Contacts of the helix formed by residues 371 - 381 (chain C) in PDB entry 3OX4
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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358C LEU* 4.2 3.1 - - - -
370C GLY* 1.3 75.8 - - - +
372C GLN* 1.3 53.6 + - - +
373C LYS* 3.6 22.2 - - + +
374C GLU* 2.6 48.8 + - - +
375C VAL* 2.7 20.2 + - - +
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Residues in contact with GLN 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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351C PRO* 2.6 31.6 + - - +
354C ALA* 3.6 3.6 - - - +
355C ASP* 2.7 45.3 - - - +
358C LEU* 3.2 21.5 - - + +
371C ASP* 1.3 73.5 - - - +
373C LYS* 1.3 57.3 + - - +
374C GLU 2.9 5.7 + - - -
375C VAL* 4.2 5.6 - - - -
376C GLU* 3.2 42.6 + - + +
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Residues in contact with LYS 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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371C ASP* 3.0 18.8 + - + +
372C GLN* 1.3 77.7 - - - +
374C GLU* 1.3 58.2 + - - +
376C GLU* 5.2 3.4 - - - -
377C GLU* 5.6 2.0 - - - +
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Residues in contact with GLU 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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291C TYR* 2.6 42.4 + - + +
368C ARG* 3.7 13.9 + - - -
369C GLN 5.0 0.7 - - - +
370C GLY* 4.2 5.2 - - - -
371C ASP* 2.6 32.1 + - - +
372C GLN 2.9 0.4 + - - -
373C LYS* 1.3 74.1 - - - +
375C VAL* 1.3 63.4 + - - +
376C GLU 3.2 1.8 - - - -
377C GLU* 3.3 31.8 + - - +
378C LEU* 3.5 5.4 + - - +
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Residues in contact with VAL 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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261C TYR* 4.8 11.7 - - + +
265C MET* 4.2 17.3 - - + -
291C TYR* 5.7 3.1 - - + +
354C ALA* 3.8 26.5 - - + +
357C ALA* 4.6 9.0 - - + -
358C LEU* 3.5 31.2 - - + -
370C GLY* 4.2 5.2 - - - -
371C ASP 2.7 30.0 + - - +
372C GLN* 4.2 3.4 - - - -
374C GLU* 1.3 73.4 - - - +
376C GLU* 1.3 63.5 + - - +
378C LEU* 3.1 25.4 - - + +
379C PHE* 3.3 7.0 + - + -
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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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350C VAL* 3.5 17.4 - - + +
351C PRO* 3.0 40.0 - - - +
354C ALA* 3.4 22.2 - - + -
372C GLN* 3.2 36.8 + - - +
373C LYS* 5.2 2.9 - - - -
374C GLU 3.2 0.4 - - - +
375C VAL* 1.3 75.2 - - - +
377C GLU* 1.3 66.3 + - - +
379C PHE* 3.0 10.1 + - - +
380C LEU* 2.9 23.9 - - + +
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Residues in contact with GLU 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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291C TYR* 6.0 1.7 - - - -
373C LYS 5.6 1.3 + - - +
374C GLU* 3.3 26.4 + - - +
375C VAL 3.3 0.4 - - - -
376C GLU* 1.3 77.7 - - - +
378C LEU* 1.3 66.7 + - - +
380C LEU* 3.0 23.9 + - + +
381C SER* 3.1 14.1 + - - -
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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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261C TYR* 4.6 18.4 - - + -
265C MET* 3.5 31.0 - - + -
284C LEU* 5.3 2.1 - - + +
287C HIS* 3.9 21.2 - - + +
288C VAL* 3.9 14.4 - - + -
291C TYR* 3.8 39.9 - - + -
374C GLU 3.5 5.1 + - - +
375C VAL* 3.1 16.8 + - + +
377C GLU* 1.3 80.9 + - - +
379C PHE* 1.3 64.7 + - - +
381C SER* 2.8 25.4 + - - -
382C ALA* 3.6 4.2 + - - +
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Residues in contact with PHE 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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265C MET* 3.4 59.0 - - + +
269C LEU* 4.6 7.2 - - + -
284C LEU* 4.7 4.0 - - + -
340C LEU* 4.1 22.2 - - + +
350C VAL* 3.8 20.9 - - + -
353C LEU* 3.7 31.0 - - + -
354C ALA* 3.4 38.6 - - + -
357C ALA* 4.5 0.9 - - + -
375C VAL* 3.3 9.8 + - + -
376C GLU 3.0 8.4 + - - +
378C LEU* 1.3 79.4 - - - +
380C LEU* 1.3 57.6 + - + +
382C ALA* 2.8 24.7 + - - +
383C PHE* 3.0 18.7 - + + -
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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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347C LYS* 4.3 18.4 + - + +
350C VAL* 3.5 33.7 - - + -
376C GLU* 2.9 25.1 - - + +
377C GLU* 3.0 17.0 + - + +
379C PHE* 1.3 75.2 - - - +
381C SER* 1.3 57.5 + - - +
382C ALA 3.0 3.7 + - - -
383C PHE* 3.5 21.6 + - + +
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Residues in contact with SER 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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287C HIS* 3.1 39.2 + - - +
377C GLU* 3.1 11.7 + - - -
378C LEU* 2.8 19.3 + - - -
380C LEU* 1.3 76.1 - - - +
382C ALA* 1.3 57.3 + - - +
383C PHE 3.6 2.4 - - - +
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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