Contacts of the helix formed by residues 371 - 378 (chain B) in PDB entry 1H3F
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 VAL 371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ILE 3.3 2.0 + - - -
370B TRP* 1.3 71.0 - - - +
372B ALA* 1.3 67.4 + - - +
374B LEU* 3.1 17.2 + - + +
375B PHE* 3.2 39.1 + - + -
391B ILE* 3.7 21.8 - - + -
398B LEU* 5.1 2.0 - - + -
403B LEU* 3.7 20.4 - - + -
405B ASP 4.1 0.2 - - - +
406B PRO 3.8 13.2 - - - +
408B LEU* 3.0 33.6 + - + +
410B VAL* 4.0 22.2 - - + -
418B LEU* 5.8 0.4 - - + -
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Residues in contact with ALA 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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370B TRP* 3.1 35.6 - - + +
371B VAL* 1.3 86.4 - - + +
373B ARG* 1.3 60.2 + - - +
375B PHE* 3.4 0.9 + - - -
376B THR* 3.0 24.8 + - - -
384B ASN* 3.5 25.8 - - + +
387B ALA* 3.8 18.0 - - + +
388B ARG* 4.2 5.8 - - + +
391B ILE* 5.4 1.1 - - + -
406B PRO 4.8 0.2 - - - +
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Residues in contact with ARG 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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363B GLU* 2.7 39.7 + - - +
369B ILE* 4.2 12.6 - - + -
370B TRP* 3.0 23.2 + - + +
372B ALA* 1.3 76.7 - - - +
374B LEU* 1.3 60.2 + - - +
376B THR* 3.2 7.5 + - - +
377B LEU* 2.8 58.8 + - + +
384B ASN* 3.0 33.8 + - - +
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Residues in contact with LEU 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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359B ILE* 3.9 30.9 - - + +
369B ILE* 4.1 25.9 - - + +
370B TRP 3.1 10.6 + - - +
371B VAL* 3.1 12.1 + - + +
373B ARG* 1.3 77.5 - - - +
375B PHE* 1.3 58.6 + - + +
377B LEU* 3.4 3.9 + - - +
378B ALA* 2.9 29.5 + - - +
398B LEU* 5.5 0.4 - - + -
410B VAL* 4.1 30.7 - - + -
412B LEU* 4.6 7.6 - - + -
416B ARG* 5.4 0.7 - - + -
418B LEU* 3.7 28.0 - - + +
428B VAL* 4.2 16.1 - - + +
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Residues in contact with PHE 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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371B VAL* 3.2 30.2 + - + -
372B ALA* 3.4 6.0 + - - +
374B LEU* 1.3 78.7 - - + +
376B THR* 1.3 61.3 + - - +
378B ALA* 3.3 1.8 + - - +
379B GLY 3.1 3.8 + - - -
380B LEU* 2.9 53.5 + - + -
381B THR* 3.3 17.2 + - + +
387B ALA* 4.5 2.7 - - + -
391B ILE* 5.8 0.2 - - + -
396B LEU* 3.6 30.3 - - + -
397B ARG 3.5 20.9 - - - -
398B LEU* 5.5 0.4 - - + -
403B LEU* 3.6 26.7 - - + -
418B LEU* 3.7 26.0 - - + -
419B GLN 3.6 21.8 - - - -
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Residues in contact with THR 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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372B ALA 3.0 6.8 + - - -
373B ARG* 3.2 10.3 + - - +
375B PHE* 1.3 78.2 - - - +
377B LEU* 1.3 63.8 + - + +
379B GLY* 3.0 14.2 + - - -
381B THR* 3.0 29.1 + - - +
382B PRO 4.1 4.7 - - - +
383B SER* 3.1 25.3 + - - +
384B ASN* 3.0 26.8 + - - +
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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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357B VAL* 3.8 15.7 - - + +
358B THR 5.6 0.9 - - - +
359B ILE* 4.0 24.0 - - + -
360B PRO* 5.4 6.3 - - + -
363B GLU* 4.4 14.4 - - + +
369B ILE* 5.9 1.6 - - + -
373B ARG* 2.8 65.2 + - + +
374B LEU* 3.8 4.5 - - + +
376B THR* 1.3 76.4 - - + +
378B ALA* 1.3 60.0 + - - +
379B GLY 3.5 0.5 + - - -
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Residues in contact with ALA 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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357B VAL* 4.0 21.8 - - - +
359B ILE* 5.2 0.2 - - - +
374B LEU 2.9 17.8 + - - +
375B PHE* 3.6 6.1 - - - +
376B THR 3.1 0.2 - - - -
377B LEU* 1.3 76.9 - - - +
379B GLY* 1.3 60.3 - - - +
380B LEU* 3.4 3.9 + - + +
418B LEU* 3.5 22.4 - - + -
426B VAL* 3.7 28.7 - - + +
428B VAL* 4.0 5.8 - - + -
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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