Contacts of the helix formed by residues 459 - 464 (chain B) in PDB entry 5NTI
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 ARG 459 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B LEU 2.9 28.3 + - - -
411B HIS* 3.5 15.3 + - - +
412B PHE* 4.3 0.8 - - - +
416B GLU* 3.0 41.3 + - - +
454B LEU* 2.7 20.2 + - + +
455B SER* 4.8 0.2 - - - +
457B THR* 3.4 37.2 - - - +
458B HIS* 1.3 74.3 - - - +
460B GLN* 1.3 60.3 + - - +
461B SER* 3.1 12.3 + - - +
462B ILE* 3.3 45.7 + - - +
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Residues in contact with GLN 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B HIS* 4.7 8.6 + - - +
454B LEU* 3.9 4.0 + - + -
455B SER* 3.3 38.6 - - - +
458B HIS 3.8 1.8 - - - -
459B ARG* 1.3 74.8 - - - +
461B SER* 1.3 63.7 + - - +
462B ILE 3.2 1.5 + - - -
463B LEU* 3.3 39.5 + - + +
464B ALA 4.6 0.9 + - - -
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Residues in contact with SER 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B HIS 4.6 3.8 + - - -
459B ARG* 4.2 9.7 + - - -
460B GLN* 1.3 77.9 - - - +
462B ILE* 1.3 66.8 + - - +
463B LEU 3.3 0.9 + - - -
464B ALA* 3.9 9.5 + - - +
465B LYS* 3.6 36.7 + - - +
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Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU* 4.3 20.4 - - + +
412B PHE* 3.7 30.5 - - + -
416B GLU* 4.0 4.3 - - + +
450B PHE* 4.7 5.4 - - + -
454B LEU* 3.8 26.5 - - + -
459B ARG* 3.3 51.6 - - - +
461B SER* 1.3 81.8 - - - +
463B LEU* 1.3 62.2 + - + +
464B ALA 3.4 0.7 - - - -
465B LYS* 3.0 26.7 + - + +
466B LEU* 3.1 19.0 + - + +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B PHE* 3.7 31.2 - - + -
451B HIS* 3.6 34.5 - - + +
454B LEU* 3.6 18.8 - - + -
460B GLN* 3.3 28.9 + - + +
462B ILE* 1.3 78.0 - - - +
464B ALA* 1.3 60.6 + - - +
465B LYS 3.2 0.7 + - - -
466B LEU* 3.6 28.8 + - + +
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Residues in contact with ALA 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B GLN 4.6 0.8 + - - +
461B SER 3.9 8.9 + - - +
462B ILE 3.4 0.2 - - - -
463B LEU* 1.3 77.7 - - - +
465B LYS* 1.3 60.8 + - + +
466B LEU 3.4 5.7 + - - +
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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