Contacts of the helix formed by residues 469 - 483 (chain G) in PDB entry 4KYI
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 469 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461G GLU* 3.0 24.7 + - - -
466G ASP* 4.5 0.2 + - - -
468G SER* 1.3 76.1 + - - +
470G VAL* 1.3 63.2 + - - +
471G GLN 3.4 0.9 - - - -
472G ASN* 3.6 15.7 - - - -
473G TYR* 3.1 43.3 + - - -
21H GLN* 3.2 35.1 + - - -
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Residues in contact with VAL 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458G ILE* 4.1 16.8 - - + +
461G GLU* 6.1 1.1 - - + +
462G MET* 4.1 24.2 - - + -
466G ASP 4.5 1.3 - - - +
467G TYR* 3.5 36.3 - - + +
468G SER 3.1 1.6 - - - -
469G SER* 1.3 77.9 - - - +
471G GLN* 1.3 65.5 + - - +
473G TYR* 3.5 4.2 + - - +
474G LEU* 3.2 31.0 + - + +
511G LEU* 4.0 25.1 - - + -
514G TYR* 4.4 15.9 - - + -
515G LEU* 5.7 0.4 - - + -
530G TRP* 4.8 2.7 - - + -
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Residues in contact with GLN 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468G SER 4.1 6.3 + - - +
470G VAL* 1.3 80.2 - - - +
472G ASN* 1.3 63.8 + - - +
474G LEU* 3.4 6.1 + - + +
475G ASP* 3.0 45.6 + - - +
514G TYR* 5.6 0.6 + - - +
530G TRP* 3.6 71.2 + - + +
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Residues in contact with ASN 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468G SER 4.8 1.0 + - - +
469G SER* 3.4 18.0 - - - +
470G VAL 3.2 0.4 - - - -
471G GLN* 1.3 79.3 - - - +
473G TYR* 1.3 62.9 + - - +
475G ASP* 3.1 14.1 + - - +
476G GLN* 3.0 34.8 + - - +
21H GLN* 3.8 16.8 - - - +
73H GLU* 3.2 25.1 + - - -
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Residues in contact with TYR 473 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454G LEU* 3.9 24.0 - - + +
457G GLN* 4.3 20.0 + - + -
458G ILE* 3.5 39.5 - - + -
461G GLU* 3.3 24.9 + - - -
469G SER* 3.1 37.0 + - - +
470G VAL* 5.0 0.2 - - - -
471G GLN 3.4 0.2 - - - -
472G ASN* 1.3 93.9 - - - +
474G LEU* 1.3 65.2 + - - +
476G GLN* 3.3 11.7 + - - +
477G ILE* 3.1 27.5 + - - +
21H GLN* 3.4 10.4 + - - -
58H PHE* 5.4 4.1 - + - -
60H THR* 5.4 3.3 + - - +
71H LYS* 4.5 3.8 + - - -
73H GLU* 4.0 22.1 - - + +
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Residues in contact with LEU 474 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458G ILE* 4.2 15.7 - - + -
470G VAL* 3.2 24.4 + - + +
471G GLN* 3.5 7.9 - - + +
472G ASN 3.2 0.2 - - - -
473G TYR* 1.3 77.6 - - - +
475G ASP* 1.3 59.9 + - - +
477G ILE* 3.3 9.4 + - + +
478G GLU 2.9 23.4 + - - -
496G PHE* 3.2 36.8 - - + -
499G CYS 6.3 0.2 - - - -
500G ILE* 4.4 13.0 - - + +
503G VAL* 5.4 7.2 - - + -
511G LEU* 5.3 11.7 - - + -
515G LEU* 5.4 0.4 - - + -
530G TRP* 4.3 22.9 - - + -
534G ILE* 4.4 23.3 - - + -
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Residues in contact with ASP 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471G GLN* 3.0 44.8 + - - +
472G ASN* 3.3 13.4 - - - +
474G LEU* 1.3 78.7 - - - +
476G GLN* 1.3 56.5 + - + +
478G GLU* 3.4 19.2 + - - +
479G ASP* 3.0 30.1 + - - +
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Residues in contact with GLN 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454G LEU* 3.4 35.2 - - + +
472G ASN* 3.0 27.5 + - - +
473G TYR* 3.6 7.5 - - - +
474G LEU 3.2 0.2 - - - -
475G ASP* 1.3 75.4 - - + +
477G ILE* 1.3 59.1 + - - +
479G ASP* 3.3 7.4 + - - +
480G ILE* 3.0 33.4 + - + +
23H LYS* 4.7 17.1 + - - +
73H GLU* 2.6 36.7 + - - +
75H TRP* 4.4 11.1 + - - -
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Residues in contact with ILE 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451G ILE* 4.1 24.0 - - + -
454G LEU* 3.7 23.1 - - + -
455G GLN* 4.1 27.6 - - + +
458G ILE* 4.8 9.0 - - + -
473G TYR 3.1 16.6 + - - +
474G LEU* 3.3 15.2 + - + +
476G GLN* 1.3 73.0 - - - +
478G GLU* 1.3 61.5 + - - +
480G ILE* 3.2 7.4 + - - +
481G LEU* 2.9 44.9 + - + +
496G PHE* 4.2 11.4 - - + -
499G CYS* 4.3 12.6 - - + -
503G VAL* 5.3 2.0 - - + -
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Residues in contact with GLU 478 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474G LEU 2.9 13.1 + - - +
475G ASP* 3.5 23.8 - - - +
476G GLN 3.3 0.2 - - - -
477G ILE* 1.3 77.4 - - - +
479G ASP* 1.3 56.7 + - - +
481G LEU* 3.3 6.8 + - + +
482G THR* 2.9 39.8 + - + +
492G LYS* 5.6 9.4 - - + -
496G PHE* 3.4 31.1 - - + -
533G LYS* 3.0 29.3 + - - -
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Residues in contact with ASP 479 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475G ASP 3.0 15.3 + - - +
476G GLN* 3.5 11.2 - - - +
477G ILE 3.2 0.2 - - - -
478G GLU* 1.3 74.0 - - - +
480G ILE* 1.3 59.7 + - + +
482G THR* 3.9 9.0 - - - +
483G VAL* 2.9 39.9 + - - +
92H ARG* 2.6 33.3 + - - +
93H GLY* 6.0 2.1 - - - -
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Residues in contact with ILE 480 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417G LEU* 5.1 0.2 - - + -
447G HIS* 3.8 30.3 - - + +
450G ALA* 3.7 27.6 - - + -
451G ILE* 3.9 20.4 - - + -
454G LEU* 4.2 17.7 - - + -
476G GLN* 3.0 19.4 + - + +
477G ILE* 3.2 7.6 + - - +
479G ASP* 1.3 75.2 - - + +
481G LEU* 1.3 59.4 + - - +
484G ASP* 3.5 20.0 + - - +
485G ALA* 3.1 26.9 + - - +
75H TRP* 5.4 2.7 - - + -
89H MET* 4.3 11.9 - - + +
92H ARG* 5.1 1.8 - - - +
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Residues in contact with LEU 481 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417G LEU* 3.7 21.1 - - + -
421G LEU* 4.9 3.1 - - + -
451G ILE* 4.1 10.3 - - + -
477G ILE* 2.9 33.2 + - + +
478G GLU* 3.6 5.2 - - - +
480G ILE* 1.3 78.8 - - - +
482G THR* 1.3 57.2 + - - +
485G ALA* 3.0 26.0 - - - +
487G MET* 3.7 37.2 - - + +
492G LYS* 4.2 10.3 - - + +
495G ALA* 3.9 9.4 - - + +
496G PHE* 3.6 44.6 - - + +
499G CYS* 4.6 1.3 - - - -
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Residues in contact with THR 482 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478G GLU* 2.9 25.4 + - + +
479G ASP* 3.8 9.2 - - - +
481G LEU* 1.3 77.0 - - - +
483G VAL* 1.3 76.3 + - + +
485G ALA 3.7 5.8 - - - +
487G MET* 5.3 6.3 + - - +
492G LYS* 3.7 32.6 + - - +
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Residues in contact with VAL 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479G ASP* 2.9 20.5 + - - +
482G THR* 1.3 93.4 - - + +
484G ASP* 1.3 68.7 + - - +
485G ALA 3.1 8.1 + - - +
486G LYS* 3.9 11.8 - - - +
92H ARG* 3.7 36.8 - - - +
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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