Contacts of the helix formed by residues 466 - 474 (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 PRO 466 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C ALA 3.4 1.1 - - - +
465C ILE* 1.3 87.1 - - - +
467C ARG* 1.3 67.3 + - - +
468C ILE* 3.9 11.2 - - + +
469C GLU* 2.9 46.0 + - + +
470C ALA* 3.1 10.0 + - - +
483C ARG* 4.4 1.1 - - - -
486C HIS* 4.0 13.5 - - + +
455E LEU* 4.7 10.3 - - + -
492E TYR* 3.6 25.4 - - + +
514E TYR* 3.9 18.8 - - - +
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Residues in contact with ARG 467 (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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466C PRO* 1.3 72.9 - - - +
468C ILE* 1.3 64.0 + - - +
470C ALA* 3.0 2.4 + - - +
471C GLN* 2.9 40.0 + - + +
483C ARG* 3.8 18.1 - - - +
486C HIS* 6.2 0.2 - - - +
504C HIS* 3.2 38.5 + - + +
1D ASP* 3.3 43.1 + - - +
2D GLU* 2.8 36.8 + - - +
3D PTR 2.7 53.0 + - - +
509E TYR* 4.7 3.8 - - + +
512E ASN* 5.8 0.7 - - - -
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Residues in contact with ILE 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C PRO* 3.9 19.7 - - + +
467C ARG* 1.3 80.8 - - - +
469C GLU* 1.3 68.6 + - + +
471C GLN* 3.6 16.3 + - + +
472C GLU* 3.6 12.5 + - - +
509E TYR* 6.1 2.2 - - + +
512E ASN 6.0 1.1 - - - +
514E TYR* 4.4 13.6 + - + +
522E SER* 3.5 35.2 - - - +
523E ASN* 4.3 17.3 - - + +
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Residues in contact with GLU 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C ILE* 3.6 28.9 - - + +
466C PRO* 2.9 28.2 + - + +
468C ILE* 1.3 81.6 - - + +
470C ALA* 1.3 66.9 + - - +
472C GLU* 3.2 17.0 + - - +
473C LEU* 3.4 17.2 + - + +
454E PRO* 3.6 22.1 - - + +
455E LEU* 2.7 42.8 + - - +
456E ALA* 5.1 1.6 + - - +
523E ASN* 6.3 1.3 - - + -
525E PRO* 5.7 1.2 - - - +
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Residues in contact with ALA 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C ILE* 3.9 14.4 - - + +
466C PRO 3.1 5.5 + - - +
467C ARG* 3.0 8.8 + - - +
469C GLU* 1.3 76.3 - - - +
471C GLN* 1.3 62.7 + - - +
473C LEU* 3.0 11.8 + - - +
474C LEU* 3.3 20.6 + - + +
481C LEU* 4.2 13.9 - - + -
483C ARG* 3.8 33.2 - - - +
495C SER* 4.4 8.1 - - - +
504C HIS* 4.8 2.9 - - + -
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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
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467C ARG* 2.9 38.0 + - + +
468C ILE* 3.8 13.9 - - + +
469C GLU 3.2 0.4 - - - -
470C ALA* 1.3 76.2 - - - +
472C GLU* 1.3 61.3 + - - +
474C LEU 3.3 3.3 - - - +
502C ARG* 2.9 66.0 + - + +
504C HIS* 3.0 30.5 + - + +
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Residues in contact with GLU 472 (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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468C ILE 3.6 10.1 + - - +
469C GLU* 3.2 13.3 + - - +
471C GLN* 1.3 80.5 - - - +
473C LEU* 1.3 60.4 + - + +
474C LEU 3.6 0.3 + - - -
475C LYS* 3.2 25.6 - - - +
502C ARG* 5.0 2.0 + - - +
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Residues in contact with LEU 473 (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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462C HIS* 3.6 33.2 - - + +
465C ILE* 3.9 15.7 - - + -
469C GLU* 3.6 16.2 - - + +
470C ALA 3.0 7.2 + - - +
472C GLU* 1.3 81.7 - - + +
474C LEU* 1.3 60.3 + - - +
475C LYS* 3.8 16.9 + - - +
479C ASP* 4.4 0.2 - - - +
481C LEU* 4.0 10.1 - - + -
550C ILE* 3.7 33.9 - - + +
551C PRO 4.9 3.1 - - - +
552C LYS 5.9 2.5 - - - -
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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
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470C ALA* 3.3 19.6 + - + +
471C GLN 3.6 0.2 + - - -
472C GLU 3.4 0.2 - - - -
473C LEU* 1.3 76.9 - - - +
475C LYS* 1.3 59.5 + - - +
479C ASP* 3.7 31.9 - - + +
480C PHE* 3.7 16.8 - - - +
481C LEU* 4.0 10.3 - - + -
495C SER* 3.6 37.9 - - - -
496C VAL 3.8 7.0 - - - +
497C TYR* 3.5 15.8 - - + -
502C ARG* 2.9 46.3 + - + -
504C HIS* 5.1 0.7 - - + -
550C ILE* 3.9 8.3 - - + -
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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