2 - - - +
671B ASP* 2.9 37.4 + - - -
577G GLN* 3.1 20.5 + - - +
578G LEU* 3.0 14.7 + - - +
580G ASP* 1.3 80.2 - - - +
582G ASP* 1.3 56.1 + - - +
583G PRO* 3.2 10.7 - - - +
655G LEU* 3.9 19.2 - - + +
658G GLN* 3.5 50.3 - - + +
659G GLY* 4.8 1.3 - - - +
662G VAL* 4.4 15.2 - - + +
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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