Contacts of the helix formed by residues 392 - 406 (chain A) in PDB entry 2WW9
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 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386A GLN 4.3 10.3 + - - -
387A ALA 5.6 0.9 + - - -
389A SER* 3.9 24.1 - - - -
390A GLY 3.6 3.2 + - - -
391A SER* 1.4 71.8 - - - +
393A ALA* 1.4 61.7 + - - +
394A ARG* 3.9 6.1 + - - +
395A ASP* 3.7 35.2 + - - -
396A VAL* 3.0 36.2 + - - +
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Residues in contact with ALA 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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386A GLN* 3.7 31.1 - - + +
391A SER 3.7 3.2 + - - -
392A SER* 1.4 70.0 + - - +
394A ARG* 1.4 63.6 + - - +
396A VAL* 5.0 0.4 - - - +
397A ALA* 3.4 25.8 + - - +
420A ASN* 4.3 17.1 + - - +
423A ILE* 6.3 3.4 - - + -
424A PRO* 5.7 6.5 - - + -
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Residues in contact with ARG 394 (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 SER* 3.4 5.5 + - - +
393A ALA* 1.4 80.0 - - - +
395A ASP* 1.4 72.1 + - - +
397A ALA* 4.2 1.3 - - - +
398A LEU* 3.2 38.8 + - + +
136K ALA 5.1 3.8 + - - -
137K ASN* 2.9 38.2 + - - +
139K ILE 5.7 1.4 + - - -
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Residues in contact with ASP 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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106A ASN* 5.5 0.5 - - - +
108A LYS* 3.4 38.8 + - - +
389A SER* 5.1 4.0 + - - -
392A SER* 3.5 25.7 + - - -
393A ALA 3.5 0.2 - - - -
394A ARG* 1.4 86.7 - - - +
396A VAL* 1.4 57.3 + - + +
398A LEU* 3.7 6.3 - - - +
399A GLU* 2.8 41.5 + - + +
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A SER* 4.2 15.7 - - - -
392A SER 3.0 30.6 + - - +
393A ALA* 5.0 0.7 - - - +
395A ASP* 1.4 76.3 - - + +
397A ALA* 1.4 62.2 + - - +
399A GLU* 4.4 10.8 - - - +
400A PHE* 3.1 51.3 + - + +
416A ALA* 5.6 3.8 - - + +
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Residues in contact with ALA 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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393A ALA 3.4 20.2 + - - +
394A ARG 4.2 1.8 - - - +
395A ASP 3.4 0.4 - - - -
396A VAL* 1.4 78.9 - - - +
398A LEU* 1.4 56.2 + - - +
400A PHE* 4.4 1.2 - - - +
401A LYS* 3.1 28.2 + - - +
414A ASN* 5.1 2.4 + - - +
416A ALA* 4.4 26.2 - - - +
417A LYS* 6.1 0.7 - - - -
420A ASN* 4.7 12.6 - - - +
37N SER 4.7 7.4 - - - +
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Residues in contact with LEU 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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394A ARG* 3.2 32.1 + - + +
395A ASP* 3.7 5.2 - - - +
397A ALA* 1.4 76.1 - - - +
399A GLU* 1.4 60.2 + - - +
401A LYS* 3.3 33.7 + - - +
402A ASP* 3.1 43.9 + - - +
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Residues in contact with GLU 399 (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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108A LYS* 3.5 26.5 + - - +
395A ASP* 2.8 25.0 + - + +
396A VAL* 4.1 12.0 - - - +
398A LEU* 1.4 70.8 - - - +
400A PHE* 1.4 72.1 + - + +
402A ASP* 4.4 2.0 - - - +
403A GLN* 3.1 32.0 + - + +
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Residues in contact with PHE 400 (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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396A VAL* 3.1 43.0 + - + +
397A ALA* 4.4 2.0 - - - +
399A GLU* 1.4 86.3 - - + +
401A LYS* 1.4 58.6 + - - +
403A GLN* 3.9 5.1 - - - +
404A GLY 2.9 24.1 + - - -
414A ASN* 4.0 14.1 - - + +
416A ALA* 5.3 6.1 - - + -
38N ARG* 3.1 25.0 + - - +
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Residues in contact with LYS 401 (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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397A ALA 3.1 19.7 + - - +
398A LEU* 3.3 28.9 - - - +
399A GLU 3.3 0.2 - - - -
400A PHE* 1.4 79.1 - - - +
402A ASP* 1.4 87.4 + - - +
405A ILE* 3.1 35.1 + - + +
414A ASN* 4.6 0.6 + - - +
68K THR* 5.2 1.4 - - - +
34N GLN* 2.8 51.2 + - + +
35N LYS 4.5 0.7 - - - +
37N SER* 3.9 11.7 - - - +
38N ARG* 3.6 39.9 - - + +
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Residues in contact with ASP 402 (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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398A LEU* 3.1 26.8 + - - +
399A GLU* 4.6 1.8 - - - +
401A LYS* 1.4 102.5 + - - +
403A GLN* 1.4 60.5 + - - +
405A ILE* 3.5 6.7 + - - +
406A THR* 3.0 32.6 + - + +
34N GLN* 3.7 16.8 + - - +
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Residues in contact with GLN 403 (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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399A GLU* 3.1 23.8 + - + +
400A PHE* 3.9 6.1 - - - +
402A ASP* 1.4 78.0 - - - +
404A GLY* 1.4 59.6 + - - +
406A THR* 3.6 5.1 + - - +
407A LEU* 3.3 47.0 + - + +
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Residues in contact with GLY 404 (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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400A PHE 2.9 17.8 + - - -
403A GLN* 1.4 72.3 - - - +
405A ILE* 1.4 62.6 + - - +
406A THR 3.1 3.3 + - - -
407A LEU* 3.4 12.2 + - - -
410A ARG 3.5 0.2 - - - +
411A ARG* 3.2 33.2 - - - +
38N ARG* 3.9 20.0 - - - -
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Residues in contact with ILE 405 (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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401A LYS* 3.1 42.5 + - + +
402A ASP* 3.9 7.9 - - - +
404A GLY* 1.4 74.8 - - - +
406A THR* 1.4 68.4 + - + +
407A LEU 3.7 0.7 - - - -
409A GLY 3.8 0.3 - - - -
410A ARG* 2.9 24.3 + - - -
411A ARG 4.9 5.8 - - - +
413A GLN* 3.6 26.7 - - - +
1677F G 5.4 0.3 + - - -
34N GLN* 4.2 19.7 - - + +
36N LEU 4.0 9.6 - - - +
38N ARG* 4.1 6.9 - - + +
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Residues in contact with THR 406 (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 ASP* 3.0 19.1 + - + +
403A GLN* 3.6 6.2 + - - +
404A GLY 3.1 0.6 - - - -
405A ILE* 1.4 94.6 - - + +
407A LEU* 1.4 53.6 + - - +
408A MET 3.2 10.9 + - - -
409A GLY 3.6 7.2 - - - -
1676F U 3.4 27.8 + - - +
1677F G 3.3 34.0 + - - +
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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