Contacts of the helix formed by residues 374 - 384 (chain C) in PDB entry 5E9W
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 TYR 374 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291C PHE* 5.0 4.2 - - - -
321C SER* 3.7 16.8 - - - -
322C PHE* 3.8 28.5 - + - -
353C LEU* 4.6 22.1 + - + +
372C LEU* 3.9 9.1 + - + +
373C VAL* 1.3 71.3 - - - +
375C PHE* 1.3 59.5 + - - +
376C PRO* 3.6 32.5 - - + +
377C LEU* 2.9 42.6 + - + +
378C LEU* 3.1 10.2 + - - +
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Residues in contact with PHE 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C THR* 5.3 2.9 - - + -
320C ASN* 6.0 0.2 - - - +
321C SER* 4.3 4.1 + - - +
322C PHE* 5.3 4.5 - - + -
373C VAL* 3.3 9.2 + - + +
374C TYR* 1.3 73.6 - - - +
376C PRO* 1.3 77.2 - - + +
378C LEU* 3.0 28.3 + - + +
379C ASN* 2.8 29.8 + - + -
389C LEU* 3.8 20.2 - - + -
392C LYS* 3.7 42.2 - - + +
468C LEU* 4.2 27.8 - - + -
470C PHE* 3.6 24.0 - + + -
472C PHE* 3.7 19.3 - + - -
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Residues in contact with PRO 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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322C PHE* 4.2 14.8 - - + -
374C TYR* 3.5 38.6 - - + +
375C PHE* 1.3 96.6 - - + +
377C LEU* 1.3 59.1 + - - +
379C ASN* 3.4 10.0 + - + +
380C GLU* 3.2 24.9 + - - +
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Residues in contact with LEU 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 PHE* 4.0 11.4 - - + -
353C LEU* 3.8 40.4 - - + +
354C PHE* 3.8 30.5 - - + -
374C TYR* 2.9 26.6 + - + +
376C PRO* 1.3 77.0 - - - +
378C LEU* 1.3 65.6 + - - +
380C GLU* 3.1 7.5 + - + +
381C MET* 2.9 43.3 + - + +
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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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287C CYS* 5.2 7.9 - - + -
291C PHE* 4.0 29.6 - - + -
301C LEU* 3.8 31.2 - - + -
314C PHE* 5.0 3.8 - - + -
318C THR* 5.2 2.2 - - + -
373C VAL* 4.3 13.2 - - + -
374C TYR 3.1 8.8 + - - +
375C PHE* 3.0 35.3 + - + +
377C LEU* 1.3 76.4 - - - +
379C ASN* 1.3 61.5 - - - +
381C MET* 3.5 3.4 + - - -
382C ALA* 3.0 25.1 + - - +
470C PHE* 4.4 20.9 - - + -
472C PHE* 4.4 13.2 - - + -
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Residues in contact with ASN 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 PHE* 2.8 23.3 + - + +
376C PRO* 3.4 15.2 + - + +
378C LEU* 1.3 78.7 - - - +
380C GLU* 1.3 64.4 + - - +
382C ALA* 3.6 7.4 + - - +
383C LYS* 3.5 35.1 + - - +
387C MET 5.3 0.7 - - - +
389C LEU* 3.6 22.0 + - - +
472C PHE* 3.6 23.9 - - - -
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Residues in contact with GLU 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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376C PRO 3.2 11.3 + - - +
377C LEU* 3.1 14.4 + - + +
379C ASN* 1.3 77.7 - - - +
381C MET* 1.3 67.4 + - + +
383C LYS* 2.3 54.0 + - - +
384C LYS* 4.1 1.7 + - - +
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Residues in contact with MET 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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291C PHE* 4.5 10.3 - - - -
294C TYR* 3.7 28.5 - - + -
297C ALA* 3.8 11.2 - - + -
298C ASP* 3.6 36.1 - - + +
301C LEU* 3.5 17.1 - - + +
354C PHE* 3.9 13.9 - - - -
377C LEU* 2.9 47.5 + - + +
378C LEU 4.0 1.3 - - - +
380C GLU* 1.3 76.1 - - + +
382C ALA* 1.3 61.0 + - - +
384C LYS* 3.2 22.3 + - - +
385C TYR* 4.0 5.0 - - - -
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Residues in contact with ALA 382 (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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301C LEU* 3.7 20.8 - - + +
305C CYS* 5.5 0.7 - - - -
314C PHE* 5.6 0.2 - - + -
378C LEU 3.0 18.5 + - - +
379C ASN 3.8 6.1 - - - +
380C GLU 3.2 0.4 - - - -
381C MET* 1.3 74.0 - - - +
383C LYS* 1.3 65.2 + - - +
385C TYR* 3.1 15.7 + - - +
387C MET* 3.3 33.9 + - + +
472C PHE* 3.9 22.7 - - + -
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Residues in contact with LYS 383 (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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379C ASN* 3.5 32.8 - - - +
380C GLU* 2.3 49.9 + - - +
382C ALA* 1.3 78.1 - - - +
384C LYS* 1.3 56.8 + - - +
386C ASN* 2.8 20.7 + - - +
387C MET 3.9 17.0 - - - +
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Residues in contact with LYS 384 (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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294C TYR* 4.1 11.2 + - - +
298C ASP* 2.7 38.7 + - - +
380C GLU 4.1 1.0 + - - +
381C MET* 3.2 16.4 + - - +
382C ALA 3.1 0.8 - - - -
383C LYS* 1.3 78.5 - - - +
385C TYR* 1.3 78.4 + - + +
386C ASN* 3.3 1.8 + - - +
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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