Contacts of the helix formed by residues 374 - 381 (chain C) in PDB entry 5ZR1
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 ALA 374 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372C ALA 3.8 0.4 + - - -
373C PRO* 1.3 74.3 - - - +
375C ASP* 1.3 65.8 + - - +
376C GLU 3.5 0.7 - - - -
377C ILE* 3.5 4.0 + - - +
378C LEU* 3.0 28.7 + - + +
429F LEU* 3.7 49.0 + - + +
430F ALA* 4.9 6.3 - - + +
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Residues in contact with ASP 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C PRO* 3.5 4.8 - - + +
374C ALA* 1.3 84.4 - - - +
376C GLU* 1.3 69.8 + - - +
378C LEU* 3.2 14.4 + - - +
379C SER* 2.8 29.6 + - - -
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Residues in contact with GLU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C LEU* 5.4 3.6 - - + +
371C HIS* 6.0 1.6 - - + +
373C PRO* 3.6 31.2 + - - +
374C ALA 3.5 0.2 - - - -
375C ASP* 1.3 81.4 + - - +
377C ILE* 1.3 64.6 + - + +
379C SER* 2.7 22.2 + - - +
380C LEU* 3.3 10.4 + - - +
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Residues in contact with ILE 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364C VAL* 3.8 27.1 - - + +
367C LEU* 3.4 50.5 - - + +
368C ILE* 3.7 21.5 - - + +
371C HIS* 4.4 2.2 - - + +
372C ALA 5.7 0.4 - - - +
373C PRO 4.1 15.7 + - - +
374C ALA 3.5 7.5 + - - +
375C ASP 3.3 0.2 - - - -
376C GLU* 1.3 76.6 - - + +
378C LEU* 1.3 59.7 + - - +
380C LEU* 3.1 11.0 + - + +
381C LEU* 3.0 32.2 + - + +
429F LEU* 3.9 20.9 - - + -
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Residues in contact with LEU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C ALA* 3.0 19.5 + - + +
375C ASP* 3.2 14.8 + - - +
377C ILE* 1.3 75.1 - - - +
379C SER* 1.3 63.0 + - - +
381C LEU* 3.3 29.6 + - + +
383C ASN* 3.3 37.2 - - + +
384C LYS* 3.9 8.0 + - - +
426F GLU* 6.4 1.1 - - + -
429F LEU* 4.8 13.2 - - + +
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Residues in contact with SER 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C ASP 2.8 15.8 + - - -
376C GLU* 2.7 29.5 + - - +
378C LEU* 1.3 73.6 - - - +
380C LEU* 1.3 59.7 + - - +
381C LEU 4.0 0.2 - - - +
384C LYS* 3.5 37.4 - - - +
387C GLY* 3.9 13.0 - - - -
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Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C PHE* 4.0 11.9 - - + -
363C PHE* 4.0 13.0 - - + -
364C VAL* 3.8 28.3 - - + -
367C LEU* 3.9 23.1 - - + -
376C GLU 3.3 9.1 + - - +
377C ILE* 3.1 12.6 + - + +
379C SER* 1.3 79.4 + - - +
381C LEU* 1.3 65.2 + - + +
387C GLY 5.4 0.7 - - - +
388C LEU* 3.3 31.2 - - + +
391C PHE* 3.6 48.0 - - + -
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Residues in contact with LEU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C SER* 6.2 0.2 - - - -
360C PHE* 4.3 22.4 - - + -
364C VAL* 4.4 19.3 - - + -
377C ILE* 3.0 32.4 + - + +
378C LEU* 3.3 18.7 + - + +
379C SER 4.0 0.7 - - - +
380C LEU* 1.3 83.7 - - + +
382C THR* 1.3 65.9 + - + +
383C ASN* 3.3 5.9 + - - +
384C LYS 3.3 18.9 + - - +
388C LEU* 4.3 6.8 - - + +
418F TYR* 4.7 1.6 - - - +
421F TRP* 5.3 3.4 - - + -
422F LYS* 3.4 36.8 - - + +
425F ILE* 5.6 3.4 - - + -
429F LEU* 5.3 8.1 - - + -
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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