Contacts of the helix formed by residues 384 - 395 (chain A) in PDB entry 1FQV
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 PRO 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A PRO* 3.9 10.5 - - + -
382A ILE 3.7 8.3 - - - +
383A VAL* 1.3 84.8 - - - +
385A ASP* 1.3 67.4 + - - +
386A GLY* 2.9 6.0 + - - +
387A THR* 3.1 29.2 - - + +
388A LEU* 2.9 19.2 + - - +
156C GLY 4.7 5.4 - - - +
158C ASN* 4.3 20.2 - - + +
181C PHE* 3.4 39.0 - - + -
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Residues in contact with ASP 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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383A VAL 3.4 2.9 + - - -
384A PRO* 1.3 70.9 - - - +
386A GLY* 1.3 61.1 + - - +
388A LEU* 3.4 14.6 + - - +
389A GLN* 3.2 31.6 + - - +
156C GLY* 4.5 18.1 + - - +
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Residues in contact with GLY 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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384A PRO* 2.9 5.2 + - - +
385A ASP* 1.3 76.1 - - - +
387A THR* 1.3 57.4 + - - -
388A LEU 2.9 9.2 + - - -
389A GLN* 2.9 15.8 + - - +
390A LEU* 3.2 16.8 + - - +
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Residues in contact with THR 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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362A PRO* 4.1 8.5 + - - +
363A GLU* 3.8 20.6 - - - +
383A VAL* 3.7 5.5 - - - +
384A PRO* 3.1 37.4 + - + +
386A GLY* 1.3 72.0 - - - +
388A LEU* 1.3 56.6 + - - +
390A LEU* 3.8 19.4 - - + +
391A LEU* 3.0 27.4 + - - +
158C ASN* 6.1 2.9 - - + +
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Residues in contact with LEU 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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379A VAL* 4.6 0.4 - - + -
383A VAL* 3.2 27.4 - - + +
384A PRO 2.9 12.3 + - - +
385A ASP* 3.4 15.9 - - - +
386A GLY 2.9 0.8 - - - -
387A THR* 1.3 77.1 + - - +
389A GLN* 1.3 69.3 + - - +
390A LEU 3.2 0.2 - - - -
391A LEU* 3.2 7.5 + - + +
392A LYS* 3.0 41.0 + - - +
400A ILE* 3.5 33.4 - - + -
401A ASN* 3.3 28.7 - - + +
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Residues in contact with GLN 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 ASP* 3.2 22.3 + - - +
386A GLY* 2.9 9.8 + - - +
388A LEU* 1.3 86.0 - - - +
390A LEU* 1.3 55.4 + - + +
392A LYS* 2.9 48.3 + - + +
393A GLU* 2.7 41.7 + - - +
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Residues in contact with LEU 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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386A GLY 3.2 13.6 + - - +
387A THR* 3.9 19.1 - - + +
388A LEU 3.2 0.2 - - - -
389A GLN* 1.3 77.1 - - + +
391A LEU* 1.3 61.6 + - - +
392A LYS 3.2 0.4 - - - -
393A GLU* 3.1 16.9 + - + +
394A ALA* 3.0 28.8 + - - +
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Residues in contact with LEU 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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362A PRO 4.7 4.3 - - - +
363A GLU 5.1 0.7 - - - +
365A LEU* 3.6 37.7 - - + +
366A LEU* 3.9 41.3 - - + +
377A LEU* 4.9 4.3 - - + -
379A VAL* 4.8 0.7 - - + -
383A VAL* 4.8 3.1 - - + -
387A THR 3.0 19.8 + - - +
388A LEU* 3.4 17.0 - - + +
390A LEU* 1.3 78.9 - - - +
392A LYS* 1.3 56.3 + - - +
394A ALA* 3.5 3.6 + - - +
395A LEU* 3.1 34.3 + - + +
400A ILE* 3.7 20.9 - - + +
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Residues in contact with LYS 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 LEU* 3.0 34.2 + - - +
389A GLN* 2.9 39.5 + - + +
390A LEU 3.2 0.2 - - - -
391A LEU* 1.3 76.1 - - - +
393A GLU* 1.3 68.3 + - - +
395A LEU 3.6 15.9 - - - +
396A PRO* 3.6 7.6 - - - +
400A ILE* 3.8 44.7 + - + +
401A ASN* 5.6 0.8 + - - +
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Residues in contact with GLU 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 GLN* 2.7 28.8 + - - +
390A LEU* 3.1 24.4 - - + +
392A LYS* 1.3 81.0 - - - +
394A ALA* 1.3 62.1 + - - +
396A PRO* 3.2 17.2 - - - +
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Residues in contact with ALA 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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366A LEU* 3.3 33.7 - - + -
390A LEU 3.0 11.7 + - - +
391A LEU* 3.8 3.6 - - - +
392A LYS 3.4 0.2 - - - -
393A GLU* 1.3 80.9 - - - +
395A LEU* 1.3 63.5 + - - +
396A PRO* 2.9 10.7 - - - +
397A HIS* 5.2 0.5 - - - -
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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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365A LEU 4.2 18.8 - - - +
366A LEU* 4.3 13.2 - - + +
368A LEU* 4.6 1.1 - - + -
369A GLY* 3.6 24.7 - - - +
377A LEU* 5.5 1.6 - - + -
391A LEU* 3.1 25.7 + - + +
392A LYS* 3.6 10.2 - - - +
394A ALA* 1.3 85.5 - - + +
396A PRO* 1.3 60.9 - - - +
397A HIS* 3.1 31.0 - - + +
398A LEU* 3.1 43.5 + - + +
400A ILE* 4.8 3.3 - - + +
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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