Contacts of the helix formed by residues 661 - 683 (chain G) in PDB entry 3HR4
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 GLU 661 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549G LYS* 5.0 7.7 + - - -
627G GLY 3.0 19.8 + - - +
628G SER* 3.8 14.5 - - - +
659G GLY 2.9 6.8 + - - -
660G ASP* 1.3 73.4 + - - +
662G LEU* 1.3 65.4 + - + +
664G GLY* 3.7 5.9 + - - -
665G GLN* 4.0 19.6 + - + +
999G FMN 2.9 36.8 + - - -
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Residues in contact with LEU 662 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628G SER* 3.0 28.0 - - - +
629G SER* 2.9 22.0 - - - +
630G MET* 4.2 22.9 - - + +
660G ASP* 3.1 8.9 + - - +
661G GLU* 1.3 84.0 - - + +
663G SER* 1.3 59.8 + - - +
664G GLY 3.2 6.0 + - - -
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Residues in contact with SER 663 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660G ASP* 3.1 29.0 + - - -
662G LEU* 1.3 76.2 - - - +
664G GLY* 1.3 60.4 + - - +
667G ASP* 5.5 2.4 - - - +
668G ALA* 6.2 1.6 - - - -
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Residues in contact with GLY 664 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660G ASP 3.1 5.3 + - - -
661G GLU 3.7 3.9 + - - -
662G LEU 3.2 5.7 + - - -
663G SER* 1.3 81.0 - - - +
665G GLN* 1.3 66.8 + - - -
666G GLU* 3.3 4.7 - - - -
667G ASP* 3.3 7.6 + - - +
668G ALA* 3.1 23.4 + - - +
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Residues in contact with GLN 665 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549G LYS* 3.6 30.0 - - - +
553G LEU* 4.4 9.4 - - + +
624G PHE* 4.5 0.5 - - - -
626G LEU* 3.4 29.8 - - + +
627G GLY 3.7 6.9 + - - -
659G GLY* 3.1 29.4 + - - +
660G ASP 3.1 11.4 + - - +
661G GLU* 4.0 17.0 + - + +
664G GLY* 1.3 72.6 - - - +
666G GLU* 1.3 67.6 + - - +
668G ALA* 3.1 9.9 + - - +
669G PHE* 3.1 13.8 + - - +
999G FMN 3.1 23.2 + - - -
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Residues in contact with GLU 666 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553G LEU* 4.1 18.8 - - + +
556G ASP* 5.6 1.7 - - - +
664G GLY* 4.9 1.8 - - - -
665G GLN* 1.3 80.4 - - - +
667G ASP* 1.3 58.5 + - - +
669G PHE* 3.4 7.6 - - - +
670G ARG* 3.0 67.8 + - - +
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Residues in contact with ASP 667 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663G SER 5.5 2.5 - - - +
664G GLY* 3.3 9.1 + - - +
665G GLN 3.3 0.6 - - - -
666G GLU* 1.3 74.7 - - - +
668G ALA* 1.3 56.1 + - - +
669G PHE 3.0 2.0 - - - -
670G ARG* 3.5 32.3 + - - +
671G SER* 2.6 45.6 + - - +
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Residues in contact with ALA 668 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624G PHE* 3.6 4.3 - - + -
657G GLY* 5.8 0.2 - - - -
658G GLU 3.4 25.6 - - - +
659G GLY* 4.1 7.9 - - - -
660G ASP* 4.3 5.2 - - + +
663G SER* 6.1 1.8 - - - -
664G GLY 3.1 13.8 + - - +
665G GLN 3.6 7.4 - - - +
667G ASP* 1.3 75.9 - - - +
669G PHE* 1.3 56.8 + - - +
671G SER* 3.3 7.8 - - - -
672G TRP* 2.9 27.9 + - - +
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Residues in contact with PHE 669 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553G LEU* 3.0 59.9 - - + -
556G ASP* 4.0 5.2 - - + -
557G LEU* 3.9 19.5 - - + -
589G VAL* 4.5 7.6 - - + -
624G PHE* 3.4 41.4 - + + -
665G GLN 3.1 8.5 + - - +
666G GLU* 3.4 12.1 - - - +
667G ASP 3.0 0.2 - - - -
668G ALA* 1.3 75.0 - - - +
670G ARG* 1.3 61.8 + - + +
671G SER 3.0 1.1 - - - -
672G TRP* 3.0 13.8 + + - +
673G ALA* 2.5 41.9 + - + +
698G TYR* 3.6 29.2 - + - -
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Residues in contact with ARG 670 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666G GLU* 3.0 53.7 + - - +
667G ASP* 3.0 38.3 + - - +
669G PHE* 1.3 79.9 - - + +
671G SER* 1.3 57.3 + - - +
674G VAL* 2.7 40.7 + - + +
698G TYR* 4.1 47.4 + - + +
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Residues in contact with SER 671 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667G ASP* 2.6 30.7 + - - +
668G ALA* 3.3 9.4 - - - -
670G ARG* 1.3 77.9 - - - +
672G TRP* 1.3 56.8 + - - +
674G VAL* 3.8 3.0 - - - +
675G GLN* 2.9 33.7 + - - +
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Residues in contact with TRP 672 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557G LEU* 3.9 24.7 - - + -
587G LEU* 3.9 19.3 - - + -
588G VAL 4.5 5.2 - - - -
589G VAL* 4.5 1.1 - - + -
622G ALA* 3.3 27.8 - - + -
623G VAL 3.7 20.1 + - - +
624G PHE* 3.6 34.1 - + + -
654G THR* 3.2 21.9 - - + +
655G PRO 3.6 11.5 + - - -
657G GLY* 3.6 21.3 - - - -
668G ALA 2.9 16.0 + - - +
669G PHE* 3.5 12.8 - + - +
671G SER* 1.3 74.9 - - - +
673G ALA* 1.3 70.0 + - + +
675G GLN* 3.0 7.0 + - + +
676G THR* 2.4 54.4 + - + +
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Residues in contact with ALA 673 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557G LEU* 4.3 5.4 - - + -
560G LEU* 3.8 10.2 - - + +
669G PHE* 2.5 33.1 + - + +
672G TRP* 1.3 80.4 - - + +
674G VAL* 1.3 53.7 + - - +
676G THR* 3.0 12.0 - - - +
677G PHE* 2.7 37.2 + - - +
698G TYR* 3.7 26.0 - - + -
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Residues in contact with VAL 674 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560G LEU* 4.6 5.4 - - - -
670G ARG* 2.7 34.8 + - + +
671G SER* 3.8 3.1 - - - +
673G ALA* 1.3 72.5 - - - +
675G GLN* 1.3 62.2 + - - +
677G PHE* 3.8 4.1 - - - +
678G LYS* 3.2 24.1 + - + +
694G ILE* 5.1 13.7 - - + -
697G LEU* 4.5 13.2 - - + +
698G TYR* 3.8 30.3 - - + -
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Residues in contact with GLN 675 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653G LEU 5.4 0.2 - - - +
654G THR* 3.3 24.3 + - + +
655G PRO* 5.1 2.3 - - - +
671G SER 2.9 18.9 + - - +
672G TRP* 3.5 4.9 - - + +
674G VAL* 1.3 79.6 - - - +
676G THR* 1.3 58.3 + - - +
678G LYS* 3.5 6.2 + - - +
679G ALA* 3.0 33.1 + - - +
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Residues in contact with THR 676 (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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557G LEU* 4.5 7.2 - - + -
561G PHE* 4.2 4.8 - - + -
585G LEU* 5.9 0.3 - - - +
587G LEU* 4.5 3.0 - - + +
622G ALA* 3.4 17.3 - - - +
653G LEU* 3.3 20.5 - - - +
654G THR* 3.2 31.7 - - - +
672G TRP* 2.4 53.5 + - + +
673G ALA* 3.0 28.0 - - - +
675G GLN* 1.3 68.7 - - - +
677G PHE* 1.3 60.2 + - - +
679G ALA 3.9 0.7 - - - -
680G ALA* 3.4 8.7 - - - +
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Residues in contact with PHE 677 (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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560G LEU* 3.5 46.7 - - + -
561G PHE* 3.5 34.1 - + + -
563G CYS* 4.3 12.1 - - + -
564G ALA* 4.6 6.1 - - + -
565G PHE* 4.0 15.5 - + - -
673G ALA 2.7 21.3 + - - +
674G VAL* 3.8 4.3 - - - +
676G THR* 1.3 72.7 - - - +
678G LYS* 1.3 68.0 + - + +
679G ALA 3.1 1.6 - - - -
680G ALA* 2.9 19.3 + - - +
681G CYS* 3.0 38.2 + - - -
689G LYS 5.9 1.6 - - - -
692G ILE* 4.7 12.1 - - + -
694G ILE* 4.5 14.1 - - + -
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Residues in contact with LYS 678 (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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674G VAL* 3.2 17.0 + - + +
675G GLN* 4.0 9.0 - - - +
677G PHE* 1.3 86.9 - - + +
679G ALA* 1.3 59.5 + - - +
681G CYS* 3.6 5.7 + - + +
682G GLU* 3.3 46.1 + - - +
689G LYS* 3.4 45.3 - - + +
690G GLN* 3.9 20.4 - - - +
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Residues in contact with ALA 679 (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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653G LEU* 3.0 39.3 - - + +
654G THR* 4.9 0.4 - - - -
675G GLN* 3.0 31.6 + - - +
676G THR* 4.4 0.2 - - - -
678G LYS* 1.3 76.0 - - - +
680G ALA* 1.3 58.4 + - - +
681G CYS 3.4 0.2 - - - -
682G GLU* 4.1 6.4 + - - +
683G THR* 2.9 23.9 + - - +
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Residues in contact with ALA 680 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561G PHE* 3.7 14.1 - - + -
565G PHE* 3.9 6.9 - - + -
585G LEU* 3.3 28.7 - - + -
653G LEU* 4.0 5.2 - - + -
676G THR 3.4 13.8 + - - +
677G PHE 2.9 10.9 + - - +
679G ALA* 1.3 81.2 - - - +
681G CYS* 1.3 57.8 + - - +
683G THR* 3.1 6.7 + - - -
684G PHE* 2.8 32.2 - - - +
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Residues in contact with CYS 681 (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 ALA* 4.9 0.7 - - - -
565G PHE* 4.2 6.3 - - - -
677G PHE* 3.0 53.3 + - - +
678G LYS* 3.6 9.8 + - + +
679G ALA 3.4 0.2 - - - -
680G ALA* 1.3 77.3 - - - +
682G GLU* 1.3 62.5 + - - +
683G THR 3.4 0.2 - - - -
684G PHE 3.9 0.7 - - - -
685G ASP* 3.4 3.3 + - - -
686G VAL* 3.2 57.2 + - + +
689G LYS* 3.9 19.7 - - + +
692G ILE* 5.6 1.6 - - - -
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Residues in contact with GLU 682 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678G LYS* 3.3 37.9 + - - +
679G ALA* 4.4 7.2 - - - +
680G ALA 3.4 0.4 - - - -
681G CYS* 1.3 78.3 - - - +
683G THR* 1.3 61.1 + - + +
684G PHE 3.2 4.7 + - - -
685G ASP* 3.6 14.9 + - - +
689G LYS* 3.4 26.7 + - - +
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Residues in contact with THR 683 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620G ARG* 3.1 43.4 + - - +
653G LEU* 3.7 10.7 - - + +
679G ALA 2.9 21.6 + - - +
680G ALA* 3.1 12.3 + - - -
682G GLU* 1.3 78.4 - - + +
684G PHE* 1.3 68.9 + - - -
685G ASP* 3.7 2.8 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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