Contacts of the helix formed by residues 374 - 378 (chain C) in PDB entry 5Y1Z
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 GLN 374 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276C ASN* 5.3 6.7 + - - -
372C ASN 3.5 10.5 + - - +
373C SER* 1.3 81.2 + - - +
375C TYR* 1.3 66.9 + - - +
376C GLN* 3.2 3.4 - - - -
377C MET* 2.9 30.1 + - - +
378C LEU* 3.5 11.9 + - + +
388C THR* 4.1 28.0 + - + +
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Residues in contact with TYR 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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323C LEU* 4.1 17.9 - - + -
361C ASN* 3.3 23.3 + - + +
362C TYR 3.3 27.4 + - - -
363C SER* 3.5 22.2 - - - -
364C PRO* 4.2 13.6 - - + +
367C THR* 6.4 0.4 - - + -
373C SER* 3.8 5.0 + - - +
374C GLN* 1.3 76.7 - - - +
376C GLN* 1.3 65.4 + - + +
377C MET 3.2 0.7 + - - -
378C LEU* 3.2 33.9 + - + +
381C PRO* 3.6 35.8 - - + +
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Residues in contact with GLN 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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278C HIS 4.7 0.7 - - - +
279C PRO* 3.4 14.7 - - + +
280C LEU* 2.7 49.0 + - - +
323C LEU* 3.8 17.8 - - + +
324C MET* 3.7 11.9 + - - +
359C VAL* 4.3 0.7 - - - +
360C PHE* 3.1 32.1 - - + -
361C ASN* 3.1 48.2 + - - +
363C SER* 5.4 0.2 - - - +
373C SER* 5.5 0.2 + - - -
374C GLN 3.0 1.2 + - - -
375C TYR* 1.3 80.2 - - + +
377C MET* 1.3 73.8 + - + +
378C LEU 3.4 0.2 - - - -
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Residues in contact with MET 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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277C PRO* 4.1 27.4 - - + +
353C ILE* 3.8 20.6 - - + -
357C PHE* 4.3 20.4 - - - -
359C VAL* 3.6 29.3 - - - +
360C PHE* 4.3 11.0 - - + -
374C GLN* 2.9 21.8 + - - +
376C GLN* 1.3 101.7 - - + +
378C LEU* 1.3 62.9 + - - +
379C LEU 3.5 0.2 + - - -
388C THR* 3.1 33.5 - - + -
389C ALA* 3.1 14.9 + - + +
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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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359C VAL* 4.0 6.6 - - - +
361C ASN* 2.8 25.5 + - - +
374C GLN* 3.9 9.4 - - + +
375C TYR* 3.2 41.1 + - + +
377C MET* 1.3 78.0 - - - +
379C LEU* 1.3 65.4 + - - +
380C ASP 3.4 10.9 + - - +
381C PRO* 4.1 11.8 - - + +
384C PRO* 3.8 46.7 - - + +
387C GLY* 3.6 15.5 - - - +
388C THR* 4.0 11.7 - - + -
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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