Contacts of the helix formed by residues 384 - 391 (chain B) in PDB entry 3W3K
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 384 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B ARG* 1.3 76.7 - - - +
385B ASP* 1.3 64.3 + - - +
386B ASP 3.3 0.7 + - - -
387B PHE* 3.5 8.1 + - - +
388B GLN* 3.7 13.3 + - - +
391B MET* 3.6 21.2 - - + +
410B ASP* 3.7 9.8 + - + +
412B LYS* 2.2 49.3 + - - +
413B LEU* 4.0 24.3 - - + +
416B ASN* 4.5 15.2 + - - +
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Residues in contact with ASP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B ARG* 3.6 18.6 + - - -
383B ARG* 3.4 7.4 - - + +
384B GLU* 1.3 77.5 - - - +
386B ASP* 1.3 71.0 + - - +
388B GLN* 2.9 35.6 + - - +
389B PRO* 4.3 2.4 - - - +
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Residues in contact with ASP 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B HIS* 3.6 13.9 - - - +
357B ILE* 3.8 29.5 + - + +
359B ILE* 3.6 22.8 + - - +
381B GLU 4.2 2.4 - - - +
382B LEU* 4.4 4.3 - - + -
383B ARG* 2.7 67.3 + - - +
384B GLU 3.2 1.0 - - - -
385B ASP* 1.3 81.9 - - - +
387B PHE* 1.3 64.5 + - - +
388B GLN 3.7 0.2 + - - -
389B PRO* 3.9 4.2 - - - +
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Residues in contact with PHE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ILE* 4.1 11.0 - - + -
359B ILE* 4.0 19.5 - - + -
374B LEU* 4.6 5.8 - - + -
379B PHE* 5.7 0.2 - + - -
382B LEU* 3.8 32.8 - - + -
383B ARG 4.0 2.8 + - - +
384B GLU 3.5 5.2 + - - +
385B ASP 3.3 0.6 - - - -
386B ASP* 1.3 83.9 - - - +
388B GLN* 1.3 64.0 + - - +
389B PRO* 3.3 4.5 - - - -
390B LEU* 3.0 28.8 + - + +
391B MET* 3.6 12.7 - - + +
399B ILE* 3.9 26.7 - - + -
401B LEU* 3.9 32.8 - - + -
413B LEU* 4.2 14.1 - - + -
414B PHE* 5.0 3.1 - + - -
417B PHE* 3.9 27.1 - + + -
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Residues in contact with GLN 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B ARG* 3.7 20.7 + - - +
384B GLU* 3.7 17.3 + - - +
385B ASP* 2.9 48.6 + - - +
387B PHE* 1.3 76.0 - - - +
389B PRO* 1.4 65.9 - - + +
390B LEU 3.3 0.7 + - - -
391B MET* 3.5 41.2 + - - +
392B GLN* 4.9 3.5 + - - +
416B ASN* 5.1 4.4 - - - +
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Residues in contact with PRO 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ILE* 4.1 12.6 - - + +
360B SER 3.6 26.7 - - - +
361B ARG* 3.7 37.7 - - + +
363B PHE* 4.0 5.4 - - + -
364B SER* 3.2 34.9 + - - +
385B ASP 4.3 1.8 - - - +
386B ASP 3.9 10.1 - - - +
387B PHE* 3.3 4.7 - - - -
388B GLN* 1.4 94.1 - - + +
390B LEU* 1.3 59.4 + - - +
391B MET 3.4 0.2 - - - -
392B GLN 4.9 1.5 + - - -
393B LEU* 4.1 3.3 - - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ILE* 4.9 7.4 - - + -
363B PHE* 3.9 24.2 - - + -
369B LEU* 4.7 1.1 - - + -
372B LEU* 3.6 33.4 - - + -
387B PHE* 3.0 45.4 + - + +
389B PRO* 1.3 77.6 - - - +
391B MET* 1.3 63.7 + - - +
392B GLN 3.3 2.0 - - - -
393B LEU* 3.1 35.2 + - + +
396B LEU* 3.9 17.5 - - + +
399B ILE* 4.3 5.8 - - + -
417B PHE* 3.6 23.9 - - + -
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Residues in contact with MET 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B GLU* 3.6 26.5 - - + +
387B PHE* 3.6 16.4 - - + +
388B GLN* 3.5 34.3 + - - +
389B PRO 3.4 2.0 - - - -
390B LEU* 1.3 78.0 - - - +
392B GLN* 1.3 69.3 - - - +
393B LEU 3.4 0.4 - - - -
413B LEU* 3.7 32.5 - - + +
416B ASN* 3.4 39.2 - - + +
417B PHE* 3.9 24.0 - - + +
418B SER* 3.0 26.3 + - - -
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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