Contacts of the helix formed by residues 483 - 496 (chain A) in PDB entry 3H8E
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 483 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A SER* 3.5 19.7 - - - +
374A ILE* 3.8 14.6 - - + -
390A THR* 4.9 3.1 - - - +
412A ASP* 3.1 16.8 - - - +
463A MET* 3.6 33.0 - - + -
465A ILE* 3.9 20.9 - - + -
482A ARG* 1.3 83.0 - - + +
484A VAL* 1.3 65.0 + - - +
485A PRO 3.2 2.7 - - - -
486A LEU* 3.2 4.4 + - + -
487A LEU* 2.9 30.1 + - + +
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Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ILE* 4.0 20.9 - - + +
182A GLY* 4.6 0.2 - - - -
183A MET* 3.8 9.0 - - + +
186A THR* 3.4 25.6 - - - +
296A SER* 3.5 23.8 - - - +
299A GLY* 4.1 4.5 - - - +
300A THR* 3.8 19.5 - - - +
303A ALA* 5.0 0.2 - - + -
481A GLY 3.0 18.9 + - - +
483A PRO* 1.3 75.5 - - - +
485A PRO* 1.4 72.0 - - + +
488A THR* 2.8 46.3 + - - +
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Residues in contact with PRO 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 3.1 28.3 - - - +
179A ILE* 3.6 25.3 - - + +
183A MET* 3.7 15.3 - - + -
410A ALA* 3.7 17.0 - - + +
411A ASP 5.6 0.2 - - - +
412A ASP* 3.7 22.2 - - + +
481A GLY 4.1 1.8 - - - +
482A ARG* 5.3 3.6 - - + -
483A PRO 3.2 0.2 - - - -
484A VAL* 1.4 94.8 - - + +
486A LEU* 1.3 57.6 + - - +
488A THR* 3.8 0.7 - - - -
489A GLN* 2.9 31.7 + - - +
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Residues in contact with LEU 486 (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 THR* 5.7 0.7 - - - -
392A LEU* 6.2 0.2 - - + -
403A LEU* 3.6 45.8 - - + +
406A ALA* 3.7 1.8 - - + +
407A GLY* 3.6 15.7 - - - +
410A ALA* 4.3 9.4 - - - -
412A ASP* 3.0 42.4 + - - +
413A ARG 4.7 0.2 - - - -
414A ALA* 4.0 21.1 - - + -
463A MET* 3.9 24.9 - - + -
483A PRO* 3.2 5.4 + - + +
485A PRO* 1.3 73.9 - - - +
487A LEU* 1.3 62.6 + - - +
489A GLN* 3.2 4.7 + - - +
490A TYR* 2.8 25.3 + - - +
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 4.3 23.8 - - + -
296A SER* 4.2 10.3 - - - +
297A VAL* 5.2 0.4 - - + -
300A THR* 3.4 32.8 - - + +
372A ILE* 4.5 5.8 - - + -
374A ILE* 3.9 23.1 - - + -
403A LEU* 4.8 5.6 - - + -
463A MET* 3.8 24.7 - - - -
483A PRO* 2.9 35.3 + - + +
486A LEU* 1.3 82.1 - - + +
488A THR* 1.4 62.2 + - - +
490A TYR* 3.2 7.6 + - + +
491A LEU* 3.0 26.6 + - + +
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Residues in contact with THR 488 (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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179A ILE* 3.8 27.6 - - + -
300A THR* 3.9 11.9 - - - +
303A ALA* 3.7 24.9 - - + +
304A VAL* 5.2 5.8 - - + -
307A LEU* 4.4 17.7 - - + -
309A LEU* 5.6 1.1 - - + -
484A VAL* 2.8 33.8 + - - +
485A PRO 3.9 0.4 - - - -
487A LEU* 1.4 72.1 - - - +
489A GLN* 1.3 60.5 + - - +
491A LEU* 3.1 5.3 + - - +
492A LEU* 2.8 33.5 + - + +
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Residues in contact with GLN 489 (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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124A TYR* 5.0 2.9 + - - -
128A ARG* 2.8 47.3 + - - +
179A ILE* 5.2 0.6 - - - +
406A ALA* 3.5 32.3 - - - +
409A ARG* 3.3 20.9 + - - +
410A ALA* 3.9 9.4 - - + +
485A PRO 2.9 18.6 + - - +
486A LEU 3.5 4.7 - - - +
488A THR* 1.3 78.0 - - - +
490A TYR* 1.4 56.3 + - - +
492A LEU* 3.2 16.2 + - - +
493A ASP* 2.8 52.2 + - - +
497A ALA 5.5 0.7 - - - +
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Residues in contact with TYR 490 (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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262A PHE* 3.3 18.9 - + + -
264A LEU* 5.7 2.0 - - + -
370A ALA* 3.3 27.2 - - - +
372A ILE* 3.7 19.3 - - + -
399A LEU* 3.5 17.6 - - + +
402A GLN* 3.6 23.2 + - + -
403A LEU* 3.6 23.1 - - + -
406A ALA* 3.6 10.5 - - + +
486A LEU 2.8 17.2 + - - +
487A LEU* 3.5 10.8 - - + +
489A GLN* 1.4 72.3 - - - +
491A LEU* 1.3 83.0 - - + +
493A ASP* 3.2 7.3 + - - +
494A ARG* 2.9 64.6 + - + +
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Residues in contact with LEU 491 (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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262A PHE* 4.0 30.1 - - + -
264A LEU* 4.6 5.8 - - + -
300A THR* 3.9 19.3 - - + -
304A VAL* 3.7 25.8 - - + -
309A LEU* 3.9 15.4 - - + +
311A VAL* 4.6 11.1 - - + +
313A LEU* 4.0 21.1 - - + -
487A LEU 3.0 9.3 + - - +
488A THR* 3.1 6.0 + - - +
490A TYR* 1.3 97.7 - - + +
492A LEU* 1.3 58.6 - - - +
494A ARG* 3.2 4.3 + - + +
495A ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 4.5 0.7 - - - +
128A ARG* 4.3 11.2 - - - +
175A HIS* 3.9 37.9 - - + +
179A ILE* 5.0 1.3 - - + -
307A LEU* 3.9 9.4 - - + -
309A LEU* 3.7 21.7 - - + +
488A THR* 2.8 34.7 + - + +
489A GLN* 3.5 26.5 - - - +
491A LEU* 1.3 71.4 - - - +
493A ASP* 1.3 63.5 + - - +
495A ALA* 3.2 2.7 + - - +
496A GLY 2.9 19.2 + - - -
497A ALA* 3.0 41.5 + - + +
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Residues in contact with ASP 493 (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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402A GLN 4.7 1.6 - - - +
406A ALA* 3.9 13.5 + - - +
409A ARG* 2.7 44.1 + - - -
489A GLN* 2.8 28.3 + - - +
490A TYR* 3.2 8.9 + - - +
492A LEU* 1.3 76.9 - - - +
494A ARG* 1.3 86.9 + - - +
496A GLY* 3.2 12.5 + - - -
497A ALA 5.2 2.5 - - - +
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Residues in contact with ARG 494 (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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262A PHE* 3.6 45.6 - - + -
311A VAL* 4.7 3.6 - - + +
369A GLN* 5.2 0.2 - - - +
402A GLN* 3.6 38.8 - - - +
490A TYR* 2.9 66.1 + - + +
491A LEU* 3.2 7.1 + - - +
493A ASP* 1.3 100.5 + - - +
495A ALA* 1.3 60.4 + - - +
496A GLY 3.5 0.3 + - - -
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Residues in contact with ALA 495 (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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309A LEU* 4.4 13.9 - - + -
310A PRO* 3.5 36.7 - - + +
311A VAL* 4.2 11.8 - - + +
491A LEU 2.9 16.8 + - - +
492A LEU 3.2 5.1 + - - +
494A ARG* 1.3 75.0 - - - +
496A GLY* 1.3 59.8 + - - +
497A ALA* 4.3 5.1 - - + +
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Residues in contact with GLY 496 (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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492A LEU 2.9 5.0 + - - -
493A ASP* 3.2 8.6 + - - -
494A ARG 3.2 4.8 + - - -
495A ALA* 1.3 80.5 - - - +
497A ALA* 1.3 58.5 + - - +
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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