Contacts of the strand formed by residues 479 - 484 (chain C) in PDB entry 6KC4
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 ASP 479 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C LEU 4.4 0.3 - - - +
474C LEU* 3.7 10.7 - - + +
475C LYS* 3.0 13.6 + - - +
476C LYS* 2.8 57.3 + - - +
478C GLY* 1.3 75.0 - - - +
480C PHE* 1.3 59.6 + - - +
496C VAL* 3.2 6.8 - - - +
497C TYR* 2.9 29.9 + - + -
548C ASN* 3.1 28.0 - - - +
550C ILE* 3.6 23.6 - - + +
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Residues in contact with PHE 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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460C TRP* 3.9 19.5 - + + +
474C LEU* 3.7 4.9 - - - -
478C GLY 3.5 10.3 - - - +
479C ASP* 1.3 76.3 - - - +
481C LEU* 1.3 67.0 + - - +
482C VAL* 5.4 0.9 - - + -
494C LEU* 4.0 15.0 - - + -
495C SER 3.2 11.9 - - - +
496C VAL* 3.8 14.4 - - + -
528C ILE* 3.7 28.3 - - + -
532C TYR* 3.9 16.4 - + - -
546C LEU* 3.8 30.3 - - + -
548C ASN 2.9 19.4 + - - -
549C PRO* 3.4 32.0 - - + +
550C ILE* 2.9 27.2 + - - +
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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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460C TRP 3.3 14.8 - - - +
462C HIS* 3.6 18.2 - - + +
465C ILE* 4.4 4.7 - - + -
470C ALA* 4.2 9.6 - - + -
473C LEU* 4.0 33.2 - - + -
474C LEU* 4.0 21.3 - - + -
480C PHE* 1.3 78.0 - - - +
482C VAL* 1.3 78.2 + - - +
483C ARG* 4.1 18.6 - - + -
494C LEU* 3.6 5.7 - - - +
495C SER* 2.9 46.5 + - - -
550C ILE* 4.5 2.7 - - + +
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Residues in contact with VAL 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C LEU* 5.1 0.2 - - + -
460C TRP* 2.9 39.3 + - + -
461C TYR* 3.6 15.6 - - + -
462C HIS* 2.8 29.3 + - - +
480C PHE* 5.4 1.1 - - + -
481C LEU* 1.3 79.7 - - - +
483C ARG* 1.3 70.2 + - - +
492C TYR* 4.3 11.0 - - + -
493C VAL 3.2 12.1 - - - +
494C LEU* 4.1 7.6 - - + -
507C ILE* 4.2 15.7 - - + -
524C ILE* 4.6 4.5 - - + -
528C ILE* 3.9 23.3 - - + -
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Residues in contact with ARG 483 (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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461C TYR* 4.7 0.9 - - - -
463C GLY 3.2 14.6 - - - +
465C ILE* 3.6 29.8 + - + +
466C PRO* 4.6 1.0 - - - +
467C ARG* 3.8 19.6 - - - +
470C ALA* 3.8 22.8 - - - +
481C LEU* 4.1 6.1 - - + -
482C VAL* 1.3 78.7 - - - +
484C GLU* 1.3 64.6 + - - +
486C HIS* 4.8 0.4 + - - +
492C TYR* 3.5 7.8 - - - +
493C VAL* 2.8 55.7 + - + +
495C SER* 3.0 14.8 + - - +
504C HIS* 3.2 28.3 + - - -
3D PTR 2.8 44.1 + - - -
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Residues in contact with GLU 484 (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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464A ALA* 3.6 26.6 - - - +
484A GLU* 5.6 0.9 - - - +
486A HIS* 5.4 8.1 + - + +
461C TYR* 3.1 23.6 + - + +
463C GLY* 2.8 20.9 + - - +
464C ALA* 3.3 26.7 + - + +
465C ILE 4.3 7.1 - - - +
483C ARG* 1.3 76.6 + - - +
485C SER* 1.3 67.5 + - - +
486C HIS* 3.7 15.0 + - + -
491C GLU 3.8 6.7 - - - +
492C TYR* 4.6 9.0 - - + +
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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