Contacts of the helix formed by residues 660 - 680 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584E PHE 4.6 6.5 - - - -
586E THR* 3.6 36.3 - - - -
587E THR* 3.7 9.3 - - - +
659E TYR* 1.3 79.7 - - - +
661E GLY* 1.3 65.6 + - - +
662E LYS* 3.1 14.6 - - - -
663E HIS* 3.2 14.3 + - - +
664E ASN* 3.3 10.4 + - - +
774E GLU* 5.5 7.3 - - - +
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Residues in contact with GLY 661 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544E GLU* 5.2 6.5 - - - -
545E ASP* 4.1 18.0 - - - -
548E CYS* 3.5 11.4 - - - +
584E PHE* 6.0 0.8 - - - +
586E THR 4.9 3.8 - - - +
659E TYR 3.9 0.2 + - - -
660E SER* 1.3 71.2 - - - +
662E LYS* 1.3 55.9 + - - +
664E ASN* 3.7 5.6 - - - +
665E GLY* 2.6 33.3 + - - -
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Residues in contact with LYS 662 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548E CYS* 4.3 9.5 - - - +
574E PHE 4.9 12.6 - - - +
584E PHE* 6.1 4.6 - - + +
660E SER* 3.1 10.0 - - - -
661E GLY* 1.3 77.6 - - - +
663E HIS* 1.3 57.7 + - - +
665E GLY* 3.2 0.5 + - - -
666E ILE* 2.8 31.2 + - - +
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Residues in contact with HIS 663 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659E TYR* 4.1 18.4 - - + -
660E SER* 3.2 12.6 + - - +
662E LYS* 1.3 81.4 - - - +
664E ASN* 1.3 62.0 + - - +
666E ILE* 3.2 5.2 + - - +
667E CYS* 2.9 25.6 + - - +
774E GLU* 5.8 3.6 - - + +
777E SER* 5.0 12.8 - - - -
778E LEU* 5.6 8.3 - - + +
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Residues in contact with ASN 664 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545E ASP* 4.1 19.5 - - + -
659E TYR* 5.5 2.0 - - + +
660E SER 3.3 8.9 + - - +
661E GLY* 3.3 7.7 + - - +
662E LYS 3.3 0.2 - - - -
663E HIS* 1.3 79.5 - - - +
665E GLY* 1.3 58.7 + - - +
667E CYS* 3.3 5.1 + - - +
668E ILE* 2.8 33.2 + - - +
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Residues in contact with GLY 665 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545E ASP 3.7 19.5 + - - -
548E CYS* 4.2 2.2 - - - -
549E ALA* 3.4 26.8 - - - +
552E LEU* 5.7 0.9 - - - -
661E GLY 2.6 22.0 + - - -
662E LYS 3.7 0.9 - - - -
664E ASN* 1.3 73.3 - - - +
666E ILE* 1.3 61.4 + - - +
668E ILE* 3.3 1.3 + - - -
669E TYR* 3.1 19.8 + - - +
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Residues in contact with ILE 666 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552E LEU* 5.5 7.4 - - + -
662E LYS 2.8 17.3 + - - +
663E HIS* 3.8 4.0 - - - +
665E GLY* 1.3 75.5 - - - +
667E CYS* 1.3 64.0 + - - +
669E TYR* 3.1 10.3 - - - +
670E PHE* 3.0 21.5 + - - +
781E ILE* 5.8 7.6 - - + -
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Residues in contact with CYS 667 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU* 5.1 15.9 - - + -
30E ILE* 5.1 8.6 - - + +
33E GLN* 5.7 1.3 - - - -
663E HIS 2.9 17.3 + - - +
664E ASN* 3.8 6.1 - - - +
666E ILE* 1.3 76.2 - - - +
668E ILE* 1.3 58.5 + - - +
670E PHE* 3.1 8.0 + - - +
671E SER* 2.8 31.2 + - - -
781E ILE* 5.9 9.4 - - + +
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Residues in contact with ILE 668 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E GLN* 5.3 9.9 - - + -
545E ASP* 6.5 1.1 - - + -
549E ALA* 4.6 8.5 - - + -
664E ASN 2.8 18.9 + - - +
665E GLY* 3.8 6.1 - - - +
667E CYS* 1.3 76.2 - - - +
669E TYR* 1.3 62.9 + - - +
671E SER* 3.3 5.7 + - - -
672E ARG* 2.9 27.6 + - - +
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Residues in contact with TYR 669 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549E ALA* 4.8 13.0 - - + +
552E LEU* 5.5 5.8 - - + -
553E ILE* 6.3 1.8 - - + +
665E GLY 3.1 12.6 + - - +
666E ILE* 3.1 13.5 - - - +
668E ILE* 1.3 76.9 - - - +
670E PHE* 1.3 62.3 + - - +
672E ARG* 3.3 4.7 + - - +
673E ILE* 3.1 23.4 + - - +
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Residues in contact with PHE 670 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ILE* 5.9 2.7 - - + -
666E ILE 3.0 9.2 + - - +
667E CYS* 3.5 11.2 - - - +
669E TYR* 1.3 81.0 - - - +
671E SER* 1.3 60.6 + - - +
673E ILE* 3.3 5.9 + - - +
674E MET* 3.3 23.9 + - - +
785E VAL* 6.5 1.3 - - + -
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Residues in contact with SER 671 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ILE* 4.1 34.1 - - - +
33E GLN* 4.8 6.5 - - - -
34E LEU* 5.0 10.2 - - - +
667E CYS 2.8 16.7 + - - -
668E ILE* 3.7 7.0 - - - -
670E PHE* 1.3 77.5 - - - +
672E ARG* 1.3 56.4 + - - +
674E MET* 3.5 2.6 + - - +
675E GLY* 2.9 30.0 + - - -
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Residues in contact with ARG 672 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489E VAL 5.2 2.2 - - - +
490E VAL* 3.8 29.0 - - + +
493E HIS* 5.0 11.2 - - + +
494E MET* 5.5 5.9 - - - +
668E ILE 2.9 17.9 + - - +
669E TYR* 3.8 4.9 - - - +
670E PHE 3.3 0.2 - - - -
671E SER* 1.3 74.7 - - - +
673E ILE* 1.3 67.5 + - - +
675E GLY* 3.4 9.2 + - - -
676E ASN 4.9 0.5 + - - -
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Residues in contact with ILE 673 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493E HIS* 4.9 13.0 - - + +
494E MET* 5.9 1.9 - - - +
669E TYR 3.1 15.5 + - - +
670E PHE* 3.9 5.4 - - - +
671E SER 3.3 0.6 - - - -
672E ARG* 1.3 79.6 - - - +
674E MET* 1.3 59.8 + - + +
675E GLY 3.5 0.5 + - - -
676E ASN* 4.5 4.9 + - - +
713E GLU* 6.0 6.3 - - + -
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Residues in contact with MET 674 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670E PHE 3.3 14.3 + - - +
671E SER* 3.7 2.9 - - - +
673E ILE* 1.3 75.5 - - + +
675E GLY* 1.3 64.9 + - - +
676E ASN 3.0 4.5 + - - -
677E ILE* 3.1 8.3 + - + +
678E TRP* 2.9 31.1 + - + +
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Residues in contact with GLY 675 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 6.4 1.8 - - - -
671E SER 2.9 18.1 + - - -
672E ARG* 3.4 4.8 + - - -
673E ILE 3.3 3.6 - - - -
674E MET* 1.3 77.1 - - - +
676E ASN* 1.3 63.3 + - - +
678E TRP* 3.7 13.0 + - - +
679E ASP* 4.6 2.3 + - - +
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Residues in contact with ASN 676 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494E MET* 5.8 8.3 - - + -
672E ARG 4.9 1.2 + - - -
673E ILE 4.5 4.9 + - - +
674E MET 3.0 1.4 + - - -
675E GLY* 1.3 78.2 - - - +
677E ILE* 1.3 62.0 + - + +
679E ASP* 4.4 3.6 + - - +
680E ALA* 4.5 8.7 + - - +
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Residues in contact with ILE 677 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674E MET* 3.1 8.3 + - + +
676E ASN* 1.3 78.6 - - + +
678E TRP* 1.3 66.8 + - - +
679E ASP 3.4 0.2 - - - -
680E ALA* 3.0 25.9 + - + +
823E PHE* 3.6 15.4 - - + +
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Residues in contact with TRP 678 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674E MET* 2.9 27.1 + - + +
675E GLY* 4.0 8.5 - - - +
676E ASN 3.4 1.4 - - - -
677E ILE* 1.3 78.4 - - - +
679E ASP* 1.3 61.6 + - - +
822E THR* 3.8 2.4 - - - -
823E PHE* 3.6 8.8 + - - -
824E LYS* 3.3 35.2 + - + +
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Residues in contact with ASP 679 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675E GLY 4.6 1.9 + - - +
676E ASN 4.4 3.9 + - - +
677E ILE 3.4 0.4 - - - -
678E TRP* 1.3 77.8 - - - +
680E ALA* 1.3 66.9 + - - +
681E SER 3.7 0.5 + - - -
822E THR* 3.4 12.8 - - - -
824E LYS* 5.9 0.4 - - - -
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Residues in contact with ALA 680 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676E ASN 4.5 7.6 + - - +
677E ILE* 3.0 20.6 + - + +
679E ASP* 1.3 82.2 - - - +
681E SER* 1.4 68.6 + - - +
701E SER* 5.5 4.9 - - - -
822E THR* 3.3 0.3 - - - -
823E PHE* 3.2 21.1 + - - +
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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