Contacts of the helix formed by residues 459 - 478 (chain S) in PDB entry 3FKS
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 GLU 459 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425S ARG* 4.4 2.7 - - - +
458S ILE* 1.3 79.0 - - + +
460S LEU* 1.3 66.9 + - - +
461S SER* 3.4 16.4 + - - +
462S ARG* 3.5 38.0 + - + -
463S ILE* 3.2 18.4 + - - +
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Residues in contact with LEU 460 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424S GLU* 3.2 50.9 - - + +
425S ARG* 3.3 30.7 - - + +
428S GLN* 4.2 17.3 + - + +
458S ILE 4.4 0.2 - - - -
459S GLU* 1.3 71.4 - - - +
461S SER* 1.3 66.5 + - - +
463S ILE* 3.1 25.6 + - - +
464S GLY 4.3 0.2 + - - -
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Residues in contact with SER 461 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428S GLN* 5.8 0.5 + - - -
459S GLU* 4.1 13.0 + - - +
460S LEU* 1.3 81.7 - - - +
462S ARG* 1.3 77.6 + - - +
463S ILE 3.4 0.3 + - - -
464S GLY* 3.9 7.4 + - - -
465S GLU* 4.8 2.1 + - - +
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Residues in contact with ARG 462 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458S ILE* 5.2 5.0 - - + +
459S GLU* 3.5 35.1 + - + +
460S LEU 3.3 0.2 - - - -
461S SER* 1.3 85.5 + - - +
463S ILE* 1.3 59.2 + - - +
464S GLY 3.2 2.5 - - - -
465S GLU* 3.1 37.2 + - + +
466S PHE* 2.9 27.9 + - - +
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Residues in contact with ILE 463 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425S ARG* 4.3 26.0 - - + +
428S GLN* 3.9 19.3 - - + +
429S LEU* 4.4 16.2 - - + +
455S LEU* 4.2 31.4 - - + +
458S ILE* 3.6 31.0 - - + +
459S GLU 3.2 13.9 + - - +
460S LEU* 3.1 18.9 + - - +
462S ARG* 1.3 78.4 - - - +
464S GLY* 1.3 64.1 + - - +
466S PHE* 3.1 19.4 + - + +
467S GLU* 3.6 6.1 + - - +
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Residues in contact with GLY 464 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428S GLN* 4.6 18.1 - - - +
460S LEU 4.3 1.0 + - - -
461S SER 3.9 6.8 + - - -
462S ARG 3.2 0.8 - - - -
463S ILE* 1.3 83.8 - - - +
465S GLU* 1.3 58.5 + - - +
466S PHE 3.6 0.2 + - - -
467S GLU* 3.8 18.0 + - - +
468S SER* 4.6 1.6 + - - -
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Residues in contact with GLU 465 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461S SER 4.8 2.1 + - - +
462S ARG* 3.1 58.5 + - + +
464S GLY* 1.3 73.4 - - - +
466S PHE* 1.3 62.9 + - - +
467S GLU 3.2 2.7 - - - -
468S SER* 2.7 26.9 + - - +
469S SER* 3.4 10.7 + - - -
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Residues in contact with PHE 466 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446S LEU* 5.4 5.2 - - + -
449S ALA* 4.8 7.6 - - + -
455S LEU* 3.5 44.4 - - + -
458S ILE* 5.5 8.1 - - + -
462S ARG 2.9 12.8 + - - +
463S ILE* 3.1 18.8 + - + +
465S GLU* 1.3 76.9 - - - +
467S GLU* 1.3 67.7 + - - +
469S SER* 3.3 10.0 + - - -
470S PHE* 3.0 60.3 + + + +
503S THR* 5.6 2.9 - - + -
506S PHE* 4.2 19.5 - + - -
507S VAL* 5.6 9.4 - - + -
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Residues in contact with GLU 467 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S LYS* 2.8 27.1 + - - -
429S LEU* 4.6 3.2 - - + +
431S LYS 4.4 2.8 - - - +
432S GLN* 5.5 1.6 - - - +
438S LEU* 3.2 28.7 - - - +
446S LEU* 3.9 29.5 - - + +
463S ILE 3.6 5.5 + - - +
464S GLY* 3.9 13.6 - - - +
465S GLU 3.2 0.2 - - - -
466S PHE* 1.3 82.0 - - - +
468S SER* 1.3 59.8 + - - +
471S LEU* 3.1 36.5 + - + +
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Residues in contact with SER 468 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464S GLY 4.6 1.5 + - - -
465S GLU* 2.7 29.7 + - - +
467S GLU* 1.3 80.5 - - - +
469S SER* 1.3 59.0 + - - +
471S LEU* 3.4 4.0 + - - +
472S SER* 3.0 29.6 + - - -
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Residues in contact with SER 469 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465S GLU 3.5 10.1 + - - -
466S PHE* 3.3 14.0 + - - -
468S SER* 1.3 80.7 + - - +
470S PHE* 1.3 60.3 + - - +
472S SER* 3.0 19.8 + - - -
473S TYR* 3.2 17.7 + - - +
506S PHE* 3.5 21.6 - - - -
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Residues in contact with PHE 470 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445S PRO* 3.6 35.7 - - + -
446S LEU* 4.6 13.7 - - + -
449S ALA* 5.3 1.3 - - + -
466S PHE* 3.0 42.3 + + + +
467S GLU* 4.5 2.7 - - - +
469S SER* 1.3 78.4 + - - +
471S LEU* 1.3 58.9 + - + +
472S SER 3.5 0.2 - - - -
473S TYR* 3.9 3.5 + + - +
474S LEU* 3.0 50.0 + - + +
499S LEU* 6.4 0.4 - - + -
502S ALA* 4.5 1.8 - - + -
503S THR* 3.6 48.9 - - + -
506S PHE* 3.4 34.8 - + + -
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Residues in contact with LEU 471 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438S LEU* 4.6 6.5 - - + -
442S GLU* 3.5 51.8 - - + +
445S PRO* 4.6 2.5 - - + -
446S LEU* 4.0 30.1 - - + -
467S GLU* 3.1 26.6 + - + +
468S SER* 3.4 5.3 + - - +
469S SER 3.2 0.2 - - - -
470S PHE* 1.3 79.3 - - + +
472S SER* 1.3 58.3 + - - +
473S TYR 3.3 1.3 - - - -
474S LEU* 3.9 22.4 - - + +
475S LYS* 3.1 38.0 + - + +
482S LEU* 5.6 2.7 - - + -
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Residues in contact with SER 472 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468S SER 3.0 14.7 + - - -
469S SER* 3.0 19.6 + - - -
471S LEU* 1.3 75.8 - - - +
473S TYR* 1.3 59.8 + - - +
475S LYS* 3.9 5.0 + - - +
476S SER* 3.2 27.9 + - - -
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Residues in contact with TYR 473 (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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469S SER 3.2 15.4 + - - +
470S PHE* 4.0 5.2 - + - +
472S SER* 1.3 81.8 + - - +
474S LEU* 1.3 71.7 + - + +
476S SER* 4.8 0.4 - - - -
477S ASN* 3.2 53.9 + - + +
478S HIS* 2.7 36.2 + + - -
502S ALA 3.9 18.1 + - - -
505S SER* 4.0 17.4 + - - -
506S PHE* 3.5 39.7 - + + -
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Residues in contact with LEU 474 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445S PRO* 3.6 36.6 - - + -
470S PHE* 3.0 37.2 + - + +
471S LEU* 4.0 13.7 - - + +
472S SER 3.4 0.2 - - - -
473S TYR* 1.3 90.9 - - + +
475S LYS* 1.3 56.6 + - - +
476S SER 2.9 7.4 + - - -
478S HIS* 2.9 56.7 + - + +
479S ASN 3.2 1.2 + - - -
481S LEU* 6.1 0.2 - - + -
482S LEU* 3.5 21.9 - - + +
499S LEU* 6.1 3.6 - - + -
502S ALA* 4.5 11.0 - - + -
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Residues in contact with LYS 475 (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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442S GLU* 4.5 28.2 + - + +
471S LEU* 3.1 24.2 + - + +
472S SER* 4.0 4.7 - - - +
473S TYR 3.5 0.2 - - - -
474S LEU* 1.3 73.4 - - - +
476S SER* 1.3 59.7 + - - +
479S ASN* 5.1 13.1 - - - +
482S LEU* 3.5 20.6 - - + -
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Residues in contact with SER 476 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472S SER 3.2 19.5 - - - -
473S TYR* 4.2 2.7 - - - -
474S LEU 2.9 0.6 - - - -
475S LYS* 1.3 78.3 - - - +
477S ASN* 1.3 77.0 + - - +
479S ASN* 5.3 3.1 - - - -
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Residues in contact with ASN 477 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473S TYR* 3.2 39.7 + - + +
474S LEU 3.4 0.4 + - - -
476S SER* 1.3 96.9 + - - +
478S HIS* 1.3 72.7 + - + +
479S ASN* 3.4 7.6 + - - +
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Residues in contact with HIS 478 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473S TYR* 2.7 50.6 + + - -
474S LEU* 2.9 30.5 + - + +
477S ASN* 1.3 85.8 - - + +
479S ASN* 1.3 62.0 + - - +
480S GLU 3.4 2.5 - - - +
481S LEU* 3.6 24.1 + - + +
482S LEU* 3.5 21.5 + - - +
502S ALA* 3.5 27.5 - - + +
505S SER* 5.9 1.1 - - - -
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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
------------------------------------------------------------
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