Contacts of the helix formed by residues 386 - 398 (chain A) in PDB entry 2WWB
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 SER 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A ILE* 3.6 25.5 + - - -
381A GLU 4.6 0.6 + - - -
384A GLY 3.7 2.2 + - - -
385A SER* 1.3 74.1 - - - +
387A ALA* 1.4 63.9 + - - +
388A LYS* 3.5 27.8 + - - +
389A ASP* 3.2 27.0 + - - +
390A VAL* 3.8 18.1 - - - +
417A ILE* 4.2 12.3 - - - -
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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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386A SER* 1.4 72.5 - - - +
388A LYS* 1.4 59.1 + - - +
389A ASP 3.4 0.2 - - - -
390A VAL* 3.3 8.8 + - - +
391A ALA* 2.9 28.9 + - - +
413A LEU* 3.7 39.1 - - + +
414A ASN* 3.9 13.5 - - + -
417A ILE* 3.9 18.4 - - + +
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Residues in contact with LYS 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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381A GLU 3.7 21.5 + - - -
382A VAL* 4.8 7.9 - - - +
386A SER* 3.5 20.4 + - - +
387A ALA* 1.4 75.9 - - - +
389A ASP* 1.4 75.5 + - - +
391A ALA* 3.6 14.9 + - - +
392A LYS* 3.5 28.2 + - - +
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Residues in contact with ASP 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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384A GLY 4.2 10.5 - - - +
386A SER* 3.2 28.5 + - - +
387A ALA 3.4 0.2 - - - -
388A LYS* 1.4 83.7 + - - +
390A VAL* 1.4 63.7 + - + +
392A LYS* 3.4 13.1 + - - +
393A GLN* 3.3 34.7 + - - +
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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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279A TYR* 3.6 27.6 - - + +
385A SER* 6.3 2.0 - - - -
386A SER 3.8 13.5 - - - +
387A ALA* 3.3 12.8 + - - +
389A ASP* 1.4 73.3 - - + +
391A ALA* 1.4 63.6 + - - +
393A GLN* 3.3 25.6 + - + +
394A LEU* 3.0 42.4 + - + +
413A LEU* 4.8 8.5 - - + -
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Residues in contact with ALA 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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387A ALA 2.9 16.3 + - - +
388A LYS* 3.7 10.8 - - - +
389A ASP 3.3 0.4 - - - -
390A VAL* 1.4 77.6 - - - +
392A LYS* 1.4 63.4 + - + +
394A LEU* 3.4 4.9 + - - +
395A LYS* 3.3 37.1 + - - +
399A MET* 5.1 0.2 - - - +
410A VAL* 6.6 0.4 - - + -
413A LEU* 3.9 21.1 - - + -
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Residues in contact with LYS 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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388A LYS* 3.5 25.9 + - - +
389A ASP* 3.4 10.5 + - - +
391A ALA* 1.4 74.7 - - + +
393A GLN* 1.4 64.1 + - + +
395A LYS* 3.3 17.6 + - - +
396A GLU* 3.6 19.2 + - - +
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Residues in contact with GLN 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 ASP* 3.4 31.1 + - - +
390A VAL* 3.3 26.2 + - + +
392A LYS* 1.4 75.8 - - + +
394A LEU* 1.4 62.4 + - + +
396A GLU* 3.4 26.9 + - - +
397A GLN* 3.6 20.9 - - - +
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Residues in contact with LEU 394 (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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267A ILE* 3.6 28.9 - - + -
268A LYS* 3.5 31.6 - - - -
279A TYR* 4.8 10.8 - - + -
390A VAL* 3.0 36.4 + - + +
391A ALA 3.7 2.7 - - - +
392A LYS 3.3 0.2 - - - -
393A GLN* 1.4 74.0 - - + +
395A LYS* 1.4 60.6 + - - +
397A GLN* 3.9 9.4 - - - +
398A GLN* 2.9 22.8 + - - -
399A MET* 3.2 36.3 + - + +
402A ARG* 3.8 1.2 + - - -
413A LEU* 3.8 20.2 - - + -
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Residues in contact with LYS 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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391A ALA* 3.3 27.6 + - - +
392A LYS* 3.6 10.8 - - - +
393A GLN 3.3 1.0 - - - -
394A LEU* 1.4 76.2 - - - +
396A GLU* 1.4 63.8 + - + +
398A GLN* 3.3 20.4 - - - +
399A MET* 4.3 13.5 - - - +
402A ARG* 3.5 35.4 + - - +
410A VAL* 4.1 23.9 - - - +
413A LEU* 6.0 1.2 - - - +
1657F C 5.6 3.8 - - - -
1658F G 5.2 10.5 - - - +
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Residues in contact with GLU 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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392A LYS* 3.6 16.4 + - - +
393A GLN* 3.4 18.6 + - - +
394A LEU 3.4 0.4 - - - -
395A LYS* 1.4 78.3 - - + +
397A GLN* 1.4 63.0 + - + +
398A GLN* 4.0 7.8 + - - +
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Residues in contact with GLN 397 (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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268A LYS* 3.9 28.2 + - - +
277A ASN* 5.7 2.6 + - - -
393A GLN* 3.6 17.1 + - - +
394A LEU* 3.9 14.0 - - - +
396A GLU* 1.4 77.6 - - + +
398A GLN* 1.4 66.3 + - - +
399A MET* 3.4 9.5 + - - +
400A VAL* 4.1 5.3 + - - +
401A MET* 3.4 18.2 - - - +
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Residues in contact with GLN 398 (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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271A ARG* 5.7 0.3 + - - -
394A LEU 2.9 11.8 + - - -
395A LYS 3.3 15.5 - - - +
396A GLU 3.4 6.2 + - - +
397A GLN* 1.4 77.7 + - - +
399A MET* 1.4 56.4 + - - +
400A VAL 3.3 1.1 - - - -
401A MET* 3.7 36.3 - - - +
402A ARG* 2.8 56.6 + - + +
1658F G 3.1 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