Contacts of the helix formed by residues 367 - 376 (chain C) in PDB entry 4LEY
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 PHE 367 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C TRP* 3.6 45.5 - + - -
319C PRO* 5.5 0.9 - - + -
322C THR* 3.7 25.8 - - + -
345C PHE* 4.4 10.3 - - + -
365C LEU* 3.9 31.4 - - + -
366C SER* 1.3 81.1 + - - +
368C SER* 1.3 60.3 + - - +
369C HIS* 3.2 11.9 - + - -
370C THR* 3.1 7.5 + - - +
371C GLU* 2.9 34.3 + - - +
467C HIS* 4.3 7.4 - + - -
469C PHE* 3.6 50.7 - + + -
470C ILE* 4.4 4.3 - - + -
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Residues in contact with SER 368 (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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197C THR* 3.7 31.5 - - - +
198C GLY 5.4 1.1 - - - -
202C GLU* 4.4 2.8 - - - +
215C MET* 4.3 8.8 - - - -
309C ILE* 6.2 0.5 - - - +
366C SER* 3.2 18.1 + - - -
367C PHE* 1.3 78.4 + - - +
369C HIS* 1.3 57.6 + - - +
371C GLU* 3.7 16.5 + - - +
372C LYS* 2.9 28.6 + - - +
424C LYS* 5.9 0.7 - - - -
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Residues in contact with HIS 369 (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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195C LEU* 3.7 26.5 - - + -
197C THR* 4.2 5.6 - - - +
215C MET* 5.1 2.6 - - - -
318C TRP* 4.6 3.2 - - - -
343C GLU* 4.6 16.4 - - + +
344C PRO* 2.9 24.1 + - + -
345C PHE* 4.7 0.9 - - - -
346C TYR* 3.4 36.2 - + - -
366C SER 3.8 3.1 - - - -
367C PHE* 3.6 23.7 - + - -
368C SER* 1.3 77.7 + - - +
370C THR* 1.3 86.0 + - - -
372C LYS* 3.2 8.6 + - - +
373C TYR* 3.0 22.9 + - - +
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Residues in contact with THR 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C TRP* 3.7 14.3 - - + -
326C LEU* 4.4 4.7 - - + -
340C LEU* 3.8 37.9 + - + +
343C GLU* 5.7 0.2 - - - +
367C PHE* 3.1 8.2 + - - -
369C HIS* 1.3 99.9 + - - +
371C GLU* 1.3 57.8 + - - +
373C TYR* 3.2 8.4 + - - +
374C ILE* 2.9 36.1 + - + +
469C PHE* 3.7 26.2 - - + -
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Residues in contact with GLU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C GLU* 4.0 1.6 - - - -
367C PHE* 2.9 28.1 + - - +
368C SER* 3.7 13.3 + - - +
370C THR* 1.3 75.1 - - - +
372C LYS* 1.3 58.2 + - - +
374C ILE* 3.3 8.7 + - - +
375C LEU* 2.9 34.8 + - - +
421C TYR* 2.7 37.5 + - - -
424C LYS* 2.5 39.4 + - - +
428C PHE* 3.8 15.0 - - + -
469C PHE* 3.7 22.4 - - + -
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Residues in contact with LYS 372 (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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195C LEU* 4.4 10.7 - - + +
196C ASN* 2.7 42.9 + - - +
197C THR* 4.6 8.1 - - + -
201C TYR* 3.9 23.4 - - + +
202C GLU* 3.8 22.4 + - + +
368C SER 2.9 18.1 + - - +
369C HIS* 3.3 7.0 - - - +
371C GLU* 1.3 74.4 - - - +
373C TYR* 1.3 64.4 + - - +
375C LEU* 3.1 4.2 + - - +
376C ASN* 3.0 38.8 + - - +
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Residues in contact with TYR 373 (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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332C LEU* 5.6 1.6 - - + -
336C VAL* 4.2 30.0 - - + +
340C LEU* 3.5 37.0 - - + -
369C HIS 3.0 12.4 + - - +
370C THR* 3.4 7.6 - - - +
372C LYS* 1.3 76.3 - - - +
374C ILE* 1.3 60.6 + - + +
376C ASN* 3.2 2.7 + - - +
377C ASN* 2.8 71.8 + - + +
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Residues in contact with ILE 374 (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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326C LEU* 3.8 29.8 - - + -
328C ILE* 4.9 3.6 - - + -
331C TRP* 3.8 27.8 - - + -
332C LEU* 4.3 14.1 - - + -
340C LEU* 4.3 11.2 - - + -
370C THR* 2.9 26.6 + - + +
371C GLU* 3.5 9.2 - - - +
372C LYS 3.3 0.4 - - - -
373C TYR* 1.3 77.9 - - + +
375C LEU* 1.3 64.6 + - - +
377C ASN 3.1 4.6 - - - +
378C HIS* 3.1 24.9 + - - +
428C PHE* 3.8 18.8 - - + -
431C TRP* 4.8 2.0 - - + -
468C TYR* 4.6 8.3 - - + -
469C PHE* 4.4 8.5 - - + -
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Residues in contact with LEU 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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202C GLU* 3.6 35.2 - - + +
204C VAL* 4.0 25.6 - - + -
371C GLU 2.9 26.2 + - - +
372C LYS 3.5 4.5 - - - +
374C ILE* 1.3 72.0 - - - +
376C ASN* 1.3 60.7 + - - +
377C ASN 3.2 0.2 - - - -
378C HIS* 2.8 28.8 + - - -
395C LYS* 3.2 20.5 - - + -
398C LEU* 4.2 6.3 - - + -
424C LYS* 4.0 8.3 - - - -
428C PHE* 3.8 28.0 - - + -
431C TRP* 4.0 22.7 - - + -
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Residues in contact with ASN 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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335A LYS* 4.0 14.7 + - - +
201C TYR 3.4 21.4 + - - -
202C GLU* 3.6 5.9 - - - +
203C HIS* 3.5 15.3 + - - -
372C LYS* 3.0 31.9 + - - +
373C TYR* 5.0 0.7 - - - -
375C LEU* 1.3 75.6 - - - +
377C ASN* 1.3 74.6 + - - +
378C HIS* 3.8 5.7 - - - -
395C LYS* 3.1 23.6 + - - +
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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