Contacts of the helix formed by residues 383 - 395 (chain A) in PDB entry 2WQI
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 GLN 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A VAL 3.3 4.6 + - - +
382A PRO* 1.3 71.9 - - - +
384A PRO* 1.3 65.7 - - + +
386A VAL* 3.1 24.5 + - - +
387A ASP* 2.7 64.1 + - - +
390A ARG* 4.1 7.9 - - - +
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Residues in contact with PRO 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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382A PRO* 3.4 11.4 - - + -
383A GLN* 1.3 94.2 - - + +
385A LEU* 1.3 61.3 + - + +
387A ASP* 3.5 11.1 + - + +
388A SER* 3.0 30.0 + - - -
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Residues in contact with LEU 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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381A VAL* 3.9 10.3 - - + -
382A PRO* 3.0 36.0 + - + +
384A PRO* 1.3 79.7 - - + +
386A VAL* 1.3 62.0 + - - +
388A SER* 3.4 8.7 + - - +
389A TYR* 2.9 30.0 + - - +
380C LEU* 4.2 30.6 - - + +
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Residues in contact with VAL 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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378A MET* 4.8 4.0 - - + +
381A VAL* 3.6 35.7 - - + +
382A PRO 3.2 5.8 + - - +
383A GLN* 3.1 20.8 + - - +
385A LEU* 1.3 77.5 - - - +
387A ASP* 1.3 62.0 + - - +
389A TYR* 3.2 2.8 + - - +
390A ARG* 2.9 66.9 + - + +
377C LEU* 4.2 24.7 - - + -
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Residues in contact with ASP 387 (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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383A GLN* 2.7 53.3 + - - +
384A PRO* 3.6 9.1 - - + +
386A VAL* 1.3 77.3 - - - +
388A SER* 1.3 56.5 + - - +
390A ARG* 3.2 11.1 + - - +
391A GLN* 2.9 29.1 + - - +
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Residues in contact with SER 388 (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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384A PRO 3.0 17.6 + - - -
385A LEU* 3.7 11.8 - - - +
387A ASP* 1.3 72.7 - - - +
389A TYR* 1.3 66.2 + - - +
391A GLN* 3.1 15.5 + - - +
392A GLN* 2.9 32.2 + - - +
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Residues in contact with TYR 389 (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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385A LEU 2.9 18.7 + - - +
386A VAL 3.4 3.4 - - - +
388A SER* 1.3 75.1 - - - +
390A ARG* 1.3 70.5 + - + +
392A GLN* 3.2 14.3 + - - +
393A GLN* 3.0 58.9 + - + +
372C LYS* 4.0 5.0 - - - -
373C GLU* 3.5 40.5 - - + +
376C GLU* 2.5 45.8 + - + -
377C LEU* 3.7 26.9 - - + -
380C LEU* 4.6 7.6 - - + -
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Residues in contact with ARG 390 (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 MET* 4.5 9.1 - - - +
383A GLN* 4.1 10.7 - - - +
386A VAL* 2.9 46.5 + - - +
387A ASP* 3.7 8.6 + - - +
389A TYR* 1.3 88.7 - - + +
391A GLN* 1.3 62.2 + - - +
393A GLN* 3.3 6.7 + - - +
394A GLN* 3.1 30.1 + - + +
373C GLU* 2.8 36.2 + - - +
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Residues in contact with GLN 391 (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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387A ASP 2.9 13.1 + - - +
388A SER* 3.1 20.7 + - - +
390A ARG* 1.3 78.7 - - - +
392A GLN* 1.3 62.9 + - + +
394A GLN* 3.4 18.6 + - - +
395A LEU* 3.6 17.9 + - + +
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Residues in contact with GLN 392 (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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388A SER* 2.9 22.3 + - - +
389A TYR* 3.2 11.7 + - + +
391A GLN* 1.3 74.4 - - + +
393A GLN* 1.3 63.0 + - - +
395A LEU* 3.0 15.5 + - + +
396A LEU* 2.9 42.5 + - + +
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Residues in contact with GLN 393 (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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389A TYR* 3.0 57.9 + - + +
390A ARG* 3.3 7.4 + - - +
392A GLN* 1.3 78.6 + - - +
394A GLN* 1.3 61.3 + - - +
396A LEU* 3.1 45.2 + - - +
369C MET* 6.4 1.3 - - + -
372C LYS* 2.7 33.7 + - - +
376C GLU* 3.6 10.1 + - - -
358D GLN* 4.5 6.4 - - - +
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Residues in contact with GLN 394 (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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390A ARG* 3.1 19.4 + - + +
391A GLN* 3.5 10.5 - - - +
392A GLN 3.2 0.2 - - - -
393A GLN* 1.3 77.7 - - + +
395A LEU* 1.3 62.9 + - + +
396A LEU 4.2 2.6 - - - +
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Residues in contact with LEU 395 (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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391A GLN* 3.7 22.0 - - + +
392A GLN* 3.0 14.6 + - + +
394A GLN* 1.3 78.5 - - + +
396A LEU* 1.3 67.5 + - + +
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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