Contacts of the helix formed by residues 660 - 680 (chain Q) in PDB entry 5IJO
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 SER 660 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584Q PHE 4.6 6.7 - - - -
586Q THR* 3.6 36.6 - - - -
587Q THR* 3.7 9.1 - - - +
659Q TYR* 1.3 79.6 - - - +
661Q GLY* 1.3 64.0 + - - +
662Q LYS* 3.1 14.6 - - - -
663Q HIS* 3.2 14.2 + - - +
664Q ASN* 3.3 10.4 + - - +
774Q GLU* 5.5 7.3 - - - +
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Residues in contact with GLY 661 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544Q GLU* 5.2 6.3 - - - -
545Q ASP* 4.1 19.1 - - - -
548Q CYS* 3.5 11.6 - - - +
584Q PHE* 6.0 1.0 - - - +
586Q THR 4.9 4.0 - - - +
659Q TYR 3.9 0.2 + - - -
660Q SER* 1.3 70.5 - - - +
662Q LYS* 1.3 55.0 + - - +
664Q ASN* 3.6 5.6 - - - +
665Q GLY* 2.6 33.1 + - - -
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Residues in contact with LYS 662 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548Q CYS* 4.3 9.5 - - - +
574Q PHE 4.9 12.1 - - - +
584Q PHE* 6.1 5.1 - - + +
660Q SER* 3.1 10.2 - - - -
661Q GLY* 1.3 76.4 - - - +
663Q HIS* 1.3 58.0 + - - +
665Q GLY* 3.2 0.7 + - - -
666Q ILE* 2.8 31.0 + - - +
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Residues in contact with HIS 663 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659Q TYR* 4.1 19.3 - - + -
660Q SER* 3.2 12.6 + - - +
662Q LYS* 1.3 81.2 - - - +
664Q ASN* 1.3 62.7 + - - +
666Q ILE* 3.2 5.7 + - - +
667Q CYS* 2.9 25.6 + - - +
774Q GLU* 5.8 3.4 - - + +
777Q SER* 5.0 13.5 - - - -
778Q LEU* 5.6 8.1 - - + +
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Residues in contact with ASN 664 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545Q ASP* 4.1 19.3 - - + -
659Q TYR* 5.5 2.2 - - + +
660Q SER 3.3 8.6 + - - +
661Q GLY* 3.3 7.7 + - - +
662Q LYS 3.3 0.2 - - - -
663Q HIS* 1.3 78.4 - - - +
665Q GLY* 1.3 57.8 + - - +
667Q CYS* 3.7 5.6 - - - +
668Q ILE* 2.8 33.0 + - - +
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Residues in contact with GLY 665 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545Q ASP 3.7 19.0 + - - -
548Q CYS* 4.2 2.9 - - - -
549Q ALA* 3.4 26.1 - - - +
552Q LEU* 5.7 0.7 - - - -
661Q GLY 2.6 22.2 + - - -
662Q LYS 3.7 1.3 - - - -
664Q ASN* 1.3 74.4 - - - +
666Q ILE* 1.3 61.3 + - - +
668Q ILE* 4.5 1.1 - - - -
669Q TYR* 3.1 19.8 + - - +
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Residues in contact with ILE 666 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552Q LEU* 5.5 8.0 - - + +
662Q LYS 2.8 16.8 + - - +
663Q HIS* 3.8 4.7 - - - +
665Q GLY* 1.3 74.2 - - - +
667Q CYS* 1.3 63.2 + - - +
669Q TYR* 3.1 10.1 - - - +
670Q PHE* 3.0 21.4 + - - +
781Q ILE* 5.8 7.2 - - + -
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Residues in contact with CYS 667 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q LEU* 5.1 16.4 - - + +
30Q ILE* 5.1 9.3 - - + +
33Q GLN* 5.7 1.1 - - - -
663Q HIS 2.9 16.8 + - - +
664Q ASN* 3.8 6.3 - - - +
666Q ILE* 1.3 76.6 - - - +
668Q ILE* 1.3 57.1 + - - +
670Q PHE* 3.1 8.0 + - - +
671Q SER* 2.8 30.5 + - - -
781Q ILE* 5.9 9.1 - - + +
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Residues in contact with ILE 668 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q GLN* 5.3 9.0 - - + -
545Q ASP* 6.5 0.9 - - + -
549Q ALA* 4.6 7.9 - - + -
664Q ASN 2.8 19.4 + - - +
665Q GLY* 3.8 5.8 - - - +
667Q CYS* 1.3 75.8 - - - +
669Q TYR* 1.3 63.1 + - - +
671Q SER* 3.3 6.0 + - - -
672Q ARG* 2.9 26.7 + - - +
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Residues in contact with TYR 669 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549Q ALA* 4.8 13.2 - - + +
552Q LEU* 5.5 5.6 - - + -
553Q ILE* 6.4 1.3 - - + -
665Q GLY 3.1 12.0 + - - +
666Q ILE* 3.1 13.5 - - - +
668Q ILE* 1.3 77.9 - - - +
670Q PHE* 1.3 62.8 + - - +
672Q ARG* 3.3 4.9 + - - +
673Q ILE* 3.1 23.2 + - - +
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Residues in contact with PHE 670 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q ILE* 6.1 2.7 - - + -
666Q ILE 3.0 8.8 + - - +
667Q CYS* 3.5 11.0 - - - +
669Q TYR* 1.3 80.8 - - - +
671Q SER* 1.3 60.9 + - - +
673Q ILE* 3.3 5.5 + - - +
674Q MET* 3.3 24.4 + - - +
785Q VAL* 6.5 1.3 - - + -
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Residues in contact with SER 671 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q ILE* 4.1 33.4 - - - +
33Q GLN* 4.8 7.0 - - - -
34Q LEU* 5.0 10.1 - - - +
667Q CYS 2.8 16.5 + - - -
668Q ILE* 3.7 7.2 - - - -
670Q PHE* 1.3 77.7 - - - +
672Q ARG* 1.3 57.2 + - - +
674Q MET* 3.7 3.0 - - - +
675Q GLY* 2.9 29.5 + - - -
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Residues in contact with ARG 672 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489Q VAL 5.2 2.5 - - - +
490Q VAL* 3.8 29.8 - - + +
493Q HIS* 5.0 10.3 - - + +
494Q MET* 5.5 5.9 + - - +
668Q ILE 2.9 17.0 + - - +
669Q TYR* 3.8 5.4 - - - +
670Q PHE 3.3 0.2 - - - -
671Q SER* 1.3 74.9 - - - +
673Q ILE* 1.3 65.5 + - - +
675Q GLY* 3.4 9.3 + - - +
676Q ASN 4.9 0.9 + - - -
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Residues in contact with ILE 673 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493Q HIS* 4.9 12.3 - - + +
494Q MET* 5.9 2.1 - - - +
669Q TYR 3.1 16.3 + - - +
670Q PHE* 3.3 5.1 + - - +
671Q SER 3.3 0.2 - - - -
672Q ARG* 1.3 80.3 - - - +
674Q MET* 1.3 60.3 + - + +
675Q GLY 3.5 0.2 + - - -
676Q ASN* 4.5 5.0 + - - +
713Q GLU* 6.0 6.5 - - + -
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Residues in contact with MET 674 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670Q PHE 3.3 14.5 + - - +
671Q SER* 3.7 2.7 - - - +
673Q ILE* 1.3 74.9 - - + +
675Q GLY* 1.3 64.9 + - - +
676Q ASN 3.0 3.9 + - - -
677Q ILE* 3.2 9.1 + - + +
678Q TRP* 2.9 30.9 + - + +
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Residues in contact with GLY 675 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q LEU* 6.4 1.6 - - - -
671Q SER 2.9 16.8 + - - -
672Q ARG* 3.4 6.7 + - - -
673Q ILE 3.3 3.4 - - - -
674Q MET* 1.3 75.8 - - - +
676Q ASN* 1.3 63.8 + - - +
678Q TRP* 3.7 13.3 + - - +
679Q ASP* 4.6 2.3 + - - +
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Residues in contact with ASN 676 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494Q MET* 5.8 8.7 - - + -
672Q ARG 4.9 1.0 + - - -
673Q ILE 4.5 4.8 + - - +
674Q MET 3.0 1.2 + - - -
675Q GLY* 1.3 78.4 - - - +
677Q ILE* 1.3 62.4 + - + +
679Q ASP* 4.4 4.9 + - - +
680Q ALA* 4.5 7.8 + - - +
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Residues in contact with ILE 677 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674Q MET* 3.2 8.8 + - + +
676Q ASN* 1.3 78.1 - - + +
678Q TRP* 1.3 66.9 + - - +
679Q ASP 3.4 0.2 - - - -
680Q ALA* 3.0 26.1 + - - +
823Q PHE* 3.6 14.8 - - + +
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Residues in contact with TRP 678 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674Q MET* 2.9 26.0 + - + +
675Q GLY* 4.0 9.0 - - - +
676Q ASN 3.4 1.8 - - - -
677Q ILE* 1.3 78.0 - - - +
679Q ASP* 1.3 61.1 + - - +
822Q THR* 3.8 2.4 - - - -
823Q PHE* 3.6 8.2 + - - -
824Q LYS* 3.3 35.4 + - + +
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Residues in contact with ASP 679 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675Q GLY 4.6 2.5 + - - +
676Q ASN 4.4 3.7 + - - +
677Q ILE 3.4 0.4 - - - -
678Q TRP* 1.3 77.2 - - - +
680Q ALA* 1.3 65.3 + - - +
681Q SER* 3.7 0.9 + - - -
822Q THR* 3.4 13.6 - - - -
824Q LYS* 5.9 0.2 - - - -
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Residues in contact with ALA 680 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676Q ASN 4.5 7.7 + - - +
677Q ILE* 3.0 20.0 + - + +
679Q ASP* 1.3 81.3 - - - +
681Q SER* 1.4 68.1 + - - +
682Q LEU 3.6 0.2 + - - -
701Q SER* 5.5 4.7 - - - -
822Q THR* 3.3 0.7 - - - -
823Q PHE* 3.2 20.6 + - - +
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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) + - + + + + + -
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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