Contacts of the helix formed by residues 460 - 465 (chain C) in PDB entry 1N8Y
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 460 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458C THR 3.8 0.2 - - - -
459C VAL* 1.3 88.6 - - + +
461C TRP* 1.3 62.6 + - - +
462C ASP* 3.3 11.2 - - - +
463C GLN* 3.1 43.9 + - + +
464C LEU* 3.8 11.1 - - + +
498C HIS* 3.7 41.7 - - + +
508C VAL* 3.9 25.6 - - + -
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Residues in contact with TRP 461 (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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422C LEU* 4.0 22.7 - - + -
432C LEU* 4.1 8.1 - - + -
434C LEU* 5.6 0.7 - - + -
440C LEU* 4.2 10.5 - - + -
445C ALA* 4.5 5.8 - - + -
447C ILE* 3.7 31.0 - - + -
456C VAL* 3.0 22.8 + - + -
457C HIS* 5.4 3.4 - - - -
459C VAL* 3.1 40.8 + - + +
460C PRO* 1.3 67.7 - - - +
462C ASP* 1.3 67.1 + - - +
463C GLN 3.0 1.2 + - - -
464C LEU* 3.1 42.7 + - + +
465C PHE* 3.2 37.8 + + + -
472C LEU* 3.8 28.0 - - + +
500C TRP* 4.0 15.7 - + - -
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Residues in contact with ASP 462 (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 PRO* 3.6 16.6 - - - +
461C TRP* 1.3 73.4 + - - +
463C GLN* 1.3 70.3 + - - +
464C LEU 3.7 0.2 + - - -
465C PHE* 3.8 28.5 + - + +
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Residues in contact with GLN 463 (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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438C ARG 3.7 4.3 - - - +
460C PRO* 3.1 39.2 + - + +
461C TRP 3.0 1.0 - - - -
462C ASP* 1.3 87.2 + - - +
464C LEU* 1.3 64.9 + - + +
465C PHE 4.3 0.2 - - - -
466C ARG* 2.8 19.7 + - - -
498C HIS* 4.5 12.1 + - - -
508C VAL* 4.9 7.6 - - - +
509C ASN* 5.8 0.7 + - - -
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Residues in contact with LEU 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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437C LEU* 3.5 35.4 - - + +
438C ARG* 3.3 23.1 - - + +
439C GLU* 3.5 0.3 - - - -
440C LEU* 2.8 37.4 + - + +
459C VAL* 4.7 1.6 - - + -
460C PRO* 3.8 18.6 - - + +
461C TRP* 3.1 38.5 + - + +
463C GLN* 1.3 80.6 - - + +
465C PHE* 1.3 63.0 + - - +
466C ARG* 2.9 13.5 + - - -
500C TRP* 3.8 25.4 - - + -
508C VAL* 6.2 1.1 - - + -
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Residues in contact with PHE 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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440C LEU* 4.0 24.2 - - + -
443C GLY 4.8 2.5 - - - -
445C ALA* 4.9 3.1 - - + -
461C TRP* 3.2 41.8 + + + -
462C ASP* 3.8 20.3 + - - +
463C GLN 3.6 0.6 - - - +
464C LEU* 1.3 76.8 - - - +
466C ARG* 1.3 77.7 + - - +
467C ASN 4.4 5.6 - - - +
470C GLN* 3.5 37.7 - - + +
471C ALA* 3.4 40.2 - - - -
472C LEU* 3.6 7.0 - - + -
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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