Contacts of the helix formed by residues 384 - 396 (chain A) in PDB entry 5FHH
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 ASP 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A GLN* 5.4 0.3 - - - +
383A ALA* 1.3 80.3 + - + +
385A GLN* 1.3 60.1 + - - +
386A THR* 2.2 33.5 + - + +
387A PHE* 2.3 38.4 + - - +
388A ILE* 3.0 18.6 + - - +
587A SER* 4.8 4.5 - - - -
588A LEU* 4.5 9.5 + - - +
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Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A ALA 3.4 4.2 + - - +
384A ASP* 1.3 69.0 - - - +
386A THR* 1.3 60.2 + - + +
388A ILE* 3.7 27.8 - - + +
389A SER* 2.6 53.8 + - - -
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Residues in contact with THR 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 ASP* 2.2 30.7 + - + +
385A GLN* 1.3 81.1 - - + +
387A PHE* 1.3 61.0 + - - +
389A SER* 3.7 5.1 + - - -
390A LEU* 3.4 17.0 + - - +
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Residues in contact with PHE 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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382A GLN* 4.0 14.4 - - + -
384A ASP* 2.3 40.8 + - - +
386A THR* 1.3 65.9 + - - +
388A ILE* 1.3 66.3 + - - +
390A LEU* 3.0 34.3 - - + +
391A LEU* 3.3 31.3 + - + +
582A LEU* 4.4 17.0 - - + -
585A ALA 3.6 15.5 - - - -
587A SER* 3.0 31.2 - - - -
588A LEU* 3.4 31.6 - - + -
591A LEU* 4.5 12.1 - - + -
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Residues in contact with ILE 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* 3.5 37.2 - - + +
382A GLN* 3.2 30.7 - - + +
383A ALA 3.6 11.0 - - - +
384A ASP 3.0 14.8 + - - +
385A GLN* 3.0 32.4 + - + +
387A PHE* 1.3 78.4 - - - +
389A SER* 1.3 61.4 + - - +
390A LEU 3.1 1.2 + - - -
391A LEU* 3.2 6.5 + - - +
392A GLN* 2.8 41.3 - - - +
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Residues in contact with SER 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 GLN* 2.6 35.5 + - - -
386A THR* 4.1 5.4 - - - -
388A ILE* 1.3 74.7 - - - +
390A LEU* 1.3 63.4 + - - +
392A GLN* 3.7 7.4 + - - +
393A ALA* 3.4 18.5 + - - +
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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 THR 3.4 11.4 + - - +
387A PHE* 3.0 39.8 + - + +
389A SER* 1.3 78.1 - - - +
391A LEU* 1.3 67.7 + - + +
393A ALA* 3.1 10.2 + - - +
394A VAL* 3.0 44.5 + - + +
403A VAL* 4.6 9.6 - - + +
406A GLN* 3.7 41.1 - - + +
407A LEU* 5.1 8.3 - - + -
582A LEU* 4.9 12.3 - - + -
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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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230A ALA 4.8 4.9 - - - +
379A VAL* 6.3 0.9 - - + -
382A GLN* 2.9 32.3 - - - +
387A PHE* 3.3 39.7 - - + +
388A ILE* 3.2 3.7 + - - +
390A LEU* 1.3 81.6 - - + +
392A GLN* 1.3 58.8 - - - +
394A VAL* 3.0 9.3 + - + +
395A ARG* 2.2 40.4 + - - +
579A TYR* 4.1 17.0 - - + +
582A LEU* 4.7 7.0 - - + -
583A SER* 3.8 34.3 - - - +
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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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229A SER* 4.8 6.7 - - - -
379A VAL* 3.9 18.2 - - - +
388A ILE* 2.8 38.9 + - - +
389A SER* 3.7 8.2 + - - +
390A LEU 3.3 0.6 - - - -
391A LEU* 1.3 81.8 - - - +
393A ALA* 1.3 57.2 + - - +
395A ARG* 3.5 22.9 - - - +
396A LEU* 2.7 51.3 + - + +
579A TYR* 5.0 1.4 + - - -
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Residues in contact with ALA 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 SER 3.4 11.0 + - - +
390A LEU* 3.1 12.0 + - - +
392A GLN* 1.3 78.6 - - - +
394A VAL* 1.3 54.9 + - - +
396A LEU* 3.9 1.5 + - - -
397A GLY 3.3 0.7 + - - -
398A ARG* 2.6 46.7 + - + +
403A VAL* 3.4 32.1 - - + -
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Residues in contact with VAL 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 LEU* 3.1 37.7 - - + +
391A LEU* 3.0 8.2 + - + +
393A ALA* 1.3 73.5 - - - +
395A ARG* 1.3 58.9 + - - +
397A GLY* 2.7 24.8 + - - -
398A ARG 4.3 3.1 - - - +
399A CYS* 5.9 0.9 - - - -
403A VAL* 4.0 12.1 - - + +
578A ALA* 4.2 19.7 - - + -
579A TYR* 4.2 13.6 - - - +
582A LEU* 5.2 10.3 - - + -
602A ARG* 4.0 23.6 - - + +
603A CYS 5.5 0.9 - - - +
604A ASP* 4.2 1.4 - - - +
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Residues in contact with ARG 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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228A GLY* 4.4 2.6 - - - -
229A SER* 2.9 32.6 - - - +
343A ASP* 2.3 30.5 + - - -
345A LEU* 3.1 39.2 - - + +
376A LEU 5.8 0.4 + - - -
391A LEU 2.2 31.2 + - - +
392A GLN* 3.0 22.1 + - - +
394A VAL* 1.3 67.9 - - - +
396A LEU* 1.3 67.0 + - + +
397A GLY 3.1 0.2 + - - -
579A TYR* 3.2 42.8 + - + +
604A ASP* 2.8 22.3 - - - +
611A TYR* 4.5 14.1 - - - -
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Residues in contact with LEU 396 (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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345A LEU* 5.4 7.4 - - + -
392A GLN* 2.7 48.6 + - + +
393A ALA* 4.6 2.7 - - - +
395A ARG* 1.3 80.4 - - + +
397A GLY* 1.3 59.7 + - - +
398A ARG* 3.5 6.6 - - + +
604A ASP* 2.8 11.9 - - - +
608A LEU* 5.3 18.4 - - + +
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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