Contacts of the helix formed by residues 370 - 379 (chain F) in PDB entry 3HX0
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 370 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F SER 3.8 3.1 + - - +
369F LEU* 1.3 78.1 - - - +
371F THR* 1.3 68.1 + - - +
372F GLN* 3.1 13.1 + - - +
373F GLN* 3.0 38.3 + - - +
374F ALA* 3.0 17.2 + - - +
12G G 4.5 27.1 - - - -
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Residues in contact with THR 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370F THR* 1.3 73.4 - - - +
372F GLN* 1.3 86.9 + - + +
374F ALA* 3.3 16.9 - - - +
375F ILE* 3.3 19.1 + - + +
460F ASP 5.7 1.5 + - - +
461F LEU 5.6 0.7 - - - +
11G T 4.9 2.5 - - - +
12G G 4.1 19.7 + - - +
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Residues in contact with GLN 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342F TRP* 3.1 37.0 - - + +
343F GLY* 4.9 5.7 - - - -
370F THR* 3.1 11.0 + - - +
371F THR* 1.3 88.4 - - + +
373F GLN* 1.3 68.3 + - + +
375F ILE* 2.8 19.4 + - - +
376F GLY 2.9 9.5 + - - -
460F ASP 5.7 0.2 - - - -
461F LEU* 3.4 34.2 - - + +
462F VAL* 4.0 6.7 - - - +
11G T 3.5 38.2 + - - -
12G G 5.1 1.2 + - - -
5H A 5.6 0.2 - - - +
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Residues in contact with GLN 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F ILE* 3.6 10.1 - - + +
342F TRP 3.3 11.2 - - - +
343F GLY* 2.8 33.6 + - - +
344F ALA* 4.9 0.4 - - + -
348F THR* 3.4 31.3 + - - +
352F TRP* 3.7 13.8 - - + -
368F SER 4.2 2.4 - - - +
369F LEU* 3.5 17.4 - - + +
370F THR* 3.0 42.0 + - - +
372F GLN* 1.3 75.0 - - + +
374F ALA* 1.3 57.7 + - - +
377F LEU* 2.8 32.6 + - - +
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Residues in contact with ALA 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369F LEU* 4.2 18.5 - - + +
370F THR 3.0 12.8 + - - +
371F THR* 3.3 14.4 - - - +
372F GLN 3.0 0.4 + - - -
373F GLN* 1.3 78.1 - - - +
375F ILE* 1.3 58.9 + - + +
377F LEU* 3.5 2.9 + - - +
378F LYS* 3.0 27.0 + - - +
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Residues in contact with ILE 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371F THR* 3.5 20.6 - - + +
372F GLN* 2.8 7.9 + - - +
374F ALA* 1.3 74.0 - - + +
376F GLY* 1.3 67.4 + - - +
378F LYS* 3.1 18.4 + - - +
379F HIS* 3.1 28.4 + - + +
383F PHE* 4.9 0.9 - - + -
459F ASP* 3.8 37.2 - - + +
460F ASP 3.1 30.3 - - - +
461F LEU* 3.8 16.4 - - + -
476F VAL* 4.0 4.9 - - + -
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Residues in contact with GLY 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F ASN 5.1 0.5 - - - +
341F ILE* 4.1 6.3 - - - -
342F TRP* 3.6 33.8 + - - +
372F GLN 2.9 11.1 + - - -
373F GLN 3.7 2.9 - - - -
375F ILE* 1.3 76.6 - - - +
377F LEU* 1.3 60.4 + - - +
379F HIS 3.6 2.1 - - - -
380F TYR* 3.1 24.4 + - - +
383F PHE* 4.0 11.4 - - - -
461F LEU* 4.9 0.6 - - - +
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Residues in contact with LEU 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F ILE* 3.8 18.5 - - + +
360F LEU* 3.8 37.2 - - + +
363F ILE* 4.4 4.0 - - + -
364F ARG* 4.1 31.4 - - + +
369F LEU* 3.5 26.7 - - + -
373F GLN 2.8 17.4 + - - +
374F ALA* 3.7 4.5 - - - +
376F GLY* 1.3 73.3 - - - +
378F LYS* 1.3 68.6 + - - +
380F TYR* 3.1 23.9 + - + +
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Residues in contact with LYS 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374F ALA 3.0 14.9 + - - +
375F ILE* 3.1 11.4 + - - +
377F LEU* 1.3 80.1 - - - +
379F HIS* 1.3 90.1 + - + +
380F TYR* 3.3 2.4 + - - +
381F SER 5.1 0.3 + - - -
459F ASP* 2.8 30.7 + - - -
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Residues in contact with HIS 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F ILE* 3.1 20.4 + - + -
376F GLY 3.6 3.8 - - - -
378F LYS* 1.3 109.3 + - + +
380F TYR* 1.3 65.3 + - - +
381F SER 3.3 2.9 + - - -
382F ASP* 3.4 10.4 + - + +
383F PHE* 3.0 44.6 + + + -
459F ASP* 3.4 14.3 + - - -
476F VAL* 3.8 17.9 - - + -
486F HIS* 3.3 42.7 + + + -
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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