Contacts of the helix formed by residues 370 - 379 (chain B) in PDB entry 5CHG
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B GLY 4.8 3.1 - - - +
369B LEU* 1.3 75.1 - - - +
371B THR* 1.3 72.3 + - - +
372B GLN* 3.7 11.7 + - + +
373B GLN* 2.8 46.3 + - + +
374B ALA* 3.0 21.5 + - - +
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Residues in contact with THR 371 (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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370B THR* 1.3 76.8 + - - +
372B GLN* 1.3 63.6 + - - +
374B ALA* 3.3 8.3 + - - +
375B ILE* 3.2 27.5 + - + +
460B ASP 4.2 15.9 - - - +
461B LEU* 4.2 22.0 - - + +
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Residues in contact with GLN 372 (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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342B TRP* 3.1 54.2 - - + +
343B GLY* 3.3 17.9 - - - -
370B THR* 3.2 11.9 + - + +
371B THR* 1.3 80.6 - - - +
373B GLN* 1.3 56.3 - - - +
375B ILE* 3.2 8.5 + - - +
376B GLY* 2.9 24.3 + - - -
461B LEU* 3.4 37.6 - - + +
474B LEU* 5.6 1.8 - - - +
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Residues in contact with GLN 373 (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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341B ILE* 3.8 4.9 - - + +
342B TRP 3.6 7.0 - - - +
343B GLY 3.3 31.1 + - - +
344B ALA* 4.3 2.8 - - + +
348B THR* 3.7 17.4 - - - +
352B TRP* 3.4 34.5 - - + -
368B SER 4.5 0.9 - - - +
369B LEU* 3.5 14.8 - - + -
370B THR* 2.8 44.9 + - + +
372B GLN* 1.3 78.8 - - - +
374B ALA* 1.3 62.3 + - - +
376B GLY* 3.1 1.6 + - - -
377B LEU* 3.1 28.7 + - + +
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Residues in contact with ALA 374 (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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572A GLU* 6.3 4.7 - - + -
575A TRP* 6.2 0.2 - - - -
369B LEU* 4.4 16.9 - - + +
370B THR 3.0 11.7 + - - +
371B THR* 3.4 13.0 - - - +
373B GLN* 1.3 76.5 - - - +
375B ILE* 1.3 64.2 - - + +
377B LEU* 3.4 6.0 + - - +
378B LYS* 3.1 21.9 + - - +
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Residues in contact with ILE 375 (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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342B TRP* 4.5 7.6 - - + -
371B THR* 3.3 24.2 - - + +
372B GLN* 3.2 8.0 + - - +
374B ALA* 1.3 75.5 - - + +
376B GLY* 1.3 64.8 + - - +
378B LYS* 3.2 9.6 + - + +
379B HIS* 3.1 35.9 + - + +
383B PHE* 4.1 5.9 - - + -
459B ASP* 3.3 30.5 - - + +
460B ASP 5.1 7.9 - - - +
461B LEU* 5.5 4.0 - - + -
476B VAL* 3.7 30.1 - - + -
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Residues in contact with GLY 376 (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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341B ILE* 3.9 7.1 - - - +
342B TRP* 3.9 29.1 + - - -
372B GLN 2.9 15.0 + - - -
373B GLN 3.1 5.5 + - - -
375B ILE* 1.3 77.1 - - - +
377B LEU* 1.3 55.7 + - - +
379B HIS 3.7 1.2 - - - -
380B TYR* 3.2 31.5 + - - +
383B PHE* 4.4 6.4 - - - +
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Residues in contact with LEU 377 (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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341B ILE* 4.0 30.5 - - + -
352B TRP* 6.1 0.4 - - + -
360B LEU* 4.2 26.5 - - + +
363B ILE* 3.7 21.1 - - + -
364B ARG* 3.6 48.0 + - + +
369B LEU* 3.7 30.3 - - + -
373B GLN* 3.1 13.9 + - + +
374B ALA 3.8 6.3 - - - +
376B GLY* 1.3 73.7 - - - +
378B LYS* 1.3 66.8 + - - +
379B HIS 3.4 0.3 + - - -
380B TYR* 3.4 17.5 + - + +
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Residues in contact with LYS 378 (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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422A LYS* 5.4 3.0 - - - +
574A ASP* 3.1 52.8 + - - +
575A TRP* 3.9 23.7 - - + +
364B ARG* 5.6 2.9 - - - +
374B ALA 3.1 13.5 + - - +
375B ILE* 3.2 15.7 + - + +
377B LEU* 1.3 78.9 - - - +
379B HIS* 1.3 85.7 + - + +
380B TYR 3.9 0.3 + - - -
458B THR 5.2 1.2 + - - -
459B ASP* 3.2 25.3 + - - +
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Residues in contact with HIS 379 (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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375B ILE* 3.1 29.8 + - + +
376B GLY 3.7 3.6 - - - -
378B LYS* 1.3 110.5 + - + +
380B TYR* 1.3 57.5 + - - +
381B SER 3.4 2.5 - - - -
382B ASP* 3.2 7.9 + - + -
383B PHE* 2.9 48.2 + + + -
459B ASP* 3.1 24.5 + - - -
476B VAL* 3.8 19.8 - - + +
486B HIS* 3.1 38.4 - + + -
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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