Contacts of the helix formed by residues 359 - 371 (chain A) in PDB entry 4D10
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 GLU 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A TYR* 5.6 1.4 + - - -
323A SER* 3.7 40.0 - - - +
326A ALA* 4.5 4.5 - - + -
327A ILE* 3.8 22.3 - - + +
355A PHE 3.3 5.9 + - - +
356A LEU* 3.0 15.3 - - - +
358A LEU* 1.3 82.4 - - - +
360A PRO* 1.3 68.5 - - - +
361A GLN* 3.3 18.8 + - - +
362A VAL* 3.7 19.9 + - + +
363A ARG* 3.5 11.3 + - - +
384A MET* 5.0 4.2 - - - +
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Residues in contact with PRO 360 (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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356A LEU 3.9 7.4 - - - +
357A GLU 4.5 4.9 - - - +
358A LEU 3.4 11.9 - - - +
359A GLU* 1.3 84.5 - - - +
361A GLN* 1.3 62.9 + - + +
363A ARG* 3.4 26.4 + - + +
364A ASP* 2.8 45.1 + - - +
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Residues in contact with GLN 361 (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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359A GLU* 3.3 17.0 - - - +
360A PRO* 1.3 85.6 - - + +
362A VAL* 1.3 57.4 + - + +
364A ASP* 3.3 3.3 + - - +
365A ILE* 3.0 36.1 + - + +
380A MET* 3.9 26.0 + - + +
383A GLU* 5.6 7.1 + - - +
384A MET* 3.9 37.6 - - + +
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Residues in contact with VAL 362 (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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326A ALA* 4.0 17.9 - - + +
327A ILE* 3.9 26.2 - - + +
330A GLY* 4.0 11.7 - - - -
331A LEU* 4.4 8.3 - - + +
356A LEU* 5.1 3.1 - - + -
359A GLU* 3.7 17.5 + - + +
360A PRO 3.4 0.2 - - - -
361A GLN* 1.3 75.8 - - - +
363A ARG* 1.3 58.2 + - - +
365A ILE* 3.2 13.2 + - + +
366A ILE* 2.9 47.3 + - + +
384A MET* 3.7 24.7 - - + -
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Residues in contact with ARG 363 (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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353A LYS* 5.4 2.9 - - - +
356A LEU* 3.4 50.3 + - + +
357A GLU* 3.2 35.8 + - - +
359A GLU 3.5 2.4 + - - -
360A PRO* 3.4 29.0 + - - +
362A VAL* 1.3 78.2 - - - +
364A ASP* 1.3 75.5 + - - +
366A ILE* 3.5 1.8 + - - +
367A PHE* 3.0 65.2 + - + -
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Residues in contact with ASP 364 (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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360A PRO* 2.8 30.5 + - - +
361A GLN 3.6 4.9 - - - +
363A ARG* 1.3 94.1 + - - +
365A ILE* 1.3 53.6 + - - +
367A PHE* 3.9 7.6 - - - +
368A LYS* 2.8 58.1 + - + +
380A MET* 4.0 21.1 - - + +
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Residues in contact with ILE 365 (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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331A LEU* 5.8 3.1 - - + -
334A LEU* 3.7 24.5 - - + -
361A GLN 3.0 24.8 + - - +
362A VAL* 3.5 14.4 - - + +
364A ASP* 1.3 75.4 - - - +
366A ILE* 1.3 58.6 + - + +
368A LYS* 4.7 1.8 - - - -
369A PHE* 2.9 28.4 + - - +
377A CYS* 3.4 22.7 - - - +
380A MET* 3.7 26.9 - - + +
381A LEU* 3.8 38.8 - - + +
384A MET* 4.2 13.9 - - + -
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Residues in contact with ILE 366 (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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330A GLY* 4.1 20.2 - - - +
334A LEU* 3.8 21.9 - - + +
342A LEU* 3.9 24.9 - - + -
346A VAL* 4.3 13.2 - - + -
347A ILE* 4.3 19.3 - - + -
356A LEU* 3.7 25.6 - - + -
362A VAL* 2.9 36.3 + - + +
363A ARG* 4.0 3.1 - - - +
365A ILE* 1.3 73.8 - - + +
367A PHE* 1.3 63.2 + - + +
369A PHE* 3.3 4.0 + - - +
370A TYR* 3.0 27.0 + - - +
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Residues in contact with PHE 367 (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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347A ILE* 3.8 40.8 - - + -
353A LYS* 4.6 23.6 - - + -
356A LEU* 5.4 6.1 - - + -
363A ARG* 3.0 52.7 + - + +
364A ASP* 4.0 7.2 - - - +
366A ILE* 1.3 81.4 - - + +
368A LYS* 1.3 56.7 + - + +
370A TYR* 3.3 5.3 + + + +
371A GLU* 2.8 49.1 + - + +
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Residues in contact with LYS 368 (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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364A ASP* 2.8 44.9 + - + +
365A ILE 4.0 0.2 - - - +
367A PHE* 1.3 71.8 - - + +
369A PHE* 1.3 61.4 + - - +
371A GLU* 4.4 5.6 - - - +
372A SER 3.4 1.6 + - - -
373A LYS* 2.8 65.8 + - + +
374A TYR 4.2 0.2 + - - -
376A SER* 3.2 40.1 + - - +
377A CYS* 3.9 9.4 - - + +
380A MET* 5.0 5.8 - - + -
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Residues in contact with PHE 369 (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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334A LEU* 3.7 28.3 - - + -
338A ASP 6.3 0.2 - - - -
339A ARG 6.2 0.4 - - - -
342A LEU* 4.1 22.7 - - + -
365A ILE 2.9 18.4 + - - +
366A ILE 3.5 5.2 - - - +
368A LYS* 1.3 77.8 - - - +
370A TYR* 1.3 63.3 + - - +
372A SER* 3.6 7.6 + - - -
374A TYR* 3.9 15.1 + + - -
377A CYS* 4.0 17.2 - - - -
405A ILE* 4.0 14.8 - - + -
408A ARG* 3.9 31.4 - - + -
409A ALA* 3.7 35.7 - - + -
412A GLN* 3.5 31.1 - - - +
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Residues in contact with TYR 370 (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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339A ARG* 3.1 73.3 + - + +
342A LEU* 5.1 6.5 - - + -
343A GLN* 2.8 46.1 + - + +
347A ILE* 3.7 29.2 - - + -
366A ILE 3.0 14.1 + - - +
367A PHE* 3.8 6.1 - + + +
369A PHE* 1.3 79.0 - - + +
371A GLU* 1.3 65.6 + - + +
372A SER* 3.2 6.2 + - - -
412A GLN* 5.0 1.1 - - - -
391B GLN* 6.3 0.7 - - + -
395B ASP* 3.5 12.2 + - - -
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Residues in contact with GLU 371 (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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367A PHE* 2.8 35.3 + - - +
368A LYS* 3.7 4.3 + - - +
369A PHE 3.4 0.4 - - - -
370A TYR* 1.3 83.2 - - + +
372A SER* 1.3 66.8 + - - -
373A LYS* 2.9 49.0 + - + +
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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