Contacts of the helix formed by residues 660 - 680 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584K PHE* 4.6 7.2 - - - -
586K THR* 3.6 35.7 - - - -
587K THR* 3.7 9.1 - - - +
659K TYR* 1.3 80.6 - - - +
661K GLY* 1.3 65.7 + - - +
662K LYS* 3.1 14.8 - - - -
663K HIS* 3.2 14.3 + - - +
664K ASN* 3.3 10.6 + - - +
774K GLU* 5.5 7.5 - - - +
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Residues in contact with GLY 661 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544K GLU* 5.2 6.3 - - - -
545K ASP* 4.1 17.5 - - - -
548K CYS* 3.5 11.7 - - - +
584K PHE* 6.0 1.0 - - - +
586K THR 4.9 3.2 - - - +
659K TYR 3.9 0.2 + - - -
660K SER* 1.3 71.6 - - - +
662K LYS* 1.3 55.2 + - - +
664K ASN* 3.6 5.2 - - - +
665K GLY* 2.6 33.4 + - - -
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Residues in contact with LYS 662 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548K CYS* 4.3 8.9 - - - +
574K PHE 4.9 11.9 - - - +
584K PHE* 6.1 5.1 - - + +
660K SER* 3.1 9.5 - - - -
661K GLY* 1.3 77.4 - - - +
663K HIS* 1.3 58.0 + - - +
665K GLY* 3.2 0.9 + - - -
666K ILE* 2.8 31.5 + - - +
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Residues in contact with HIS 663 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659K TYR* 4.1 17.9 - - + -
660K SER* 3.2 13.0 + - - +
662K LYS* 1.3 79.9 - - - +
664K ASN* 1.3 62.8 + - - +
666K ILE* 3.2 5.7 + - - +
667K CYS* 2.9 25.9 + - - +
774K GLU* 5.8 3.1 - - + +
777K SER* 5.0 13.7 - - - -
778K LEU* 5.6 8.5 - - + +
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Residues in contact with ASN 664 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545K ASP* 4.1 19.3 - - + -
659K TYR* 5.5 2.4 - - + +
660K SER 3.3 8.0 + - - +
661K GLY* 3.3 7.5 + - - +
662K LYS 3.3 0.4 - - - -
663K HIS* 1.3 79.9 - - - +
665K GLY* 1.3 59.3 + - - +
667K CYS* 3.3 5.4 + - - +
668K ILE* 2.8 33.0 + - - +
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Residues in contact with GLY 665 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545K ASP 3.7 18.2 - - - -
548K CYS* 4.2 2.2 - - - -
549K ALA* 3.4 26.6 - - - +
552K LEU* 5.7 0.7 - - - -
661K GLY 2.6 22.3 + - - -
662K LYS 3.7 1.1 - - - -
664K ASN* 1.3 73.5 - - - +
666K ILE* 1.3 60.9 + - - +
668K ILE* 3.3 1.7 + - - -
669K TYR* 3.1 20.3 + - - +
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Residues in contact with ILE 666 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552K LEU* 5.5 6.1 - - - -
662K LYS 2.8 16.2 + - - +
663K HIS* 3.8 4.9 - - - +
665K GLY* 1.3 75.9 - - - +
667K CYS* 1.3 62.5 + - - +
669K TYR* 3.1 10.3 - - - +
670K PHE* 3.0 21.0 + - - +
781K ILE* 5.8 7.0 - - + -
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Residues in contact with CYS 667 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K LEU* 5.1 15.0 - - + -
30K ILE* 5.1 8.9 - - + +
33K GLN* 5.7 5.2 - - + -
663K HIS 2.9 17.0 + - - +
664K ASN* 3.8 5.8 - - - +
666K ILE* 1.3 75.8 - - - +
668K ILE* 1.3 57.7 + - - +
670K PHE* 3.1 8.6 + - - +
671K SER* 2.8 31.5 + - - -
781K ILE* 5.9 8.7 - - + +
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Residues in contact with ILE 668 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K GLN* 5.3 9.2 - - + -
545K ASP* 6.5 1.1 - - + -
549K ALA* 4.6 8.1 - - + -
664K ASN 2.8 18.4 + - - +
665K GLY* 3.8 6.5 - - - +
667K CYS* 1.3 75.4 - - - +
669K TYR* 1.3 62.9 + - - +
671K SER* 3.3 6.0 + - - -
672K ARG* 2.9 27.4 + - - +
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Residues in contact with TYR 669 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549K ALA* 4.8 13.0 - - + +
552K LEU* 5.5 5.8 - - + -
553K ILE* 6.4 1.1 - - + -
665K GLY 3.1 12.6 + - - +
666K ILE* 3.1 14.4 - - - +
668K ILE* 1.3 76.5 - - - +
670K PHE* 1.3 63.0 + - - +
672K ARG* 3.8 4.5 - - - +
673K ILE* 3.1 23.2 + - - +
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Residues in contact with PHE 670 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE* 5.9 0.2 - - - -
666K ILE 3.0 8.4 + - - +
667K CYS* 3.5 10.8 - - - +
669K TYR* 1.3 81.6 - - - +
671K SER* 1.3 61.6 + - - +
673K ILE* 3.3 5.9 + - - +
674K MET* 3.3 24.1 + - - +
785K VAL* 6.5 1.1 - - + -
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Residues in contact with SER 671 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K ILE* 4.1 33.4 - - - +
33K GLN* 4.8 7.0 - - - -
34K LEU* 5.0 9.0 - - - -
667K CYS 2.8 17.0 + - - -
668K ILE* 3.7 7.0 - - - -
670K PHE* 1.3 76.8 - - - +
672K ARG* 1.3 57.5 + - - +
674K MET* 3.7 3.2 - - - +
675K GLY* 2.9 29.8 + - - -
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Residues in contact with ARG 672 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489K VAL 5.2 2.2 - - - +
490K VAL* 3.8 30.0 - - + +
493K HIS* 5.0 10.7 - - + +
494K MET* 5.5 5.5 - - - +
668K ILE 2.9 18.1 + - - +
669K TYR* 3.8 5.4 - - - +
670K PHE 3.3 0.2 - - - -
671K SER* 1.3 74.3 - - - +
673K ILE* 1.3 67.2 + - - +
675K GLY* 3.4 9.3 + - - -
676K ASN 4.9 0.7 + - - -
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Residues in contact with ILE 673 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493K HIS* 4.9 13.4 - - + +
494K MET* 5.9 2.4 - - - +
669K TYR 3.1 15.7 + - - +
670K PHE* 3.3 5.8 + - - +
671K SER 3.3 0.2 - - - -
672K ARG* 1.3 78.6 - - - +
674K MET* 1.3 59.8 + - + +
675K GLY 3.5 0.3 + - - -
676K ASN* 4.5 5.4 + - - +
713K GLU* 6.0 6.5 - - + -
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Residues in contact with MET 674 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670K PHE 3.3 13.8 + - - +
671K SER* 4.2 2.9 - - - +
673K ILE* 1.3 75.5 - - + +
675K GLY* 1.3 64.3 + - - +
676K ASN 3.0 4.1 + - - -
677K ILE* 3.1 8.0 + - + +
678K TRP* 2.9 31.1 + - + +
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Residues in contact with GLY 675 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671K SER 2.9 18.0 + - - -
672K ARG* 3.4 6.1 + - - -
673K ILE 3.3 3.4 - - - -
674K MET* 1.3 75.4 - - - +
676K ASN* 1.3 64.6 + - - +
678K TRP* 3.7 13.5 + - - +
679K ASP* 4.6 2.3 + - - +
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Residues in contact with ASN 676 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494K MET* 5.8 8.3 - - + -
672K ARG 4.9 1.0 + - - -
673K ILE 4.5 4.5 + - - +
674K MET 3.0 1.6 + - - -
675K GLY* 1.3 78.4 - - - +
677K ILE* 1.3 61.9 + - + +
678K TRP 3.6 0.2 + - - -
679K ASP* 4.4 3.6 + - - +
680K ALA* 4.5 8.3 + - - +
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Residues in contact with ILE 677 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674K MET* 3.1 9.0 + - + +
676K ASN* 1.3 78.2 - - + +
678K TRP* 1.3 66.4 + - - +
679K ASP 3.4 0.2 - - - -
680K ALA* 3.0 25.8 + - - +
823K PHE* 3.6 15.6 - - + +
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Residues in contact with TRP 678 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674K MET* 2.9 25.8 + - + +
675K GLY* 4.0 9.2 - - - +
676K ASN 3.4 1.8 - - - -
677K ILE* 1.3 77.9 - - - +
679K ASP* 1.3 60.7 + - - +
822K THR* 3.8 2.3 - - - -
823K PHE* 3.6 8.9 + - - -
824K LYS* 3.3 34.7 + - + +
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Residues in contact with ASP 679 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675K GLY 4.6 2.1 + - - +
676K ASN 4.4 3.9 + - - +
677K ILE 3.4 0.2 - - - -
678K TRP* 1.3 76.7 - - - +
680K ALA* 1.3 67.4 + - - +
681K SER 3.7 0.7 + - - -
822K THR* 3.4 13.2 - - - -
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Residues in contact with ALA 680 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676K ASN 4.5 8.1 + - - +
677K ILE* 3.0 19.2 + - - +
679K ASP* 1.3 81.8 - - - +
681K SER* 1.4 67.8 + - - +
682K LEU 3.6 0.2 + - - -
701K SER* 5.5 4.3 - - - -
822K THR* 3.3 0.5 - - - -
823K PHE* 3.2 20.8 + - - +
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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) + - + + + + + -
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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