Contacts of the helix formed by residues 396 - 406 (chain A) in PDB entry 2AY6
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 THR 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.5 37.3 - - + +
391A GLY 4.5 2.9 - - - +
392A LEU* 3.3 17.6 - - - -
393A ASN* 2.7 48.6 + - - +
395A ASN* 1.3 79.3 - - + +
397A ILE* 1.3 61.6 + - - +
398A PRO 3.4 0.2 - - - -
399A ILE* 3.2 12.2 + - + +
400A LEU* 3.0 22.2 + - - +
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Residues in contact with ILE 397 (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 LEU* 3.8 28.3 - - + +
336A GLN* 3.7 35.9 - - + +
337A LEU* 3.9 28.1 - - + +
340A GLU* 4.0 18.2 - - + +
392A LEU* 3.9 17.7 - - + -
393A ASN 2.9 27.4 + - - +
394A ASP* 4.9 1.1 - - - +
396A THR* 1.3 76.7 - - - +
398A PRO* 1.4 69.7 - - + +
400A LEU* 3.3 2.4 + - - +
401A ALA* 2.9 23.2 + - - +
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Residues in contact with PRO 398 (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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340A GLU* 3.6 28.6 - - - +
344A LEU* 6.0 0.2 - - - +
394A ASP 3.3 25.4 - - - +
395A ASN 3.5 8.3 - - - +
396A THR 3.4 4.3 - - - -
397A ILE* 1.4 93.0 - - + +
399A ILE* 1.3 57.6 + - + +
401A ALA* 3.3 1.9 + - - +
402A ARG* 2.9 31.2 + - - +
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Residues in contact with ILE 399 (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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31A GLY 5.5 3.6 - - - +
33A ILE* 3.9 23.8 - - + -
377A PHE* 4.7 18.0 - - + +
379A ILE* 4.0 16.4 - - + -
395A ASN 3.3 24.7 - - - +
396A THR* 3.4 5.8 - - + +
398A PRO* 1.3 76.7 - - + +
400A LEU* 1.3 57.2 + - - +
402A ARG* 3.2 11.3 + - - +
403A ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 400 (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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33A ILE* 6.0 0.7 - - + -
35A LEU* 4.1 16.2 - - + -
337A LEU* 4.0 25.1 - - + -
363A LEU* 5.1 1.3 - - + -
373A ILE* 5.1 0.9 - - + -
379A ILE* 3.6 29.8 - - + +
381A MET* 4.5 13.2 - - + -
387A ILE* 4.6 15.3 - - + -
392A LEU* 4.2 16.4 - - + -
396A THR 3.0 12.1 + - - +
397A ILE 3.7 3.8 - - - +
399A ILE* 1.3 79.6 - - - +
401A ALA* 1.3 63.5 + - - +
403A ALA* 3.3 3.7 + - + +
404A ILE* 3.0 55.1 + - + +
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Residues in contact with ALA 401 (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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337A LEU* 4.4 3.8 - - + +
340A GLU* 3.4 35.0 - - + +
341A LEU* 3.8 30.8 - - + +
344A LEU* 4.8 6.3 - - + -
397A ILE 2.9 12.2 + - - +
398A PRO 3.6 1.8 - - - +
400A LEU* 1.3 76.0 - - - +
402A ARG* 1.3 65.3 + - - +
404A ILE* 3.4 4.5 + - - +
405A ILE* 3.2 23.7 + - - +
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Residues in contact with ARG 402 (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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344A LEU* 4.9 15.6 - - + +
377A PHE* 3.4 31.6 - - + -
398A PRO 2.9 18.1 + - - +
399A ILE* 3.5 9.2 - - - +
401A ALA* 1.3 76.7 - - - +
403A ALA* 1.3 57.4 + - - +
405A ILE* 3.8 5.8 - - - +
406A GLU* 2.8 47.0 + - + +
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Residues in contact with ALA 403 (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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373A ILE* 4.0 17.7 - - + -
377A PHE* 3.4 42.8 - - + -
379A ILE* 4.3 4.5 - - + -
399A ILE 2.9 15.0 + - - +
400A LEU* 3.6 4.7 - - + +
401A ALA 3.2 0.2 - - - -
402A ARG* 1.3 74.7 - - - +
404A ILE* 1.3 67.1 + - - +
407A VAL* 2.9 30.5 + - - +
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Residues in contact with ILE 404 (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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337A LEU* 4.9 0.7 - - + -
341A LEU* 4.1 26.0 - - + -
350A PHE* 3.7 34.1 - - + -
363A LEU* 4.1 30.5 - - + -
373A ILE* 4.8 9.2 - - + +
400A LEU* 3.0 51.0 + - + +
401A ALA* 3.7 4.5 - - - +
403A ALA* 1.3 74.9 - - - +
405A ILE* 1.3 63.5 + - - +
407A VAL 3.5 3.3 + - - -
408A GLY 3.5 0.2 + - - -
409A VAL* 3.3 41.8 + - + +
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Residues in contact with ILE 405 (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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341A LEU* 4.3 14.4 - - + +
344A LEU* 3.2 55.4 - - + +
345A SER* 3.5 18.6 - - - +
349A ARG* 5.2 3.4 - - - +
350A PHE* 4.7 8.1 - - + -
401A ALA 3.2 13.9 + - - +
402A ARG* 3.8 5.8 - - - +
404A ILE* 1.3 80.2 - - - +
406A GLU* 1.3 67.1 + - - +
408A GLY* 3.0 15.2 + - - -
409A VAL 5.1 4.3 - - - +
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Residues in contact with GLU 406 (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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376A GLU* 5.0 5.9 - - - +
377A PHE* 3.7 29.8 - - + -
402A ARG* 2.8 37.9 + - + +
403A ALA 3.9 0.2 - - - +
405A ILE* 1.3 78.6 - - + +
407A VAL* 1.3 60.0 + - - +
408A GLY 3.2 1.3 + - - -
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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