Contacts of the helix formed by residues 374 - 386 (chain A) in PDB entry 1DQU
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 GLY 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A SER 3.1 12.7 + - - -
247A GLU* 3.4 19.0 - - - +
373A GLY* 1.3 73.7 - - - -
375A THR* 1.3 57.0 + - - -
376A GLN* 3.0 4.0 - - - -
377A CYS* 2.3 32.4 + - - +
378A ALA 2.7 10.3 + - - -
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Residues in contact with THR 375 (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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247A GLU* 4.5 1.4 - - - +
374A GLY* 1.3 69.1 - - - -
376A GLN* 1.3 70.3 + - - +
378A ALA* 3.0 8.7 + - - -
379A ILE* 2.9 50.4 + - + +
394A MET* 4.2 7.3 - - + +
403A GLN* 3.7 26.4 + - - +
406A GLU* 3.9 23.7 + - + +
407A PHE* 4.4 18.2 - - + +
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Residues in contact with GLN 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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263A PHE* 4.0 16.6 - - + -
374A GLY* 2.8 2.7 + - - -
375A THR* 1.3 83.8 - - - +
377A CYS* 1.3 66.1 + - - +
379A ILE* 4.0 11.5 - - - +
380A ASN* 2.9 25.1 + - - +
406A GLU* 5.5 1.9 - - - +
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Residues in contact with CYS 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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246A SER* 3.4 21.8 - - - -
263A PHE* 3.6 16.6 - - + -
371A TYR* 3.0 45.3 - - - -
372A GLN 3.6 19.7 - - - +
373A GLY* 4.3 1.5 - - - -
374A GLY* 2.3 28.5 + - - +
376A GLN* 1.3 71.3 - - - +
378A ALA* 1.3 60.7 + - - +
380A ASN* 3.0 17.9 + - - +
381A ARG* 3.1 15.7 + - - +
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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
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244A THR* 4.5 6.2 - - + +
246A SER* 3.4 14.7 - - - -
374A GLY 2.7 9.4 + - - +
375A THR* 3.2 17.3 - - - +
377A CYS* 1.3 74.9 - - - +
379A ILE* 1.3 58.7 + - - +
381A ARG* 3.2 2.1 + - - +
382A ALA* 2.8 28.9 + - - +
394A MET* 3.5 22.7 - - + -
407A PHE* 3.5 21.9 - - + -
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Residues in contact with ILE 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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375A THR* 2.9 28.6 + - + +
376A GLN* 4.1 11.9 - - - +
378A ALA* 1.3 73.9 - - - +
380A ASN* 1.3 58.5 + - - +
382A ALA* 3.8 7.2 - - - -
383A VAL* 2.5 45.2 + - + +
406A GLU* 3.8 3.4 - - + +
407A PHE* 3.6 28.7 - - + -
410A GLY* 3.2 49.8 - - - +
411A VAL* 3.4 7.4 - - + +
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Residues in contact with ASN 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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217A ILE* 4.4 7.5 - - - +
259A ARG* 3.7 22.2 + - - +
262A PRO* 5.8 0.2 - - - +
263A PHE* 3.3 36.0 - - + -
371A TYR* 4.6 5.1 + - - -
376A GLN 2.9 15.2 + - - +
377A CYS* 3.0 12.8 + - - +
379A ILE* 1.3 80.4 - - - +
381A ARG* 1.3 69.7 + - - +
383A VAL* 3.7 5.3 + - - +
384A ALA* 3.6 12.3 + - - +
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Residues in contact with ARG 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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198A ASP* 3.7 14.8 - - - +
214A LEU* 3.6 21.4 - - - +
215A VAL 2.6 30.9 + - - +
216A PRO 4.2 2.0 - - - -
217A ILE* 3.6 22.0 - - + -
244A THR* 4.0 2.0 - - - +
246A SER* 3.4 17.2 + - - +
252A ILE* 3.0 26.7 - - - +
260A ASP* 3.2 14.8 + - - -
371A TYR* 3.2 16.6 + - - -
377A CYS* 3.1 13.8 + - - +
378A ALA 3.9 3.1 - - - +
380A ASN* 1.3 72.3 - - - +
382A ALA* 1.3 59.3 + - - +
383A VAL 3.0 1.1 - - - -
384A ALA* 2.3 31.0 + - - +
385A TYR* 2.8 49.3 + - + -
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Residues in contact with ALA 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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244A THR* 5.1 3.0 + - + -
378A ALA 2.8 22.3 + - - +
379A ILE* 3.6 5.6 - - - +
381A ARG* 1.3 72.7 - - - +
383A VAL* 1.3 57.2 + - - +
385A TYR* 3.0 13.6 + - - +
386A ALA* 2.8 30.6 + - - +
392A ILE* 4.0 16.2 - - + +
407A PHE* 3.8 12.3 - - + -
411A VAL* 3.8 24.9 - - + -
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Residues in contact with VAL 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 ILE* 2.5 47.3 + - + +
380A ASN* 3.8 6.1 - - - +
381A ARG 2.8 1.4 + - - -
382A ALA* 1.3 73.8 - - - +
384A ALA* 1.3 61.9 + - - +
386A ALA* 3.6 3.4 - - - +
387A PRO* 3.7 0.2 - - - +
410A GLY 4.6 1.1 - - - +
411A VAL* 4.5 10.5 - - - +
414A VAL* 2.8 40.8 - - + -
415A TRP* 3.0 38.3 + - + +
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Residues in contact with ALA 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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217A ILE* 4.0 27.1 - - + -
221A ILE* 4.1 7.7 - - + +
259A ARG* 4.4 12.8 - - - +
380A ASN 3.6 6.7 + - - +
381A ARG* 2.3 27.9 + - - +
383A VAL* 1.3 70.8 - - - +
385A TYR* 1.3 61.2 + - - +
387A PRO* 2.9 25.4 - - - +
388A PHE* 3.8 8.5 - - - -
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Residues in contact with TYR 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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198A ASP* 3.3 37.6 + - - +
217A ILE* 3.8 31.3 - - + -
220A HIS* 3.6 34.3 - + - +
221A ILE* 3.9 12.6 - - + -
224A LEU* 4.4 12.8 - - + +
242A ALA* 4.4 14.1 - - + -
243A ARG 4.4 0.9 - - - -
244A THR* 4.0 9.0 - - - -
381A ARG* 2.8 44.7 + - + -
382A ALA* 3.4 11.2 - - - +
384A ALA* 1.3 77.9 - - - +
386A ALA* 1.3 50.8 + - - +
387A PRO 2.7 14.3 - - - -
388A PHE* 2.9 22.8 + - - +
389A ALA* 3.6 8.2 + - - +
392A ILE* 4.5 4.9 - - + -
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Residues in contact with ALA 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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29A TYR* 4.8 3.3 - - - +
382A ALA 2.8 15.5 + - - +
383A VAL* 3.6 0.4 - - - +
385A TYR* 1.3 73.0 - - - +
387A PRO* 1.3 62.1 - - + +
388A PHE 3.5 0.4 - - - -
389A ALA 3.9 6.2 - - - +
392A ILE* 4.2 10.5 - - + +
411A VAL* 5.4 1.6 - - + -
415A TRP* 3.1 44.9 - - + +
418A GLN* 3.0 35.7 + - + +
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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