Contacts of the helix formed by residues 359 - 364 (chain A) in PDB entry 2N5T
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 ALA 359 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A MET* 3.3 40.5 - - - +
335A ASP* 3.4 25.4 - - - +
336A ILE 2.7 18.6 + - - +
358A ARG* 1.3 70.3 - - - +
360A ILE* 1.3 60.9 + - - +
362A ILE* 3.0 18.9 + - - +
363A ALA 3.4 0.2 + - - -
391A PRO* 3.7 8.3 - - + -
392A MET* 3.4 20.6 - - + -
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Residues in contact with ILE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A THR* 4.2 6.5 - - - +
334A MET* 4.3 2.4 + - - +
358A ARG 3.0 0.8 + - - -
359A ALA* 1.3 74.8 - - - +
361A ARG* 1.3 68.4 + - + +
362A ILE 3.1 2.5 - - - -
363A ALA* 3.8 7.0 - - + +
364A MET* 3.0 36.3 + - + +
370A LEU* 4.9 6.7 - - + -
390A PHE* 3.4 38.6 - - + -
391A PRO* 3.3 22.4 - - + +
392A MET* 3.8 20.0 - - + +
393A ILE* 4.6 5.2 - - + +
398A GLU* 4.6 9.9 - - + +
402A LEU* 3.4 33.2 - - + -
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Residues in contact with ARG 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A PHE 5.8 0.2 + - - -
355A LEU 4.4 0.2 - - - -
356A GLY 2.9 26.4 + - - +
357A TRP* 3.2 24.7 + - + -
358A ARG* 3.0 20.8 + - - +
360A ILE* 1.3 87.6 - - + +
362A ILE* 1.3 57.8 + - - +
364A MET* 4.3 3.8 - - - +
365A ASP* 3.3 19.8 + - - +
392A MET* 4.6 16.2 + - - +
394A ILE* 3.7 20.8 - - - +
398A GLU* 4.6 5.6 + - - +
461B LEU 2.7 28.7 + - - -
462B ALA* 2.8 23.8 + - - +
463B VAL* 3.2 16.9 - - - +
470B ILE* 3.7 7.0 - - + +
472B HIS* 6.1 0.8 - - + -
473B LEU* 3.2 30.2 - - + +
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Residues in contact with ILE 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A MET* 3.6 15.3 - - + -
336A ILE* 3.8 29.8 - - + +
337A GLY* 5.2 0.4 - - - -
347A PHE* 4.0 33.4 - - + -
357A TRP* 3.4 44.4 - - + +
359A ALA 3.0 10.6 + - - +
361A ARG* 1.3 76.4 - - - +
363A ALA* 1.3 63.2 + - - +
364A MET 3.0 1.8 - - - -
365A ASP* 2.7 18.9 + - - +
366A ARG* 2.8 15.5 + - + +
369A ILE* 3.8 19.7 - - + -
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Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A MET* 3.8 28.0 - - + -
359A ALA 3.4 4.3 + - - +
360A ILE* 3.5 10.3 + - + +
362A ILE* 1.3 80.9 - - - +
364A MET* 1.3 57.3 + - - +
366A ARG 3.2 25.7 - - - +
367A ARG* 3.5 3.1 + - - +
369A ILE* 4.4 0.9 - - - -
370A LEU* 3.3 48.6 - - + +
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Residues in contact with MET 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A ILE* 3.0 29.1 + - + +
361A ARG* 4.5 4.9 - - - +
363A ALA* 1.3 78.3 - - - +
365A ASP* 1.3 66.1 + - - +
366A ARG 3.3 0.9 - - - -
367A ARG* 4.5 22.4 + - - +
370A LEU* 4.7 5.4 - - + -
398A GLU* 4.4 25.4 - - + +
401A ALA* 3.9 27.8 - - + -
402A LEU* 3.6 33.7 - - + -
405A GLU* 6.0 1.8 - - - +
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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