Contacts of the helix formed by residues 652 - 666 (chain S) in PDB entry 5IJ7
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 LEU 652 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASN* 5.6 1.1 - - - +
265A ASP* 3.4 8.5 - - - -
608S GLU 4.6 0.7 - - - +
609S GLY* 3.4 37.9 - - - +
612S GLU* 3.7 28.5 - - + -
613S VAL* 3.7 12.3 - - + -
616S LEU* 4.5 7.0 - - + -
647S ILE* 2.9 31.9 + - + +
650S LYS* 3.7 29.6 - - + +
651S ASN* 1.3 79.0 - - - +
653S CYS* 1.3 58.7 + - - +
654S ARG 3.4 3.4 - - - -
655S ASN* 4.5 1.8 - - + +
656S PHE* 3.0 30.1 + - - +
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Residues in contact with CYS 653 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 3.6 5.5 + - - +
647S ILE* 3.9 7.6 - - - -
648S ILE* 4.0 32.3 - - - -
651S ASN* 3.7 3.8 - - - +
652S LEU* 1.3 77.8 - - - +
654S ARG* 1.4 61.5 + - + +
656S PHE* 3.6 8.1 - - - +
657S MET* 3.4 21.7 + - - +
681S LEU* 3.8 24.5 - - + +
685S GLN* 4.0 16.8 - - - -
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Residues in contact with ARG 654 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 3.2 42.1 + - + -
265A ASP* 3.1 41.8 + - - +
435A ALA* 4.3 12.5 - - - +
439A MET* 3.7 11.4 - - + +
651S ASN* 3.7 15.4 + - - -
653S CYS* 1.4 76.8 - - + +
655S ASN* 1.4 61.1 + - - +
656S PHE 3.2 1.6 - - - -
657S MET* 3.1 13.6 + - + +
658S LEU* 3.0 28.9 + - - +
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Residues in contact with ASN 655 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 3.7 10.7 - - - +
264A ILE* 3.6 15.3 - - - +
265A ASP* 2.8 35.7 + - - +
281A PHE* 3.5 11.3 - - + -
609S GLY* 3.5 30.8 - - - +
610S GLU* 3.7 21.4 + - - +
613S VAL* 3.7 21.7 - - + +
652S LEU* 3.9 3.7 - - - +
654S ARG* 1.4 71.5 - - - +
656S PHE* 1.3 59.1 + - - +
658S LEU* 3.3 12.0 + - - +
659S HIS* 3.1 22.7 + - - +
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Residues in contact with PHE 656 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613S VAL* 4.0 9.4 - - + +
617S TRP* 6.0 0.2 - + - -
636S CYS* 4.8 2.7 - - + -
639S PHE* 3.5 37.2 - + + -
640S VAL* 3.6 31.2 - - + -
647S ILE* 4.2 15.3 - - + -
652S LEU 3.0 19.1 + - - +
653S CYS 3.6 4.9 - - - +
655S ASN* 1.3 72.6 - - - +
657S MET* 1.3 61.1 + - - +
659S HIS* 3.2 13.3 + + + +
660S LEU* 3.0 58.5 + - + +
677S ALA* 4.3 9.4 - - + -
678S VAL* 5.1 2.9 - - + -
681S LEU* 3.7 30.1 - - + -
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Residues in contact with MET 657 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A MET* 3.3 41.5 - - + -
443A LEU* 3.8 8.1 - - + -
457A LEU* 3.3 48.2 - - + +
458A ILE* 4.8 0.2 - - - -
653S CYS 3.4 12.3 + - - +
654S ARG* 3.1 19.9 + - + +
656S PHE* 1.3 79.8 - - - +
658S LEU* 1.3 56.8 + - - +
660S LEU* 3.3 13.3 + - - +
661S VAL* 3.0 34.7 + - + +
674S ILE* 5.5 2.9 - - + -
678S VAL* 4.4 22.7 - - + -
682S ARG* 4.7 1.3 - - - -
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Residues in contact with LEU 658 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ILE* 3.8 28.0 - - + -
277A SER* 3.7 26.5 - - - +
278A LEU* 3.4 15.4 - - + +
281A PHE* 3.8 19.3 - - + -
439A MET* 3.9 18.8 - - + -
442A VAL* 3.9 34.3 - - + -
610S GLU* 5.3 0.9 - - + +
654S ARG 3.0 13.3 + - - +
655S ASN* 3.4 13.0 - - - +
656S PHE 3.3 0.2 - - - -
657S MET* 1.3 74.1 - - - +
659S HIS* 1.3 57.4 + - - +
661S VAL* 3.5 2.8 + - - -
662S SER* 3.0 29.3 + - - -
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Residues in contact with HIS 659 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 3.9 18.3 - - + -
292A TYR* 2.8 33.9 - + - -
613S VAL* 3.9 12.3 - - + +
617S TRP* 3.4 39.5 + + + -
636S CYS* 4.8 4.3 - - - -
639S PHE* 5.2 1.1 - + - -
655S ASN 3.1 12.8 + - - +
656S PHE* 3.2 26.7 + + - +
658S LEU* 1.3 75.9 - - - +
660S LEU* 1.4 57.2 + - - +
662S SER* 3.3 4.3 + - - -
663S MET* 2.9 62.4 + - + +
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Residues in contact with LEU 660 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636S CYS* 4.1 20.6 - - + -
656S PHE* 3.0 52.6 + - + +
657S MET* 3.5 8.7 - - - +
659S HIS* 1.4 79.1 - - - +
661S VAL* 1.4 55.9 + - - +
663S MET* 3.4 2.7 + - - -
664S HIS* 3.1 22.2 + - - +
669S ILE* 3.2 32.6 - - + +
673S SER 4.7 0.9 - - - +
674S ILE* 3.9 18.6 - - + +
677S ALA* 4.0 20.6 - - + -
678S VAL* 3.9 23.3 - - + -
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Residues in contact with VAL 661 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 3.5 27.8 - - - +
278A LEU* 3.8 14.6 - - + -
442A VAL* 3.7 21.5 - - + -
443A LEU* 4.5 17.0 - - + -
446A THR* 4.0 10.8 - - - +
657S MET* 3.0 24.2 + - + +
658S LEU* 3.5 1.1 + - - -
659S HIS 3.4 0.2 - - - -
660S LEU* 1.4 72.5 - - + +
662S SER* 1.3 57.4 + - - +
664S HIS* 3.1 4.7 + - - +
665S ASP* 2.8 37.7 + - - +
674S ILE* 4.0 19.1 - - + -
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Residues in contact with SER 662 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 4.3 2.0 - - - -
281A PHE* 3.6 25.0 + - - +
282A HIS* 3.6 11.1 - - - -
285A PHE* 5.0 1.0 - - - +
292A TYR* 4.4 4.6 + - - -
658S LEU 3.0 18.0 + - - -
659S HIS* 3.4 6.5 - - - -
661S VAL* 1.3 75.9 - - - +
663S MET* 1.4 57.0 + - - +
665S ASP* 3.1 13.8 + - - +
666S PHE* 2.9 54.2 + - - -
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Residues in contact with MET 663 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE* 3.6 30.3 - - - -
292A TYR* 5.4 0.2 - - - -
617S TRP* 3.3 20.0 - - + -
632S MET* 3.7 7.9 - - + -
636S CYS* 3.5 15.7 - - - -
659S HIS* 2.9 51.2 + - + +
660S LEU* 3.5 10.1 - - - +
661S VAL 3.2 0.2 - - - -
662S SER* 1.4 72.5 - - - +
664S HIS* 1.3 62.2 + - - +
666S PHE* 3.4 5.5 + - - +
667S ASN 3.4 4.2 + - - -
668S LEU* 3.0 44.1 + - + +
669S ILE* 3.7 16.3 + - + -
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Residues in contact with HIS 664 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ARG* 2.9 67.7 + - + +
446A THR* 3.5 32.5 + - + +
660S LEU 3.1 13.3 + - - +
661S VAL 3.3 7.9 - - - +
663S MET* 1.3 76.4 - - - +
665S ASP* 1.4 69.8 + - - +
667S ASN* 3.1 6.2 + - - -
669S ILE* 3.3 25.5 + - + +
670S SER 4.1 0.4 - - - -
671S ILE* 3.5 33.2 + - + -
674S ILE* 3.8 12.1 - - + -
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Residues in contact with ASP 665 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ARG* 2.7 32.9 + - - -
278A LEU* 3.5 6.6 - - - +
282A HIS* 2.9 27.0 + - - +
305A THR 3.3 0.3 - - - +
306A TYR* 3.5 23.1 - - - +
307A LYS* 3.0 24.9 + - - +
308A ARG* 4.2 3.9 + - - +
446A THR* 4.4 0.7 + - - -
661S VAL 2.8 19.9 + - - +
662S SER* 3.1 8.1 + - - +
664S HIS* 1.4 84.9 - - - +
666S PHE* 1.3 59.3 + - - +
667S ASN* 3.3 10.9 + - - -
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Residues in contact with PHE 666 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE 4.1 1.6 - - - -
282A HIS* 3.5 27.1 - + - -
285A PHE* 3.6 36.3 - + + -
287A ARG* 3.7 40.8 + - + -
301A ALA* 4.0 10.3 - - + -
305A THR* 3.4 35.1 - - - +
306A TYR* 3.6 19.7 - + + -
662S SER* 2.9 43.5 + - - +
663S MET 3.8 6.5 - - - +
664S HIS 3.3 0.6 - - - -
665S ASP* 1.3 73.6 - - - +
667S ASN* 1.4 68.3 + - - +
668S LEU* 3.4 16.3 - - + +
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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