Contacts of the helix formed by residues 362 - 369 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360B GLY 3.7 6.5 - - - +
361B VAL* 1.3 77.5 - - - +
363B LEU* 1.3 65.1 + - - +
364B ASP* 3.3 9.6 + - - +
365B ASP* 3.0 40.6 + - - +
366B ILE* 3.1 18.3 + - - +
414B PHE* 5.1 0.7 - - - -
417B GLU* 3.7 23.1 - - - +
418B ASN* 3.3 12.1 - - - +
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Residues in contact with LEU 363 (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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226B LEU* 4.1 19.6 - - + +
228B GLU* 5.7 2.5 - - - +
343B CYS* 4.6 9.9 - - - -
346B GLY* 5.7 2.5 - - - +
349B LEU* 4.0 37.9 - - + -
362B THR* 1.3 74.9 - - - +
364B ASP* 1.3 62.7 + - - +
366B ILE* 3.2 12.6 + - + +
367B ARG* 3.0 32.4 + - - +
414B PHE* 4.7 1.6 - - + -
418B ASN* 3.1 35.8 + - + +
420B LEU* 4.4 19.3 - - + -
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Residues in contact with ASP 364 (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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362B THR* 3.1 9.3 + - - +
363B LEU* 1.3 78.5 - - - +
365B ASP* 1.3 63.4 + - - +
367B ARG* 3.1 37.8 + - - +
368B LYS* 2.4 66.7 + - - +
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Residues in contact with ASP 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B GLY 3.8 4.7 - - - +
361B VAL* 3.5 19.3 - - + +
362B THR* 3.0 37.4 + - - +
364B ASP* 1.3 77.6 - - - +
366B ILE* 1.3 62.2 + - - +
368B LYS* 3.3 10.6 + - - +
369B ILE* 3.3 24.7 + - - +
380B PRO* 6.2 3.6 - - + -
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Residues in contact with ILE 366 (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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225B THR* 3.3 24.9 - - + +
226B LEU* 4.3 13.2 - - + -
341B ALA* 4.1 18.2 - - + -
349B LEU* 4.1 28.5 - - + -
356B PHE* 4.0 31.6 - - + -
361B VAL* 4.3 2.9 - - + -
362B THR 3.1 14.8 + - - +
363B LEU* 3.2 16.8 + - + +
365B ASP* 1.3 76.0 - - - +
367B ARG* 1.3 63.5 + - - +
369B ILE* 3.0 20.5 + - + +
384B LEU* 4.1 23.6 - - + -
414B PHE* 4.3 3.6 - - + -
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Residues in contact with ARG 367 (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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224B SER* 3.5 23.8 + - - +
225B THR* 3.8 12.8 + - - -
226B LEU* 3.8 22.5 - - + +
228B GLU* 2.8 50.8 + - - -
363B LEU* 3.0 16.7 + - - +
364B ASP* 3.1 48.5 + - - +
366B ILE* 1.3 76.4 - - - +
368B LYS* 1.3 60.5 + - + +
369B ILE 3.6 0.9 + - - +
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Residues in contact with LYS 368 (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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364B ASP* 2.4 53.2 + - - +
365B ASP* 3.8 10.1 - - - +
366B ILE 3.1 0.4 - - - -
367B ARG* 1.3 78.3 - - + +
369B ILE* 1.3 64.9 + - - +
370B GLU* 3.3 6.1 + - - +
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Residues in contact with ILE 369 (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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225B THR* 2.7 29.6 + - + -
340B LEU* 3.8 20.0 - - + -
365B ASP 3.3 11.1 + - - +
366B ILE* 3.0 23.6 + - + +
367B ARG 4.0 1.0 - - - +
368B LYS* 1.3 77.0 - - - +
370B GLU* 1.3 71.9 + - - +
371B ARG* 4.1 1.6 - - - +
380B PRO* 3.8 29.4 - - + -
381B MET* 4.0 17.3 - - + +
384B LEU* 3.7 30.5 - - + -
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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