Contacts of the helix formed by residues 371 - 379 (chain C) in PDB entry 1P7L
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 ASP 371 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280C TYR* 3.0 32.8 + - - -
369C LYS* 4.0 11.4 - - - +
370C THR* 1.3 71.4 - - - +
372C LYS* 1.3 63.5 + - + +
373C ALA 3.2 5.7 + - - -
374C GLN* 4.2 9.2 + - - +
375C LEU* 4.5 9.4 + - - +
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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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280C TYR* 3.0 33.3 + - + +
284C ASN* 3.2 9.8 + - - +
332C PHE* 4.0 30.9 + - + +
333C PHE* 3.5 31.2 - - + -
343C MET* 6.1 0.9 - - + -
371C ASP* 1.3 79.6 - - - +
373C ALA* 1.3 52.2 + - - +
374C GLN 3.6 0.2 - - - -
375C LEU* 3.3 13.8 + - - +
376C LEU* 2.6 44.8 + - + +
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Residues in contact with ALA 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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284C ASN* 2.9 25.4 + - - +
287C ALA* 3.8 13.5 - - + -
288C ALA* 3.5 32.1 - - - +
370C THR 4.4 9.4 - - - +
371C ASP 3.2 1.8 - - - -
372C LYS* 1.3 74.9 - - - +
374C GLN* 1.3 58.3 + - - +
376C LEU* 2.6 24.8 + - - +
377C ARG* 2.7 14.2 + - - +
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Residues in contact with GLN 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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287C ALA 5.3 3.6 - - - +
288C ALA* 5.8 0.3 - - - -
371C ASP 4.2 6.3 + - - +
372C LYS 3.6 0.2 - - - -
373C ALA* 1.3 83.0 - - - +
375C LEU* 1.3 57.7 + - + +
377C ARG* 3.1 20.9 - - - +
378C ASP* 3.1 31.4 + - - +
382C LEU* 6.6 0.4 - - + -
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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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332C PHE* 3.3 37.0 - - + -
371C ASP 4.5 8.0 + - - +
372C LYS* 3.3 15.5 + - - +
373C ALA 3.0 0.8 - - - -
374C GLN* 1.3 76.9 - - + +
376C LEU* 1.3 61.9 + - - +
377C ARG 2.9 6.3 + - - -
378C ASP* 3.3 30.1 + - + +
379C ALA 3.5 7.3 + - - -
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Residues in contact with LEU 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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284C ASN* 4.0 26.9 - - + +
285C ILE* 4.2 13.9 - - + +
288C ALA* 3.9 7.2 - - + -
290C LEU* 3.6 20.1 - - + +
328C LEU* 3.2 37.3 - - + +
332C PHE* 3.5 31.6 - - + -
333C PHE* 3.5 28.9 - - + -
372C LYS* 2.6 27.1 + - + +
373C ALA 2.6 6.6 + - - +
375C LEU* 1.3 72.1 - - - +
377C ARG* 1.3 60.1 + - - +
379C ALA* 3.9 4.9 + - - +
380C ALA 4.3 1.7 + - - -
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Residues in contact with ARG 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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287C ALA 5.7 0.4 - - - -
288C ALA* 2.8 40.6 + - - +
289C GLY* 4.1 11.3 + - - -
290C LEU* 5.1 4.8 - - + +
373C ALA 2.7 6.4 + - - +
374C GLN* 3.1 28.9 - - - +
375C LEU 2.9 0.2 - - - -
376C LEU* 1.3 77.1 - - - +
378C ASP* 1.3 56.1 + - - +
379C ALA 3.1 2.0 - - - -
380C ALA 2.5 41.6 + - - +
381C GLY 4.3 6.3 + - - -
382C LEU* 3.5 31.5 + - + -
383C LYS* 3.8 9.5 + - - -
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Residues in contact with ASP 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 GLN* 3.1 16.8 - - - +
375C LEU* 3.3 27.4 + - + +
377C ARG* 1.3 76.7 - - - +
379C ALA* 1.3 57.6 + - - +
380C ALA* 2.9 9.2 + - - -
381C GLY 4.4 0.5 + - - -
382C LEU* 3.1 42.3 + - + +
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Residues in contact with ALA 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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324C GLN* 4.4 4.5 - - - +
328C LEU* 3.2 33.8 - - + +
332C PHE* 3.9 23.1 - - + -
375C LEU 3.5 2.4 + - - -
376C LEU 4.0 5.6 - - - +
377C ARG 3.1 0.4 - - - -
378C ASP* 1.3 76.3 - - - +
380C ALA* 1.3 61.0 + - - +
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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