Contacts of the helix formed by residues 384 - 390 (chain A) in PDB entry 2YWB
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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243A HIS* 4.4 0.2 - - - -
245A LEU* 3.6 10.4 - - - +
288A ARG* 3.6 35.9 - - + +
291A ILE* 3.9 31.0 - - + -
382A PRO* 3.5 5.4 - - + -
383A GLY* 1.3 88.3 - - - +
385A GLY* 1.3 65.5 + - - +
386A LEU 3.5 0.3 + - - -
387A ALA* 3.1 20.8 + - + +
388A VAL* 3.7 28.0 - - + -
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Residues in contact with GLY 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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243A HIS* 4.7 0.7 - - - -
245A LEU* 3.5 5.6 - - - -
381A PHE* 3.4 31.9 - - - -
382A PRO* 2.9 19.0 + - - +
383A GLY 3.0 3.1 + - - -
384A PRO* 1.3 80.1 - - - +
386A LEU* 1.3 62.2 + - - -
387A ALA 3.1 0.5 + - - -
388A VAL* 3.2 20.6 - - - +
389A ARG* 4.3 3.2 + - - +
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Residues in contact with LEU 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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245A LEU* 2.9 19.5 + - - +
246A LEU 3.7 11.9 - - - +
247A ARG* 4.7 7.2 - - + -
381A PHE* 3.7 17.5 - - + -
385A GLY* 1.3 68.3 - - - -
387A ALA* 1.3 63.7 + - - +
388A VAL 3.1 0.7 - - - -
389A ARG* 3.0 34.0 + - - +
390A VAL* 3.4 16.1 + - - +
399A LEU* 3.8 21.3 - - + +
402A LEU* 4.0 26.7 - - + -
403A ARG* 3.4 37.0 - - + +
406A ASP* 5.0 7.9 - - + +
427A ALA 5.5 0.2 - - - +
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Residues in contact with ALA 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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245A LEU* 3.7 24.4 - - + +
278A LEU* 4.2 9.2 - - + -
287A LYS* 3.0 33.0 + - + +
291A ILE* 4.6 7.6 - - + -
384A PRO* 3.1 16.5 + - + +
386A LEU* 1.3 77.6 - - - +
388A VAL* 1.3 60.3 + - + +
389A ARG 3.2 0.9 + - - -
390A VAL 3.6 3.3 - - - +
394A VAL* 3.6 25.1 - - + +
503A GLU* 3.4 0.2 - - - +
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Residues in contact with VAL 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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284A PRO 5.0 0.7 - - - +
287A LYS* 5.0 8.5 - - + -
288A ARG* 3.9 32.3 - - + +
382A PRO* 4.3 7.4 - - + -
384A PRO* 3.7 33.2 - - + -
385A GLY 3.2 16.4 + - - +
387A ALA* 1.3 77.9 - - + +
389A ARG* 1.3 60.2 + - + +
390A VAL 3.5 1.3 - - - -
391A LEU* 5.1 0.2 - - - +
501A GLU* 4.2 15.9 - - - +
502A TRP* 4.7 3.3 + - - +
503A GLU* 2.9 49.6 + - + +
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Residues in contact with ARG 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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247A ARG* 3.1 28.1 - - - +
380A PRO 4.4 0.8 + - - -
381A PHE* 3.4 22.2 - - - -
382A PRO* 3.5 17.6 - - - +
385A GLY 4.3 6.3 - - - +
386A LEU* 3.0 23.1 + - - +
388A VAL* 1.3 78.4 - - - +
390A VAL* 1.3 59.9 + - - +
391A LEU* 4.0 1.1 - - - -
402A LEU* 3.6 10.8 - - + +
406A ASP* 4.3 3.6 + - - -
424A GLN* 4.3 12.1 + - - +
426A LEU* 3.4 24.4 - - - +
427A ALA 3.5 22.0 - - - +
428A VAL* 3.3 16.1 - - + -
429A LEU 2.8 26.3 + - - -
501A GLU* 2.8 44.0 + - - +
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Residues in contact with VAL 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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287A LYS* 2.7 31.7 + - - -
386A LEU 3.4 15.0 + - - +
387A ALA 3.7 4.0 + - - +
389A ARG* 1.3 80.6 - - - +
391A LEU* 1.3 62.4 + - - +
392A GLY 3.2 3.3 + - - +
393A GLU 3.8 23.1 - - - +
394A VAL* 4.4 8.3 - - + -
398A ARG* 4.0 27.8 - - + +
399A LEU* 4.5 15.0 - - + -
402A LEU* 3.7 19.3 - - + -
429A LEU* 3.7 12.6 - - + +
431A PRO* 5.1 1.6 - - + -
503A GLU* 3.3 3.6 - - - +
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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