Contacts of the helix formed by residues 455 - 471 (chain q) in PDB entry 6FF7
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 ARG 455 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453q GLN* 3.1 8.5 - - - +
454q PRO* 1.3 81.6 - - - +
456q ARG* 1.3 65.4 + - - +
457q VAL* 4.4 4.0 - - + +
458q ALA* 3.2 18.8 + - + +
459q ALA* 3.1 18.8 + - - +
498q THR* 5.3 1.1 - - - -
677q ILE* 5.4 9.0 - - + -
681q SER* 4.8 11.0 - - - -
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Residues in contact with ARG 456 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454q PRO 4.1 1.6 + - - -
455q ARG* 1.3 72.0 - - - +
457q VAL* 1.3 59.5 + - - +
459q ALA* 3.0 9.1 + - - +
460q MET* 2.9 29.9 + - - +
482q ILE* 5.0 15.9 - - + -
498q THR* 5.3 9.5 - - - -
650q ALA* 4.7 14.6 - - + +
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Residues in contact with VAL 457 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455q ARG* 3.2 3.0 - - + +
456q ARG* 1.3 80.3 - - - +
458q ALA* 1.3 58.1 + - - +
460q MET* 4.0 4.4 - - - +
461q SER* 2.9 34.5 + - - -
649q TYR 4.9 13.5 - - - +
650q ALA* 4.9 11.7 + - - +
657q GLN* 5.6 10.1 - - + +
677q ILE* 5.2 13.9 - - + -
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Residues in contact with ALA 458 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453q GLN* 4.2 11.9 - - + -
455q ARG* 3.2 16.3 + - + +
457q VAL* 1.3 77.2 - - - +
459q ALA* 1.3 58.9 + - - +
461q SER* 4.8 2.7 - - - -
462q VAL* 2.9 36.6 + - + +
677q ILE* 6.3 0.2 - - - +
681q SER* 4.0 37.4 - - - +
682q LEU* 5.3 6.7 - - - -
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Residues in contact with ALA 459 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453q GLN* 4.1 9.1 - - + +
455q ARG 3.1 10.7 + - - +
456q ARG* 3.0 11.0 + - - +
458q ALA* 1.3 77.1 - - - +
460q MET* 1.3 63.6 + - - +
462q VAL* 4.2 1.1 - - - +
463q ALA* 3.1 25.8 + - - +
480q TYR* 4.1 4.7 - - + +
481q SER 5.2 2.0 - - - +
482q ILE* 6.2 2.7 - - + -
496q TYR* 3.9 12.6 - - - +
497q MET* 4.1 34.1 - - - +
498q THR 4.4 2.2 - - - +
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Residues in contact with MET 460 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456q ARG 2.9 15.6 + - - +
457q VAL* 4.0 4.9 - - - +
459q ALA* 1.3 78.5 - - - +
461q SER* 1.3 62.5 + - - +
463q ALA* 3.4 2.8 + - - +
464q ALA* 3.1 21.5 + - - +
480q TYR* 4.5 10.5 - - + -
654q SER* 5.2 16.2 - - - -
657q GLN* 6.3 2.7 - - + -
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Residues in contact with SER 461 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457q VAL* 2.9 18.2 + - - -
458q ALA* 4.2 2.7 - - - -
460q MET* 1.3 74.6 - - - +
462q VAL* 1.3 66.0 + - - +
464q ALA* 3.2 8.4 + - - +
465q ARG* 3.0 21.5 + - - +
657q GLN* 5.3 14.6 - - - +
658q ALA* 6.5 0.7 - - - -
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Residues in contact with VAL 462 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430q THR* 5.1 17.3 - - - +
431q THR* 6.0 5.0 - - - +
458q ALA* 2.9 20.4 + - + +
459q ALA* 4.2 2.7 - - - +
461q SER* 1.3 74.9 - - - +
463q ALA* 1.3 62.1 + - - +
465q ARG* 3.1 8.0 + - - +
466q VAL* 2.8 31.5 + - + +
496q TYR* 5.5 4.5 - - + -
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Residues in contact with ALA 463 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459q ALA 3.1 19.1 + - - +
460q MET 3.7 4.3 - - - +
462q VAL* 1.3 76.8 - - - +
464q ALA* 1.3 59.2 + - - +
466q VAL* 3.2 5.9 + - - +
467q ALA* 2.9 31.1 + - - +
474q LEU* 5.6 2.5 - - + -
478q VAL* 4.5 5.9 - - + +
479q GLY* 3.9 18.8 - - - +
480q TYR* 3.8 20.9 - - + -
496q TYR* 4.3 7.6 - - + +
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Residues in contact with ALA 464 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460q MET 3.1 11.2 + - - +
461q SER* 3.4 11.7 - - - +
463q ALA* 1.3 81.0 - - - +
465q ARG* 1.3 61.0 + - - +
467q ALA* 3.4 7.1 + - - +
468q ARG* 3.3 17.0 + - - +
474q LEU* 5.0 10.1 - - + -
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Residues in contact with ARG 465 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431q THR* 5.9 6.3 - - - -
461q SER 3.0 14.0 + - - +
462q VAL* 3.1 10.7 + - - +
464q ALA* 1.3 74.5 - - - +
466q VAL* 1.3 60.5 + - - +
468q ARG* 3.0 11.2 + - - +
469q GLU* 2.9 25.1 + - - +
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Residues in contact with VAL 466 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431q THR* 4.9 21.7 - - - +
462q VAL 2.8 20.6 + - - +
463q ALA* 3.9 5.8 - - - +
465q ARG* 1.3 70.3 - - - +
467q ALA* 1.3 61.3 + - - +
469q GLU* 3.0 10.0 + - - +
470q MET* 2.8 32.3 + - - +
478q VAL* 4.8 7.0 - - + -
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Residues in contact with ALA 467 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463q ALA 2.9 17.0 + - - +
464q ALA 3.6 6.5 - - - +
465q ARG 3.2 0.2 - - - -
466q VAL* 1.3 76.5 - - - +
468q ARG* 1.3 57.7 + - - +
470q MET* 3.3 2.8 + - - -
471q GLY 2.8 22.9 + - - -
472q VAL* 2.9 27.9 + - - +
473q LYS 4.4 0.7 - - - -
474q LEU* 4.0 26.0 - - + +
478q VAL* 4.0 18.1 - - + +
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Residues in contact with ARG 468 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464q ALA 3.3 8.5 + - - +
465q ARG* 3.0 12.8 + - - +
467q ALA* 1.3 77.1 - - - +
469q GLU* 1.3 64.2 + - - +
471q GLY* 3.0 14.2 + - - +
472q VAL 4.9 0.9 - - - -
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Residues in contact with GLU 469 (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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431q THR* 6.3 2.7 - - - -
465q ARG 2.9 12.2 + - - +
466q VAL* 3.0 12.7 + - - +
468q ARG* 1.3 76.9 - - - +
470q MET* 1.3 59.5 + - - +
471q GLY 3.7 0.2 + - - -
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Residues in contact with MET 470 (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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466q VAL 2.8 16.4 + - - +
467q ALA* 3.9 5.6 - - - +
469q GLU* 1.3 77.8 - - - +
471q GLY* 1.3 62.0 + - - +
472q VAL* 4.4 10.3 - - + +
477q GLU* 6.1 2.0 - - + -
478q VAL* 5.7 3.8 - - + -
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Residues in contact with GLY 471 (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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467q ALA 2.8 6.1 + - - -
468q ARG* 3.0 13.9 + - - -
469q GLU 3.3 0.6 + - - -
470q MET* 1.3 79.7 - - - +
472q VAL* 1.3 58.8 + - - +
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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
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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