Contacts of the helix formed by residues 394 - 415 (chain B) in PDB entry 4P22
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 LEU 394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 3.8 13.7 - - + -
63A GLY* 3.1 25.8 - - - +
64A HIS* 2.5 21.3 - - + +
65A GLU* 3.8 25.1 - - + +
191B THR* 4.9 1.2 - - - +
193B GLY 3.9 15.8 + - - +
194B LEU* 3.5 31.6 - - + -
393B ASP* 1.3 81.6 - - - +
395B ALA* 1.3 64.8 + - - +
396B PRO* 4.1 1.6 - - + -
397B ILE* 3.1 23.3 + - + +
398B ASN* 3.0 28.1 + - - +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A HIS* 2.7 17.4 + - + -
90A ASN* 3.8 13.9 - - - +
93A LEU* 3.6 38.8 - - + -
94A GLY 4.4 0.9 - - - +
86B GLU* 5.1 2.1 - - - +
113B SER 4.7 1.8 - - - +
114B SER* 4.4 13.2 - - - +
393B ASP 3.7 1.0 + - - -
394B LEU* 1.3 70.0 - - - +
396B PRO* 1.4 70.2 - - + +
398B ASN* 3.5 1.4 + - - +
399B ALA* 3.0 25.9 + - - +
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Residues in contact with PRO 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY* 4.5 3.4 - - - +
64A HIS* 3.9 12.8 - - + -
90A ASN* 4.5 8.0 - - + +
403A GLY* 3.7 10.9 - - - +
406A ALA* 3.9 6.7 - - + -
407A GLN* 3.5 31.1 + - + +
410A MET* 4.1 33.4 - - + -
394B LEU* 3.5 7.9 - - + -
395B ALA* 1.4 92.5 - - + +
397B ILE* 1.3 63.2 + - + +
399B ALA* 3.6 5.6 - - + +
400B PHE* 3.1 26.2 + - - +
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Residues in contact with ILE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY* 5.6 2.5 - - - +
407A GLN* 4.3 24.0 - - + +
191B THR* 3.3 24.5 - - + +
193B GLY 3.9 19.3 - - - +
194B LEU* 4.4 14.1 - - + +
195B PHE 5.0 4.7 - - - +
394B LEU* 3.1 34.3 + - + +
396B PRO* 1.3 81.9 - - + +
398B ASN* 1.3 62.7 + - - +
399B ALA 3.1 0.3 + - - -
400B PHE* 3.1 3.9 + - + -
401B ILE* 2.8 38.2 + - + +
426B PHE* 4.8 4.3 - - + -
428B ALA* 4.4 13.2 - - + -
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Residues in contact with ASN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY 4.3 2.0 - - - +
83B LEU* 3.5 34.1 - - - +
86B GLU* 4.0 6.1 - - + +
114B SER* 3.1 29.9 + - - +
191B THR* 3.1 34.7 + - - +
393B ASP* 3.3 24.3 + - - +
394B LEU 3.0 20.5 + - - +
395B ALA 4.1 2.2 - - - +
397B ILE* 1.3 76.7 - - - +
399B ALA* 1.3 52.2 - - - +
402B GLY* 2.7 32.1 + - - -
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 5.6 0.9 - - - +
89A LYS* 4.5 1.3 - - - +
90A ASN* 3.3 32.3 - - - +
399A ALA* 3.7 16.5 - - - +
403A GLY* 4.1 3.4 - - - -
86B GLU* 4.0 21.3 - - - +
395B ALA 3.0 18.9 + - - +
396B PRO 3.6 4.7 - - - +
397B ILE 3.1 0.2 - - - -
398B ASN* 1.3 78.3 - - - +
400B PHE* 1.3 56.5 + - - +
402B GLY 3.3 1.9 + - - -
403B GLY* 2.8 23.6 + - - -
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Residues in contact with PHE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ALA 4.2 1.1 - - - -
400A PHE* 3.3 46.8 - + - +
403A GLY* 3.5 17.9 - - - -
404A LEU* 3.6 17.3 - - + -
407A GLN* 3.7 13.2 - - - +
396B PRO 3.1 12.4 + - - +
397B ILE* 3.8 7.6 - - - -
399B ALA* 1.3 77.0 - - - +
401B ILE* 1.3 80.7 + - + +
403B GLY* 3.2 9.5 + - - -
404B LEU* 3.2 31.1 + - + +
426B PHE* 3.2 55.2 - + + -
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Residues in contact with ILE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.9 19.3 - - + -
189B ALA* 4.8 0.4 - - + -
190B ASP 4.4 12.6 - - - +
191B THR* 4.3 2.5 - - - +
196B GLY* 3.9 31.0 - - - -
197B GLN 4.5 2.2 - - - +
198B LEU* 4.0 24.0 - - + +
397B ILE* 2.8 28.7 + - + +
398B ASN 4.3 1.8 - - - +
400B PHE* 1.3 94.3 - - + +
402B GLY* 1.3 57.4 + - - +
403B GLY 3.4 0.2 + - - -
404B LEU* 3.4 12.1 + - + +
405B ALA* 3.0 27.4 + - - +
424B LEU* 6.0 2.0 - - + +
426B PHE* 4.5 8.1 - - + -
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Residues in contact with GLY 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.7 12.1 - - - +
86B GLU* 4.4 5.8 - - - -
87B ILE* 3.8 15.8 - - - +
90B ASN* 3.0 17.3 + - - -
398B ASN 2.7 25.1 + - - -
399B ALA 3.5 2.5 - - - -
401B ILE* 1.3 71.0 - - - +
403B GLY* 1.3 63.5 + - - +
405B ALA 4.2 0.7 - - - -
406B ALA* 3.3 15.4 + - - +
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Residues in contact with GLY 403 (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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396A PRO* 3.6 21.4 - - - +
400A PHE* 3.9 9.2 - - - -
90B ASN* 3.7 9.4 - - - -
399B ALA 2.8 14.0 + - - -
400B PHE 3.2 4.8 + - - -
402B GLY* 1.3 76.8 - - - +
404B LEU* 1.3 63.1 + - - +
406B ALA* 3.1 6.1 + - - +
407B GLN* 3.0 24.3 + - - +
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LYS* 5.5 8.1 - - - +
400A PHE* 3.7 24.6 - - + +
426A PHE* 4.9 6.7 - - + -
198B LEU* 5.1 9.0 - - + -
400B PHE* 3.2 30.1 + - + +
401B ILE* 3.6 15.5 - - + +
403B GLY* 1.3 76.5 - - - +
405B ALA* 1.3 61.9 + - - +
407B GLN* 3.1 30.2 + - - +
408B GLU* 3.1 28.1 + - - +
420B ILE* 5.7 3.6 - - + -
424B LEU* 4.2 24.2 - - + -
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.6 29.4 - - + -
187B VAL* 4.5 7.0 - - + +
189B ALA* 4.1 5.4 - - + -
198B LEU* 3.9 22.8 - - + +
401B ILE 3.0 17.7 + - - +
404B LEU* 1.3 75.6 - - - +
406B ALA* 1.3 62.6 + - - +
408B GLU* 3.2 11.5 + - - +
409B VAL* 3.0 26.0 + - + +
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Residues in contact with ALA 406 (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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396A PRO* 4.2 5.8 - - + -
87B ILE* 4.3 6.8 - - - +
90B ASN* 3.5 21.3 - - + -
91B ILE* 3.3 26.8 - - + +
402B GLY 3.3 18.4 + - - +
403B GLY 3.1 5.7 + - - +
405B ALA* 1.3 78.0 - - - +
407B GLN* 1.3 64.9 + - - +
409B VAL* 3.1 2.6 + - - -
410B MET* 3.0 28.1 + - - +
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Residues in contact with GLN 407 (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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396A PRO* 3.7 16.0 + - + +
397A ILE* 3.7 23.3 - - + +
400A PHE* 3.7 32.1 - - - +
426A PHE* 4.3 4.2 - - - -
428A ALA* 3.8 22.5 - - - +
403B GLY 3.0 11.9 + - - +
404B LEU* 3.1 25.8 + - + +
406B ALA* 1.3 74.3 - - - +
408B GLU* 1.3 68.5 + - - +
410B MET* 3.1 13.2 + - - +
411B LYS* 2.9 35.7 + - - +
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Residues in contact with GLU 408 (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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187B VAL* 4.1 6.1 - - + -
198B LEU* 4.2 5.6 - - + -
200B CYS* 3.5 25.3 - - - -
202B PHE* 3.4 10.7 - - + -
404B LEU* 3.1 16.0 + - - +
405B ALA* 3.3 7.9 - - - +
407B GLN* 1.3 76.0 - - - +
409B VAL* 1.3 65.5 + - - +
411B LYS* 3.0 29.4 + - - +
412B ALA 2.9 19.6 + - - -
419B PRO* 3.2 14.0 - - - +
420B ILE* 2.9 49.9 + - + +
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Residues in contact with VAL 409 (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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75B VAL* 3.9 28.7 - - + -
87B ILE* 4.6 3.4 - - + -
91B ILE* 3.5 29.4 - - + -
96B VAL* 4.9 0.2 - - + -
161B VAL* 4.3 6.5 - - + -
163B VAL* 3.4 29.4 - - + -
187B VAL* 4.6 9.0 - - + -
405B ALA 3.0 17.2 + - - +
406B ALA* 3.1 7.8 + - - +
408B GLU* 1.3 74.0 - - - +
410B MET* 1.3 63.7 + - - +
412B ALA* 3.1 10.0 + - - +
413B CYS* 2.9 25.6 + - - -
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Residues in contact with MET 410 (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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396A PRO* 3.7 17.3 - - + -
62B LEU* 2.9 41.9 - - + +
63B GLY* 4.6 5.2 - - - +
64B HIS* 4.3 4.3 - - + -
90B ASN 3.6 14.4 - - - +
91B ILE* 3.6 20.6 - - + +
94B GLY* 3.4 34.3 - - - +
96B VAL* 4.2 15.9 - - - -
406B ALA 3.0 18.0 + - - +
407B GLN* 3.2 11.2 - - - +
409B VAL* 1.3 76.8 - - - +
411B LYS* 1.3 65.7 + - + +
413B CYS* 3.0 17.5 + - - +
414B SER 3.1 3.1 + - - -
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Residues in contact with LYS 411 (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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428A ALA 4.6 9.0 + - - -
429A LEU* 3.6 25.4 - - + +
62B LEU* 3.6 23.3 - - + -
202B PHE* 4.0 11.5 - - + -
320B PHE* 4.8 8.1 - - - -
407B GLN* 2.9 27.9 + - - +
408B GLU* 3.0 32.3 + - - +
410B MET* 1.3 75.2 - - + +
412B ALA* 1.3 57.1 + - - +
415B GLY* 2.4 41.5 + - - +
417B PHE* 4.6 6.5 - - + +
418B MET 2.8 29.9 + - - +
419B PRO* 3.9 11.2 - - + +
420B ILE* 5.5 0.4 - - - +
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Residues in contact with ALA 412 (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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73B SER* 4.8 0.5 + - - -
161B VAL* 4.1 19.5 - - + +
185B LYS* 3.0 44.9 + - + +
202B PHE* 3.5 31.1 - - + -
408B GLU 2.9 6.1 + - - +
409B VAL* 3.1 10.3 + - - +
411B LYS* 1.3 78.2 - - - +
413B CYS* 1.3 62.1 + - - +
415B GLY 4.3 0.9 + - - -
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Residues in contact with CYS 413 (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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71B GLN* 6.1 0.7 - - - +
72B THR* 3.9 9.2 + - - -
73B SER* 3.1 43.0 + - - +
75B VAL* 3.8 17.9 - - - -
96B VAL* 4.0 19.7 - - + -
161B VAL* 3.8 13.0 - - - -
185B LYS* 5.4 0.3 + - - -
409B VAL* 2.9 18.5 + - - -
410B MET* 3.0 8.2 + - - +
412B ALA* 1.3 79.9 - - - +
414B SER* 1.3 61.4 + - - +
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Residues in contact with SER 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 5.5 5.9 - - - +
62B LEU* 3.3 27.4 - - - +
71B GLN* 6.2 0.4 - - - -
72B THR* 5.9 0.4 - - - -
410B MET 3.1 3.6 + - - -
413B CYS* 1.3 80.8 - - - +
415B GLY* 1.3 60.3 + - - +
416B LYS 3.8 1.9 + - - -
417B PHE* 4.9 2.4 - - - -
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Residues in contact with GLY 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.7 11.4 - - - -
185B LYS* 5.4 1.4 + - - -
206B MET* 3.7 22.2 - - - +
207B ILE* 4.1 1.2 - - - +
411B LYS* 2.4 37.0 + - - +
412B ALA 4.3 1.7 + - - +
413B CYS 3.8 0.4 - - - -
414B SER* 1.3 70.0 - - - +
416B LYS* 1.3 58.7 + - - +
417B PHE 3.1 10.3 + - - +
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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
------------------------------------------------------------
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