Contacts of the helix formed by residues 375 - 386 (chain A) in PDB entry 5UC7
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 ASN 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A VAL* 1.3 69.4 - - - +
376A ILE* 1.3 65.0 + - - +
377A ALA* 3.4 8.3 + - - +
378A ALA* 3.2 28.5 + - + +
379A LEU* 2.9 23.0 + - - +
425A THR* 3.8 8.7 + - - +
426A PHE 2.7 26.1 + - - +
427A PHE* 3.9 11.6 + - - +
428A SER* 4.3 9.6 - - - +
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Residues in contact with ILE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.9 20.4 - - + -
374A VAL* 3.5 24.2 + - + +
375A ASN* 1.3 72.0 + - - +
377A ALA* 1.3 58.0 + - - +
379A LEU* 3.8 3.5 - - - +
380A GLN* 2.8 34.1 + - - +
391A ARG* 3.8 32.1 - - - +
392A PRO* 3.9 22.7 - - + +
393A PHE* 4.4 11.4 - - + -
394A GLY 4.9 2.7 - - - +
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.9 30.6 - - + +
25A PRO* 4.6 13.7 - - + -
375A ASN* 3.3 6.8 + - - +
376A ILE* 1.3 80.1 - - - +
378A ALA* 1.3 62.6 + - - +
380A GLN* 3.8 4.9 - - - +
381A GLN* 3.1 28.3 + - - +
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASN* 3.2 28.9 + - + +
377A ALA* 1.3 80.1 - - - +
379A LEU* 1.3 62.4 + - - +
381A GLN* 3.4 6.1 + - - +
382A PHE* 3.0 22.0 + - - +
385A ARG* 4.9 1.2 + - - -
425A THR* 4.1 8.1 - - + +
426A PHE* 4.0 24.0 - - + -
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A VAL* 3.6 28.3 - - + -
375A ASN 2.9 13.4 + - - +
376A ILE 3.9 2.2 - - - +
378A ALA* 1.3 74.4 - - - +
380A GLN* 1.3 62.2 + - - +
382A PHE* 3.2 5.9 + - + +
383A PHE* 2.8 50.1 + - + -
392A PRO* 3.6 27.1 - - + -
397A ILE* 4.0 13.2 - - + -
420A ALA* 3.6 30.7 - - + +
426A PHE* 3.7 31.0 - - + +
427A PHE* 5.3 0.9 - - + -
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Residues in contact with GLN 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO 5.9 0.7 - - - +
27A PHE* 3.7 24.5 - - + -
376A ILE* 2.8 17.5 + - - +
377A ALA* 3.8 5.2 - - - +
379A LEU* 1.3 78.5 - - - +
381A GLN* 1.3 57.0 + - - +
383A PHE* 3.3 3.6 + - - +
384A VAL* 3.0 35.8 + - - +
389A TRP* 3.2 30.9 - - + -
390A VAL 2.6 28.7 + - - +
391A ARG* 2.7 42.1 + - - +
392A PRO* 3.6 10.2 - - - +
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Residues in contact with GLN 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO* 6.2 5.0 - - + +
27A PHE* 3.8 32.5 - - + -
377A ALA 3.1 18.3 + - - +
378A ALA* 3.7 6.1 - - - +
380A GLN* 1.3 76.2 - - - +
382A PHE* 1.3 62.6 + - - +
384A VAL* 3.4 2.2 + - - +
385A ARG* 2.9 52.7 + - - +
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A ALA 3.0 11.4 + - - +
379A LEU* 3.2 8.3 + - + +
381A GLN* 1.3 76.3 - - - +
383A PHE* 1.3 80.1 + + - +
385A ARG* 3.1 24.8 + - - +
386A GLN* 3.0 61.6 + - + +
416A ALA* 3.5 21.3 - - - -
419A GLU* 3.8 28.3 - - + -
420A ALA* 4.0 11.7 - - + -
426A PHE* 3.5 40.6 - + + -
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Residues in contact with PHE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A LEU* 2.8 49.2 + - + +
380A GLN* 3.8 5.2 - - - +
382A PHE* 1.3 77.0 - + - +
384A VAL* 1.4 58.8 + - - +
386A GLN* 2.9 19.9 + - - +
387A GLY 3.2 0.2 + - - -
388A VAL* 3.1 45.6 + - + +
390A VAL* 3.5 50.7 - - + +
392A PRO* 4.4 5.4 - - + -
397A ILE* 4.1 13.5 - - + -
416A ALA* 4.0 31.9 - - + -
417A VAL* 4.2 4.9 - - + -
420A ALA* 4.0 19.1 - - + -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 4.0 30.1 - - + -
39A LEU* 4.0 14.4 - - + -
43A GLU* 3.9 23.1 - - - +
45A LEU* 3.8 13.2 - - + +
380A GLN* 3.0 20.3 + - - +
381A GLN* 3.9 3.4 - - - +
383A PHE* 1.4 74.0 - - - +
385A ARG* 1.3 59.4 + - + +
387A GLY* 2.9 20.6 + - - -
388A VAL 3.7 4.7 - - - +
389A TRP* 3.7 34.1 - - + -
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Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLU* 5.7 0.7 - - - -
378A ALA 4.9 1.0 + - - -
381A GLN* 2.9 52.3 + - - +
382A PHE* 3.4 39.4 - - - +
384A VAL* 1.3 76.0 - - + +
386A GLN* 1.3 67.7 + - - +
387A GLY 3.2 1.3 + - - -
426A PHE* 4.1 12.7 - - - -
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Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A PHE* 3.0 55.2 + - + +
383A PHE* 2.9 9.8 + - - +
385A ARG* 1.3 85.3 + - - +
387A GLY* 1.3 60.8 + - - +
388A VAL* 3.6 5.5 + - + +
412A ARG* 3.2 16.9 + - - +
416A ALA* 4.4 18.9 - - + +
419A GLU* 4.2 17.3 + - - -
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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