Contacts of the helix formed by residues 492 - 507 (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 LYS 492 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478C GLU* 4.6 20.0 - - + +
481C LEU* 4.0 25.1 - - + +
482C THR* 4.2 23.8 - - + +
487C MET* 4.1 9.2 - - + +
488C ASP 3.2 8.3 + - - +
489C ASP* 3.2 46.0 + - - +
490C ILE 3.2 0.6 - - - -
491C GLN* 1.3 79.7 - - - +
493C GLU* 1.3 71.8 + - + +
494C LYS 3.5 0.2 - - - -
495C ALA* 4.0 1.6 - - - -
496C PHE* 3.2 27.0 + - - +
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Residues in contact with GLU 493 (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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489C ASP 4.3 9.9 - - - +
490C ILE* 3.6 10.2 + - - +
492C LYS* 1.3 89.4 - - + +
494C LYS* 1.3 59.9 + - - +
496C PHE* 3.8 4.7 - - - +
497C ALA* 2.8 32.7 + - - +
533C LYS* 5.6 6.6 - - - +
537C LEU* 4.1 25.5 - - + +
544C TRP* 3.9 21.7 - - + -
553C ALA* 5.6 3.5 + - - +
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Residues in contact with LYS 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C PHE* 6.3 1.0 - - - -
414C ASP* 4.4 14.6 + - - +
418C MET* 3.7 14.3 - - + +
490C ILE* 3.7 31.0 + - + +
491C GLN* 4.2 14.8 - - - +
493C GLU* 1.3 75.8 - - - +
495C ALA* 1.3 58.2 + - - +
497C ALA* 4.4 0.2 - - - -
498C LEU* 3.0 29.5 + - - +
544C TRP* 3.6 39.5 - - + +
545C VAL* 3.3 34.6 - - - +
546C VAL 5.2 0.2 - - - -
547C SER 2.9 25.9 + - - -
548C LEU* 5.4 1.0 - - - +
549C PHE* 4.2 10.9 + - + +
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Residues in contact with ALA 495 (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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418C MET* 3.6 15.3 - - + +
421C LEU* 4.3 8.7 - - + +
481C LEU* 3.8 22.7 - - + -
487C MET* 3.8 16.6 - - + -
491C GLN 3.7 16.9 + - - +
492C LYS 3.8 2.7 + - - +
493C GLU 3.2 0.2 - - - -
494C LYS* 1.3 77.4 - - - +
496C PHE* 1.3 59.6 + - - +
498C LEU* 3.4 4.0 + - - +
499C CYS* 3.0 33.8 + - - -
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Residues in contact with PHE 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C LEU* 3.2 40.2 - - + -
475C ASP* 5.8 0.2 - - - -
477C ILE* 4.0 22.4 - - + -
478C GLU* 3.8 33.7 - - + -
481C LEU* 3.5 9.6 - - + +
492C LYS 3.2 17.1 + - - +
493C GLU* 3.4 4.5 + - - +
495C ALA* 1.3 76.1 - - - +
497C ALA* 1.3 61.2 + - - +
499C CYS* 3.1 3.6 + - + +
500C ILE* 2.9 44.0 + - + +
533C LYS* 3.9 6.5 - - - -
534C ILE* 3.8 30.5 - - + -
537C LEU* 3.5 19.7 - - + -
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Residues in contact with ALA 497 (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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493C GLU 2.8 18.9 + - - +
494C LYS* 3.8 4.0 - - - +
496C PHE* 1.3 77.4 - - - +
498C LEU* 1.3 56.9 + - - +
500C ILE* 3.2 3.4 + - - +
501C LYS* 2.8 36.6 + - - +
537C LEU* 3.4 39.6 - - + +
540C ALA* 4.5 3.8 - - + -
544C TRP* 4.7 1.3 - - + -
545C VAL* 4.0 17.0 - - + -
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Residues in contact with LEU 498 (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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364C VAL* 3.7 22.9 - - + +
418C MET* 3.6 25.8 - - + -
421C LEU* 3.6 38.1 - - + -
422C TYR* 4.1 10.8 - - + +
494C LYS 3.0 18.4 + - - +
495C ALA 3.6 3.8 - - - +
497C ALA* 1.3 75.6 - - - +
499C CYS* 1.3 57.7 + - - +
501C LYS* 3.4 7.4 + - - +
502C GLN* 2.9 56.1 + - + +
542C ILE* 5.0 2.5 - - + -
545C VAL* 4.4 16.1 - - + +
546C VAL* 5.5 0.2 - - + -
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Residues in contact with CYS 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LEU* 4.0 21.8 - - - -
451C ILE* 3.7 28.9 - - + -
455C GLN* 3.3 17.1 + - - +
474C LEU* 6.1 1.1 - - + -
477C ILE* 4.2 22.0 - - + -
481C LEU* 4.7 1.3 - - - -
495C ALA 3.0 24.1 + - - +
496C PHE* 3.1 11.4 + - + +
498C LEU* 1.3 76.8 - - - +
500C ILE* 1.3 60.0 + - - +
502C GLN* 3.4 1.2 + - - -
503C VAL* 3.1 30.7 + - - +
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Residues in contact with ILE 500 (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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474C LEU* 4.5 9.6 - - + -
496C PHE* 2.9 32.9 + - + +
497C ALA* 3.6 6.3 - - - +
499C CYS* 1.3 73.2 - - - +
501C LYS* 1.3 60.9 + - - +
503C VAL* 3.4 6.2 + - - +
504C ASN* 2.9 28.4 + - - +
511C LEU* 4.1 16.2 - - + +
515C LEU* 5.0 0.4 - - + -
534C ILE* 3.7 45.3 - - + +
537C LEU* 3.9 23.8 - - + -
538C LEU* 3.7 28.3 - - + -
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Residues in contact with LYS 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C LEU* 4.7 2.0 - - - +
362C GLU* 3.0 36.5 + - - +
364C VAL* 3.7 16.4 - - + +
497C ALA 2.8 22.0 + - - +
498C LEU* 3.6 7.6 - - - +
500C ILE* 1.3 77.6 - - - +
502C GLN* 1.3 61.4 + - - +
504C ASN* 3.5 2.3 + - - +
505C PHE* 3.0 22.9 + - - +
537C LEU 3.8 10.3 - - - +
538C LEU* 2.8 42.4 + - + +
539C TRP 4.7 0.2 - - - -
540C ALA 2.9 26.2 + - - -
542C ILE* 4.2 20.2 - - + +
545C VAL* 4.3 13.7 - - + -
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Residues in contact with GLN 502 (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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364C VAL* 3.6 20.4 + - + -
365C TYR* 3.3 39.8 + - + +
421C LEU* 2.3 37.6 + - - +
455C GLN* 3.1 27.4 + - - +
498C LEU* 2.9 35.3 + - - +
499C CYS 3.7 4.0 - - - +
501C LYS* 1.3 73.5 - - - +
503C VAL* 1.3 54.9 + - - +
505C PHE* 3.0 6.2 + - - +
506C LEU* 2.8 39.7 + - + +
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Residues in contact with VAL 503 (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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455C GLN* 3.6 37.5 - - + +
458C ILE* 3.9 33.0 - - + -
459C VAL* 3.7 10.2 - - + +
462C MET* 4.3 5.2 - - + -
474C LEU* 5.6 2.5 - - + -
477C ILE* 5.4 1.3 - - + -
499C CYS 3.1 22.5 + - - +
500C ILE* 3.7 5.4 - - - +
502C GLN* 1.3 74.9 - - - +
504C ASN* 1.3 58.2 + - - +
506C LEU* 3.1 9.1 + - - +
507C SER* 2.8 31.2 + - - -
511C LEU* 3.8 19.1 - - + -
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Residues in contact with ASN 504 (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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359C LEU* 4.1 17.6 + - - +
360C ASN* 4.5 5.7 + - - +
500C ILE 2.9 18.6 + - - +
501C LYS 3.7 5.4 - - - +
503C VAL* 1.3 76.2 - - - +
505C PHE* 1.3 60.1 + - - +
507C SER* 3.1 8.7 + - - -
508C GLU 3.2 0.2 + - - -
509C GLY* 2.9 54.8 + - - -
511C LEU* 4.0 9.3 + - + -
512C GLU* 3.6 17.5 + - - +
538C LEU* 3.6 36.1 - - + +
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Residues in contact with PHE 505 (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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359C LEU 6.0 0.4 - - - -
360C ASN* 4.3 25.5 - - + +
362C GLU 5.2 5.4 - - - -
364C VAL* 4.0 22.0 - - + -
365C TYR* 4.6 18.2 - + - -
501C LYS 3.0 12.9 + - - +
502C GLN* 3.0 8.8 + - - +
504C ASN* 1.3 75.6 - - - +
506C LEU* 1.3 83.2 + - + +
508C GLU* 3.1 18.2 + - - +
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Residues in contact with LEU 506 (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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365C TYR* 3.8 26.9 - - + +
452C LEU* 5.2 7.0 - - + -
455C GLN* 4.8 17.0 - - + +
456C GLU* 5.3 6.5 - - + -
459C VAL* 3.4 27.0 - - + +
463C ASN* 5.3 1.2 + - - -
502C GLN* 2.8 27.4 + - + +
503C VAL* 3.1 8.7 + - - +
505C PHE* 1.3 90.0 - - + +
507C SER* 1.3 58.0 + - - +
508C GLU* 3.3 5.1 + - - +
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Residues in contact with SER 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C VAL* 3.8 14.4 - - - -
462C MET* 3.7 25.4 - - - +
463C ASN* 4.7 5.6 - - - +
503C VAL 2.8 22.2 + - - -
504C ASN* 3.1 13.0 + - - -
506C LEU* 1.3 76.7 - - - +
508C GLU* 1.3 69.1 + - - +
510C LYS* 3.2 29.3 - - - +
511C LEU 3.7 12.6 + - - -
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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