Contacts of the helix formed by residues 650 - 666 (chain J) in PDB entry 1O1F
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 650 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475J PHE* 4.3 6.3 - - - -
479J CYS* 5.7 0.2 - - - -
533J PHE* 4.1 27.5 + - - -
537J GLU* 2.6 24.7 + - - +
599J ASN* 2.7 29.2 + - - -
648J THR* 3.3 1.4 - - - -
649J VAL* 1.0 82.3 - - - +
651J ALA* 1.3 64.3 + - - +
652J LEU 3.2 2.7 + - - -
653J PHE* 3.6 10.1 - - - +
654J ARG* 3.2 28.1 + - - +
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Residues in contact with ALA 651 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47 GLU* 4.9 12.2 - - + +
537J GLU* 3.9 11.7 - - - +
641J LYS* 5.0 10.3 - - - +
646J PHE* 5.4 2.5 - - + -
647J GLN 4.9 4.3 - - - +
648J THR* 2.9 37.9 - - + +
650J SER* 1.3 78.0 - - - +
652J LEU* 1.3 62.5 + - + +
654J ARG* 4.1 9.6 + - - +
655J GLU* 3.7 19.3 + - - +
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Residues in contact with LEU 652 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47 GLU* 5.3 1.3 - - - +
646J PHE* 2.6 54.1 - - + -
648J THR 4.9 4.3 - - - +
649J VAL* 5.6 8.5 - - + +
650J SER* 3.2 0.8 - - - +
651J ALA* 1.3 76.0 - - + +
653J PHE* 1.3 57.8 - - - +
654J ARG 2.8 2.5 - - - -
655J GLU* 2.3 45.1 + - - +
656J ASN* 2.6 36.1 + - - +
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Residues in contact with PHE 653 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J TYR* 5.5 9.6 - + + -
269J LEU* 3.6 31.6 - - + -
479J CYS* 3.2 58.1 - - + -
482J PHE* 4.2 6.7 - + - -
483J THR* 3.3 13.7 - - + -
533J PHE* 4.8 5.6 - + - -
649J VAL 4.3 6.4 + - - +
650J SER* 3.6 20.4 - - - +
652J LEU* 1.3 76.6 - - - +
654J ARG* 1.3 61.0 + - + +
656J ASN* 3.7 7.4 - - + +
657J LEU* 2.7 57.2 + - + +
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Residues in contact with ARG 654 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3507 SER 4.9 2.4 + - - -
3537 GLN* 4.9 13.7 - - - +
482J PHE* 4.7 10.8 - - + -
527J GLU* 3.9 26.5 + - + +
528J MLY 5.3 1.6 + - - -
533J PHE* 3.5 43.9 - - + +
534J SER* 4.9 8.1 + - - +
537J GLU* 2.9 34.1 + - - -
650J SER 3.2 17.4 + - - +
651J ALA* 4.1 10.3 + - - +
652J LEU 2.8 0.8 + - - -
653J PHE* 1.3 83.0 - - + +
655J GLU* 1.3 48.5 + - - +
657J LEU* 3.0 7.6 + - - +
658J ASN* 2.6 47.6 + - - +
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Residues in contact with GLU 655 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17 ASP* 1.5 62.1 + - + +
27 GLU* 4.4 9.0 - - - +
47 GLU* 3.2 19.7 - - - +
651J ALA 3.7 9.0 + - - +
652J LEU* 2.3 40.2 + - + +
654J ARG* 1.3 72.6 - - - +
656J ASN* 1.3 64.9 + - - +
658J ASN* 3.7 7.0 - - - +
659J MLY 3.2 24.4 + - - +
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Residues in contact with ASN 656 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266J GLU* 4.6 5.4 - - - +
267J THR 5.4 2.7 - - - +
268J TYR* 4.2 25.2 + - + -
652J LEU* 2.6 37.3 + - - +
653J PHE* 3.8 7.6 + - + +
655J GLU* 1.3 76.6 + - - +
657J LEU* 1.3 58.9 + - - +
658J ASN 3.0 9.4 + - - -
659J MLY 3.1 31.8 + - - +
660J LEU* 3.0 23.5 + - - +
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Residues in contact with LEU 657 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J TYR* 5.0 2.2 - - - -
482J PHE* 3.5 39.9 - - + -
483J THR* 3.9 30.3 - - + +
486J MLY 4.3 12.2 - - + -
653J PHE* 2.7 41.5 + - + +
654J ARG* 3.3 7.0 - - - +
656J ASN* 1.3 72.7 - - - +
658J ASN* 1.3 61.3 + - - +
660J LEU* 3.9 16.2 - - + -
661J MET* 3.4 32.7 + - + +
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Residues in contact with ASN 658 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27 GLU* 5.9 2.8 + - - +
486J MLY 3.1 34.9 - - - -
527J GLU* 4.7 2.0 + - - +
654J ARG* 2.6 31.6 + - - +
655J GLU* 3.7 8.1 - - - +
656J ASN 3.0 0.2 - - - -
657J LEU* 1.3 77.7 - - - +
659J MLY 1.3 63.6 + - - +
660J LEU 2.9 4.9 - - - -
661J MET* 3.5 3.0 + - - +
662J ALA* 3.1 25.8 + - - +
665J ARG* 5.6 0.7 + - - -
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Residues in contact with MLY 659 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266J GLU* 2.5 44.0 + - - +
655J GLU 3.2 14.9 + - - +
656J ASN* 3.5 26.7 - - - +
658J ASN* 1.3 78.8 + - - +
660J LEU* 1.3 60.3 + - - +
662J ALA* 3.8 5.9 - - - +
663J ASN* 3.3 32.4 + - - +
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Residues in contact with LEU 660 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J PHE* 3.9 28.5 - - + -
268J TYR* 3.5 35.7 - - + +
462J LEU* 4.3 17.7 - - + -
464J ILE* 4.5 8.5 - - + -
483J THR* 5.2 2.5 - - + -
487J LEU* 5.5 2.7 - - + -
656J ASN 3.0 16.7 + - - +
657J LEU* 3.8 21.5 - - + +
659J MLY 1.3 74.6 + - - -
661J MET* 1.3 54.6 + - + +
662J ALA 2.9 4.3 - - - -
663J ASN* 2.8 27.2 + - - +
664J LEU* 2.8 36.1 + - + +
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Residues in contact with MET 661 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486J MLY 4.2 28.9 - - + +
487J LEU* 3.6 35.4 - - - -
490J PHE* 4.2 30.3 - - + -
657J LEU* 3.4 30.7 + - + +
658J ASN* 3.5 3.3 + - - +
660J LEU* 1.3 79.2 - - + +
662J ALA* 1.3 56.3 + - - +
664J LEU* 3.5 14.7 - - + +
665J ARG* 3.1 53.9 + - - +
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Residues in contact with ALA 662 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658J ASN 3.1 19.0 + - - +
659J MLY 3.8 7.9 - - - +
660J LEU 2.9 0.8 - - - -
661J MET* 1.3 74.1 - - - +
663J ASN* 1.3 67.6 + - - +
664J LEU 3.1 1.3 - - - -
665J ARG* 3.3 20.8 + - - +
666J SER* 3.1 17.2 + - - -
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Residues in contact with ASN 663 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J PHE* 4.2 21.3 - - + -
251J ARG* 3.6 36.7 + - - +
458J PHE* 4.3 11.4 - - + -
659J MLY 3.3 25.1 + - - +
660J LEU* 2.8 11.0 + - - +
662J ALA* 1.3 79.7 - - - +
664J LEU* 1.3 62.2 + - - +
665J ARG 3.4 0.5 + - - -
666J SER* 3.7 11.7 + - - -
667J THR* 2.7 21.8 + - - -
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Residues in contact with LEU 664 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174J SER* 4.7 14.4 - - - +
176J LEU* 4.4 12.6 - - + -
249J PHE* 4.0 29.6 - - + -
462J LEU* 4.7 6.1 - - + -
487J LEU* 3.9 15.5 - - + -
490J PHE* 3.3 34.3 - - + -
660J LEU* 2.8 28.3 + - + +
661J MET* 3.5 35.0 - - + +
663J ASN* 1.3 79.8 - - - +
665J ARG* 1.3 53.9 + - - +
667J THR* 2.8 23.9 - - - +
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Residues in contact with ARG 665 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486J MLY 4.8 18.0 - - - -
489J GLN* 5.8 2.4 + - - -
490J PHE* 4.3 19.5 - - + -
658J ASN 5.6 0.6 + - - -
661J MET* 3.1 49.8 + - - +
662J ALA* 3.3 13.7 + - - +
663J ASN 3.2 0.6 - - - -
664J LEU* 1.3 72.7 - - - +
666J SER* 1.3 51.6 + - - +
667J THR 2.6 24.9 + - - +
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Residues in contact with SER 666 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J ASN* 3.2 30.0 + - - +
458J PHE* 5.0 4.4 - - - -
662J ALA 3.1 15.2 + - - -
663J ASN* 3.7 9.8 + - - -
664J LEU 3.6 0.4 - - - -
665J ARG* 1.3 73.1 - - - +
667J THR* 1.3 60.3 + - - +
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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
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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