Contacts of the helix formed by residues 463 - 469 (chain C) in PDB entry 5COX
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 LEU 463 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461C GLN 3.6 2.2 + - - -
462C SER* 1.3 71.8 + - - +
464C ASN* 1.3 67.0 + - - +
466C TYR* 3.4 6.8 + - + +
467C ARG* 3.0 26.2 + - + +
475C TYR* 3.8 28.3 - - + -
481C LEU* 4.1 3.4 - - + -
498C ILE* 5.3 2.0 - - + -
501C MET* 3.0 22.7 + - + +
502C GLU 3.1 23.2 + - - +
503C LEU* 3.9 17.7 - - + +
506C ALA* 3.6 28.3 - - + -
521C THR* 3.8 33.4 - - + +
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Residues in contact with ASN 464 (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 SER* 3.0 9.2 + - - +
463C LEU* 1.3 79.6 - - - +
465C GLU* 1.3 66.6 + - + +
467C ARG* 2.8 18.6 + - - +
468C LYS* 2.8 22.8 + - + +
474C PRO* 3.0 16.4 - - + +
475C TYR* 2.9 42.0 + - - +
498C ILE* 3.3 11.9 + - - +
499C ASP* 2.7 40.3 - - + +
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Residues in contact with GLU 465 (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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39C ASN* 4.1 25.9 - - - +
42C GLN* 4.5 3.1 + - - -
152C LEU* 4.5 8.4 - - + +
163C MET 6.0 1.1 - - - +
461C GLN* 4.1 23.3 - - + +
462C SER* 3.1 31.1 + - - +
464C ASN* 1.3 79.9 - - - +
466C TYR* 1.3 58.6 + - - +
468C LYS* 3.1 35.8 + - - +
469C ARG* 2.8 28.4 + - - +
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Residues in contact with TYR 466 (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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150C ARG* 3.5 16.6 + - - -
151C ALA* 4.7 2.2 - - + -
152C LEU* 3.7 24.1 - - + +
380C GLU* 3.0 43.0 + - + -
460C TYR* 3.6 16.4 - + - -
461C GLN* 3.4 34.9 + - + +
462C SER 3.2 21.0 + - - -
463C LEU* 3.7 7.0 - - + +
465C GLU* 1.3 79.9 - - + +
467C ARG* 1.3 62.4 + - + +
469C ARG* 3.7 4.9 - - - -
470C PHE* 3.1 36.8 + + - +
503C LEU* 4.4 19.7 - - + -
521C THR* 6.3 0.4 - - + -
525C LEU* 4.0 27.8 - - + +
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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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463C LEU* 3.0 27.0 + - + +
464C ASN* 2.8 12.2 + - - +
466C TYR* 1.3 73.3 - - - +
468C LYS* 1.3 61.1 + - - +
470C PHE 3.1 7.8 + - - -
472C LEU* 2.6 52.5 + - + +
473C LYS* 2.6 37.7 + - - +
474C PRO* 3.8 4.9 - - + +
475C TYR* 3.6 48.0 + - - +
520C GLU* 2.7 31.9 + - - -
521C THR* 2.6 41.0 + - + +
525C LEU* 5.4 0.4 - - - -
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Residues in contact with LYS 468 (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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42C GLN* 2.9 39.3 + - - +
464C ASN* 2.8 25.7 + - + +
465C GLU* 3.1 38.2 + - - +
467C ARG* 1.3 75.4 - - - +
469C ARG* 1.3 58.9 + - - +
471C SER* 2.8 22.6 + - - +
472C LEU 3.5 8.9 + - - -
474C PRO* 4.2 23.6 - - + -
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Residues in contact with ARG 469 (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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44C ARG* 3.1 48.0 - - - +
123C LEU* 2.3 39.8 + - - +
124C ILE* 4.3 6.5 - - - +
125C ASP* 4.8 7.7 + - - +
151C ALA* 2.5 43.4 + - - +
152C LEU* 3.2 30.1 - - + -
465C GLU 2.8 12.6 + - - +
466C TYR* 3.5 11.2 - - - +
468C LYS* 1.3 76.8 - - - +
470C PHE* 1.3 79.2 + - + +
471C SER* 3.2 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