Contacts of the helix formed by residues 459 - 464 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410D LEU 2.7 28.9 + - - -
411D HIS* 3.0 16.2 + - - +
412D PHE 4.0 0.6 - - - +
416D GLU* 2.7 35.5 + - - +
454D LEU* 2.9 29.7 + - + +
457D THR* 3.1 30.3 - - - +
458D HIS* 1.3 75.8 - - - +
460D GLN* 1.3 64.0 + - - +
461D SER* 3.1 9.4 - - - +
462D ILE* 3.2 46.5 - - + +
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Residues in contact with GLN 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D HIS* 3.2 59.4 + - + +
454D LEU* 3.8 8.2 + - + -
455D SER* 4.0 20.6 - - - +
458D HIS* 3.8 1.8 - - - +
459D ARG* 1.3 75.9 - - - +
461D SER* 1.3 64.7 + - - +
462D ILE 3.1 1.2 + - - -
463D LEU* 3.1 23.5 + - - +
464D ALA 4.5 0.3 + - - -
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Residues in contact with SER 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D HIS 4.9 2.3 + - - -
459D ARG* 4.1 7.8 - - - +
460D GLN* 1.3 79.3 - - - +
462D ILE* 1.3 69.1 + - - +
463D LEU 3.2 1.7 + - - -
464D ALA* 3.3 21.1 + - - +
465D LYS* 3.8 14.9 - - - +
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Residues in contact with ILE 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410D LEU* 4.2 17.2 - - + +
412D PHE* 3.4 28.0 - - + -
454D LEU* 3.8 18.2 - - + -
459D ARG* 3.2 61.7 - - + +
460D GLN 3.1 1.6 + - - -
461D SER* 1.3 81.4 - - - +
463D LEU* 1.3 60.4 + - - +
464D ALA 3.2 2.7 - - - -
465D LYS* 3.0 32.0 + - + +
466D LEU* 3.3 16.2 + - + +
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Residues in contact with LEU 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423D LEU* 5.3 4.5 - - + -
447D GLU* 5.7 1.3 - - + +
450D PHE* 3.7 33.7 - - + -
451D HIS* 3.4 53.2 - - + +
454D LEU* 3.6 22.4 - - + -
460D GLN* 3.1 14.9 + - - +
462D ILE* 1.3 77.8 - - - +
464D ALA* 1.3 61.1 + - - +
466D LEU* 3.5 32.3 - - + +
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Residues in contact with ALA 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D GLN 4.5 0.4 + - - -
461D SER* 3.3 13.5 + - - +
462D ILE 3.2 0.2 - - - -
463D LEU* 1.3 78.3 - - - +
465D LYS* 1.3 61.4 + - + +
466D LEU 3.2 6.9 + - - +
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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