Contacts of the helix formed by residues 362 - 369 (chain A) in PDB entry 3H60
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A GLY 3.8 5.6 - - - +
361A VAL* 1.3 77.6 - - - +
363A LEU* 1.3 65.4 + - - +
364A ASP* 3.3 11.0 + - - +
365A ASP* 2.8 43.3 + - - +
366A ILE* 3.2 18.9 + - - +
414A PHE* 5.1 0.4 - - - -
417A GLU* 3.6 28.5 - - + +
418A ASN* 3.3 11.9 - - - +
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Residues in contact with LEU 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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226A LEU* 4.0 21.4 - - + +
228A GLU* 5.6 3.8 - - - +
343A CYS* 4.6 10.1 - - - -
346A GLY* 5.8 3.1 - - - +
349A LEU* 3.8 39.3 - - + -
362A THR* 1.3 73.1 - - - +
364A ASP* 1.3 61.8 + - - +
366A ILE* 3.2 11.9 + - + +
367A ARG* 3.0 33.5 + - - +
414A PHE* 4.8 2.2 - - + -
418A ASN* 3.1 36.5 + - + +
420A LEU* 4.4 16.8 - - + -
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Residues in contact with ASP 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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362A THR* 3.1 9.8 + - - +
363A LEU* 1.3 79.3 - - - +
365A ASP* 1.3 61.3 + - - +
367A ARG* 3.3 35.5 + - - +
368A LYS* 2.2 63.4 + - - +
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Residues in contact with ASP 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLY 3.7 4.9 - - - +
361A VAL* 3.4 19.2 - - + +
362A THR* 2.8 38.1 + - - +
364A ASP* 1.3 75.1 - - - +
366A ILE* 1.3 63.1 + - - +
368A LYS* 3.2 19.1 + - - +
369A ILE* 3.3 17.1 + - - +
380A PRO* 6.3 2.9 - - + -
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Residues in contact with ILE 366 (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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225A THR* 3.2 26.1 - - + +
226A LEU* 4.4 11.9 - - + -
340A LEU* 5.1 0.2 - - + -
341A ALA* 4.3 18.4 - - + -
349A LEU* 4.3 21.3 - - + -
356A PHE* 3.7 34.5 - - + -
361A VAL* 4.2 3.6 - - + -
362A THR 3.2 15.8 + - - +
363A LEU* 3.2 16.1 + - + +
365A ASP* 1.3 74.0 - - - +
367A ARG* 1.3 63.6 + - - +
368A LYS 3.1 1.0 + - - -
369A ILE* 3.2 18.9 + - + +
384A LEU* 3.9 25.6 - - + -
414A PHE* 4.5 3.4 - - + -
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Residues in contact with ARG 367 (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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224A SER* 3.4 23.9 + - - +
225A THR* 3.9 11.8 + - - -
226A LEU* 3.8 19.4 - - + +
228A GLU* 2.5 52.3 + - - -
363A LEU* 3.0 19.3 + - - +
364A ASP* 3.3 49.3 + - - +
366A ILE* 1.3 76.8 - - - +
368A LYS* 1.3 60.5 + - + +
369A ILE 3.7 1.0 + - - +
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Residues in contact with LYS 368 (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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364A ASP* 2.2 49.9 + - - +
365A ASP* 3.7 10.1 - - - +
366A ILE 3.1 0.6 - - - -
367A ARG* 1.3 75.4 - - + +
369A ILE* 1.3 68.2 + - - +
370A GLU* 3.3 3.8 + - - +
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Residues in contact with ILE 369 (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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225A THR* 2.8 27.9 + - + -
340A LEU* 3.8 20.9 - - + -
365A ASP 3.3 13.4 + - - +
366A ILE* 3.2 21.2 + - + +
367A ARG 4.2 1.0 - - - +
368A LYS* 1.3 77.7 - - - +
370A GLU* 1.3 71.4 + - - +
371A ARG* 3.3 1.5 + - - -
380A PRO* 4.1 25.1 - - + -
381A MET* 4.0 18.2 - - + +
384A LEU* 3.9 27.8 - - + -
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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