Contacts of the helix formed by residues 469 - 483 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C GLU* 2.3 38.8 + - - -
467C TYR 3.5 0.4 - - - -
468C SER* 1.3 75.4 + - - +
470C VAL* 1.3 63.0 + - - +
471C GLN 3.3 1.8 - - - -
472C ASN* 3.2 10.7 + - - -
473C TYR* 3.0 39.6 + - - -
21D GLN* 3.3 36.0 + - - -
71D LYS* 3.9 0.2 + - - -
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Residues in contact with VAL 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C ILE* 4.1 18.0 - - + +
461C GLU* 5.0 1.5 + - + +
462C MET* 3.8 25.4 - - + -
466C ASP 4.7 2.2 - - - +
467C TYR* 3.4 34.3 - - + +
468C SER 3.2 1.4 - - - -
469C SER* 1.3 78.0 - - - +
471C GLN* 1.3 63.1 + - - +
473C TYR* 3.5 3.3 + - + +
474C LEU* 3.2 30.2 + - + +
511C LEU* 3.8 26.0 - - + -
514C TYR* 4.1 15.5 - - + -
530C TRP* 4.2 5.8 - - + -
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Residues in contact with GLN 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C TYR 4.8 0.2 + - - -
468C SER 4.2 6.3 + - - +
469C SER 3.3 0.2 - - - -
470C VAL* 1.3 80.1 - - - +
472C ASN* 1.3 62.6 + - - +
474C LEU* 3.5 2.1 + - - +
475C ASP* 2.8 47.3 + - - +
514C TYR* 5.2 1.3 + - - +
530C TRP* 3.0 73.3 + - + +
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Residues in contact with ASN 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C SER 4.8 1.0 + - - +
469C SER* 3.2 19.1 + - - +
470C VAL 3.2 0.6 - - - -
471C GLN* 1.3 78.4 - - - +
473C TYR* 1.3 64.8 + - - +
475C ASP* 3.1 9.8 + - - +
476C GLN* 3.0 37.2 + - - +
21D GLN* 3.1 16.3 + - - +
73D GLU* 2.9 27.7 + - - -
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Residues in contact with TYR 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C LEU* 4.1 23.6 - - + +
457C GLN* 3.9 23.8 + - + -
458C ILE* 3.6 37.7 - - + -
461C GLU* 2.9 29.6 + - - -
469C SER* 3.0 36.6 + - - +
470C VAL 4.1 0.7 - - - +
472C ASN* 1.3 76.6 - - - +
474C LEU* 1.3 61.5 + - - +
476C GLN* 3.1 17.6 + - - +
477C ILE* 2.9 33.8 + - - +
21D GLN* 4.4 0.5 + - - -
58D PHE* 5.1 4.3 - + - -
60D THR* 4.9 2.8 + - - -
71D LYS* 3.8 9.0 + - - -
73D GLU* 3.7 31.2 + - + +
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Residues in contact with LEU 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C ILE* 3.9 19.7 - - + -
470C VAL* 3.2 29.9 + - + +
471C GLN* 3.8 4.7 - - - +
472C ASN 3.3 0.2 - - - -
473C TYR* 1.3 75.5 - - - +
475C ASP* 1.3 63.9 + - - +
477C ILE* 3.5 8.1 + - + -
478C GLU* 3.3 12.0 + - - +
496C PHE* 3.2 42.3 - - + -
499C CYS* 6.1 0.4 - - + -
500C ILE* 4.5 14.1 - - + +
503C VAL* 5.6 2.2 - - + -
511C LEU* 5.1 12.3 - - + -
530C TRP* 4.1 15.5 - - + -
534C ILE* 3.8 35.2 - - + -
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Residues in contact with ASP 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C GLN* 2.8 32.6 + - - +
472C ASN* 3.1 12.6 + - - +
474C LEU* 1.3 81.0 - - - +
476C GLN* 1.3 63.0 + - + +
478C GLU* 3.5 11.8 + - - +
479C ASP* 3.3 24.9 + - - +
496C PHE* 5.8 0.3 - - - -
530C TRP* 5.5 1.7 - - - -
534C ILE* 5.7 2.9 - - - +
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Residues in contact with GLN 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C LEU* 3.9 23.6 - - + +
472C ASN* 3.0 40.6 + - - +
473C TYR* 3.1 16.5 + - - +
475C ASP* 1.3 75.4 - - + +
477C ILE* 1.3 64.5 + - - +
479C ASP* 3.3 20.9 - - - +
480C ILE* 3.5 13.5 - - - +
23D LYS* 5.1 10.7 + - - +
73D GLU* 3.1 27.6 + - - +
75D TRP* 4.7 7.8 + - - -
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Residues in contact with ILE 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C ILE* 3.9 33.2 - - + -
454C LEU* 3.7 24.7 - - + -
455C GLN* 4.2 15.3 - - + -
458C ILE* 4.5 14.1 - - + -
473C TYR 2.9 18.8 + - - +
474C LEU* 3.7 14.1 - - + +
475C ASP 3.3 0.4 - - - -
476C GLN* 1.3 74.7 - - - +
478C GLU* 1.3 65.2 + - - +
480C ILE* 3.0 20.0 + - - +
481C LEU* 3.2 21.9 + - + +
496C PHE* 4.0 18.8 - - + -
499C CYS* 4.2 11.4 - - + -
503C VAL* 5.4 0.9 - - + -
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Residues in contact with GLU 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C LEU 3.3 12.6 + - - +
475C ASP* 3.9 11.2 - - - +
476C GLN 3.4 0.2 - - - -
477C ILE* 1.3 80.7 - - - +
479C ASP* 1.3 61.8 + - - +
481C LEU* 3.2 18.8 + - + +
482C THR* 3.2 26.4 + - + +
492C LYS* 4.6 21.5 - - + +
496C PHE* 3.8 24.0 - - + -
533C LYS* 3.0 32.4 + - - +
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Residues in contact with ASP 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C ASP 3.3 13.5 + - - +
476C GLN* 3.3 15.3 - - - +
477C ILE 3.1 0.4 - - - -
478C GLU* 1.3 78.9 - - - +
480C ILE* 1.3 58.4 + - + +
482C THR* 4.3 5.0 - - - +
483C VAL* 2.8 46.3 + - + +
484C ASP* 5.1 1.6 - - - -
92D ARG* 3.1 34.4 + - - -
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Residues in contact with ILE 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417C LEU* 5.0 0.7 - - + -
447C HIS* 3.8 30.3 - - + +
450C ALA* 3.8 23.3 - - + -
451C ILE* 3.7 32.1 - - + +
454C LEU* 4.7 9.0 - - + -
476C GLN 3.5 16.4 - - - +
477C ILE* 3.0 7.1 + - - +
479C ASP* 1.3 77.8 - - + +
481C LEU* 1.3 58.5 + - - +
482C THR 3.4 0.2 + - - -
484C ASP* 4.0 26.7 - - + +
485C ALA* 2.8 33.6 + - + +
75D TRP* 6.1 0.7 - - + -
89D MET* 4.5 5.4 - - + -
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Residues in contact with LEU 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417C LEU* 4.3 4.5 - - + -
421C LEU* 4.7 2.9 - - + -
451C ILE* 3.7 25.8 - - + -
477C ILE* 3.4 23.8 - - + +
478C GLU* 3.2 11.2 + - + +
479C ASP 3.2 1.0 - - - -
480C ILE* 1.3 77.7 - - - +
482C THR* 1.3 57.7 + - - +
485C ALA 2.9 15.1 - - - +
487C MET* 3.2 47.0 - - + +
492C LYS* 4.0 11.4 - - + +
495C ALA* 3.8 11.4 - - + +
496C PHE* 3.5 44.0 - - + +
499C CYS* 4.7 0.4 - - - -
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Residues in contact with THR 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C GLU* 3.2 22.2 - - + +
479C ASP* 3.9 5.8 - - - +
481C LEU* 1.3 77.7 - - - +
483C VAL* 1.3 74.3 + - + +
485C ALA 4.1 3.8 - - - -
486C LYS* 4.4 8.5 - - - +
487C MET 4.6 9.3 + - - +
489C ASP* 5.4 2.4 + - - -
492C LYS* 4.2 24.3 - - + +
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Residues in contact with VAL 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C ASP* 2.8 27.9 + - + +
482C THR* 1.3 91.5 - - + +
484C ASP* 1.3 77.5 + - - +
485C ALA 4.5 0.4 - - - -
486C LYS* 4.0 14.6 + - - +
92D ARG* 4.4 19.3 - - - +
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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