Contacts of the helix formed by residues 454 - 459 (chain C) in PDB entry 5NC5
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 VAL 454 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C SER* 3.1 21.5 + - - +
451C ALA* 3.9 7.2 - - - +
453C PHE* 1.3 75.3 - - - +
455C PRO* 1.3 77.6 - - + +
456C MET 2.9 1.6 + - - -
457C ALA* 3.0 19.7 + - - +
458C PHE* 4.0 11.8 - - + -
471C SER* 4.5 3.8 - - - -
475C VAL* 4.4 15.0 - - + -
1107C D12 3.9 35.9 - - + -
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Residues in contact with PRO 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C ALA 3.1 18.8 - - - +
452C VAL 4.3 1.1 - - - +
453C PHE 4.1 0.7 - - - -
454C VAL* 1.3 94.3 - - + +
456C MET* 1.3 60.6 + - - +
457C ALA 3.3 0.7 + - - -
458C PHE* 3.4 11.4 + - + +
459C PHE* 3.4 18.0 - - - -
876C LEU* 4.2 1.8 - - + -
879C ILE* 4.0 18.2 - - + +
880C SER* 3.6 25.1 - - - +
883C VAL* 3.9 27.1 - - + -
1107C D12 4.2 20.4 - - + +
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Residues in contact with MET 456 (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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452C VAL 4.8 0.8 + - - +
453C PHE* 2.9 48.2 - - + +
455C PRO* 1.3 75.2 - - - +
457C ALA* 1.3 65.5 + - - +
458C PHE 3.1 3.1 + - - -
459C PHE* 3.3 16.3 + - - +
464C GLY 4.6 1.2 - - - +
467C TYR* 3.2 67.3 - - + +
470C PHE* 4.8 1.3 - - + -
471C SER* 3.8 6.3 - - - -
876C LEU* 3.6 22.2 - - + -
929C VAL* 4.0 16.6 - - + -
932C LEU* 3.9 19.5 - - + -
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Residues in contact with ALA 457 (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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454C VAL* 3.0 14.5 + - - +
456C MET* 1.3 83.8 - - - +
458C PHE* 1.3 53.1 + - + +
459C PHE 3.2 0.9 - - - -
468C ARG* 2.6 49.9 + - + +
471C SER* 3.4 20.9 - - - +
1101C DD9 3.8 20.1 - - + +
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Residues in contact with PHE 458 (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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1106B DD9 3.9 41.5 - - + -
454C VAL* 4.0 21.8 - - + -
455C PRO 3.4 2.2 + - - +
456C MET 3.1 1.0 - - - -
457C ALA* 1.3 78.6 - - + +
459C PHE* 1.3 69.2 + - - +
468C ARG* 4.4 0.9 - - - +
1101C DD9 3.1 32.1 - - + -
1104C D10 3.4 51.4 - - + +
1107C D12 3.6 62.0 - - + +
1110C DD9 4.9 3.1 - - + -
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Residues in contact with PHE 459 (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 PRO 3.4 22.2 - - - -
456C MET* 3.3 13.0 + - - +
457C ALA 3.2 3.2 - - - -
458C PHE* 1.3 84.2 - - - +
460C GLY* 1.3 58.0 + - - +
464C GLY* 3.8 14.1 - - - -
467C TYR* 4.3 6.3 - + + -
468C ARG* 3.0 24.9 + - - -
872C GLN* 3.8 43.5 - - + +
875C SER* 4.4 10.1 - - - -
876C LEU* 3.6 46.0 - - + -
879C ILE* 4.7 4.9 - - + -
1104C D10 4.5 6.7 - - - +
1107C D12 4.0 29.6 - - + -
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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