Contacts of the helix formed by residues 394 - 414 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A THR* 5.0 2.8 - - - +
193A GLY* 3.8 27.6 - - - +
194A LEU* 4.0 17.0 - - + -
392A GLY* 4.2 4.2 + - - -
393A ASP* 1.3 86.7 - - - +
395A ALA* 1.3 67.0 + - - +
396A PRO* 3.3 2.7 - - + -
397A ILE* 2.8 33.6 + - + +
398A ASN* 3.1 18.4 + - - +
60B TYR* 4.4 5.4 - - + +
63B GLY* 4.3 13.7 - - - +
64B HIS* 2.7 17.3 - - + +
65B GLU* 3.8 38.8 - - + +
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 5.1 2.1 - - - +
114A SER* 3.9 16.3 + - - +
393A ASP 4.0 0.6 + - - -
394A LEU* 1.3 69.6 - - - +
396A PRO* 1.3 62.2 - - + +
398A ASN* 3.4 2.4 + - - +
399A ALA* 2.8 32.9 + - - +
64B HIS* 2.5 16.7 + - + +
90B ASN* 3.9 11.7 - - - +
93B LEU* 3.5 42.4 - - + -
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Residues in contact with PRO 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 3.4 4.5 - - + -
395A ALA* 1.3 92.8 - - + +
397A ILE* 1.3 57.6 + - + +
399A ALA* 3.5 4.0 + - + -
400A PHE* 3.0 29.1 + - - +
63B GLY* 4.0 2.9 - - - +
64B HIS* 3.4 16.4 - - + -
90B ASN* 4.3 9.9 - - + +
403B GLY* 3.6 12.8 - - - +
406B ALA* 4.2 4.9 - - + -
407B GLN* 3.7 28.7 + - + +
410B MET* 3.7 33.0 - - + -
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Residues in contact with ILE 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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191A THR* 3.8 13.5 - - + +
193A GLY 3.7 25.1 - - - +
194A LEU* 4.7 7.6 - - + +
195A PHE 4.7 1.3 - - - +
394A LEU* 2.8 33.5 + - + +
396A PRO* 1.3 69.8 - - + +
398A ASN* 1.3 55.6 + - - +
400A PHE* 3.0 4.0 + - - +
401A ILE* 2.8 52.5 + - + +
426A PHE* 4.7 6.3 - - + -
428A ALA* 3.5 29.6 - - + -
407B GLN* 3.7 20.9 - - + +
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Residues in contact with ASN 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY* 4.1 5.3 - - - -
83A LEU* 3.6 25.1 - - - +
86A GLU* 4.0 15.0 - - + +
114A SER* 2.6 30.8 + - - +
191A THR* 3.1 31.4 - - - +
393A ASP* 3.4 18.9 + - - +
394A LEU 3.1 11.1 + - - +
395A ALA* 3.7 6.1 - - - +
397A ILE* 1.3 78.5 - - - +
399A ALA* 1.3 55.4 + - - +
402A GLY* 2.7 33.4 + - - -
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Residues in contact with ALA 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 4.1 20.2 - - - +
90A ASN* 5.1 0.7 + - - -
395A ALA 2.8 17.0 + - - +
396A PRO 3.8 3.1 - - - +
398A ASN* 1.3 73.6 - - - +
400A PHE* 1.3 58.0 + - - +
402A GLY 3.6 0.7 - - - -
403A GLY* 2.9 25.1 + - - -
86B GLU* 5.2 0.7 - - - +
89B LYS* 4.3 1.6 - - - +
90B ASN* 3.3 39.5 - - - +
399B ALA* 3.7 15.5 - - + +
403B GLY* 4.1 2.5 - - - -
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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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322A LYS* 5.6 4.0 - - - -
396A PRO 3.0 17.9 + - - +
397A ILE 3.0 3.5 + - - +
399A ALA* 1.3 75.4 - - - +
401A ILE* 1.3 84.2 + - + +
403A GLY* 3.0 16.1 + - - -
404A LEU* 3.2 27.5 + - + +
426A PHE* 3.3 56.3 - + + -
400B PHE* 3.3 47.6 - + - +
403B GLY* 3.9 12.3 - - - -
404B LEU* 3.7 19.1 - - + -
407B GLN* 3.7 11.9 - - - +
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Residues in contact with ILE 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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83A LEU* 3.9 24.0 - - + -
189A ALA* 4.6 11.7 - - + -
190A ASP 4.5 5.8 - - - +
191A THR* 4.0 6.5 - - - +
196A GLY* 3.8 21.8 - - - -
197A GLN 4.6 5.2 - - - +
198A LEU* 4.8 9.4 - - + -
397A ILE* 2.8 31.1 + - + +
398A ASN 4.5 0.9 - - - +
400A PHE* 1.3 101.7 - - + +
402A GLY* 1.3 56.9 + - - +
404A LEU* 3.1 11.5 + - + +
405A ALA* 2.8 32.6 + - - +
426A PHE* 3.7 18.6 - - + -
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Residues in contact with GLY 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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83A LEU* 3.8 3.8 - - - +
86A GLU* 4.4 6.1 - - - -
87A ILE* 3.9 23.2 - - - +
90A ASN* 3.1 19.3 + - - -
398A ASN 2.7 25.5 + - - -
399A ALA 3.6 1.3 - - - -
401A ILE* 1.3 70.9 - - - +
403A GLY* 1.3 64.1 + - - +
405A ALA* 3.9 0.9 - - - +
406A ALA* 3.2 15.9 + - - +
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Residues in contact with GLY 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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90A ASN* 4.0 7.6 - - - -
399A ALA 2.9 13.6 + - - -
400A PHE 3.0 6.2 + - - -
402A GLY* 1.3 77.2 - - - +
404A LEU* 1.3 61.2 + - - +
406A ALA* 3.2 11.1 + - - +
407A GLN* 3.2 19.7 + - - +
396B PRO 3.7 10.8 - - - +
400B PHE* 3.5 22.2 - - - -
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Residues in contact with LEU 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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198A LEU* 3.6 17.3 - - + -
400A PHE* 3.2 36.0 + - + +
401A ILE* 3.1 8.8 + - + +
403A GLY* 1.3 75.5 - - - +
405A ALA* 1.3 64.0 + - - +
407A GLN* 3.3 22.3 + - - +
408A GLU* 3.1 26.6 + - - +
420A ILE* 5.5 2.0 - - + -
424A LEU* 4.1 23.8 - - + -
426A PHE* 6.3 0.7 - - + -
400B PHE* 3.6 26.5 - - + -
426B PHE* 5.3 4.7 - - + -
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Residues in contact with ALA 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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87A ILE* 3.7 32.3 - - + -
187A VAL* 4.3 5.4 - - + +
189A ALA* 4.1 15.7 - - + -
198A LEU* 4.1 15.8 - - + +
401A ILE 2.8 17.7 + - - +
404A LEU* 1.3 77.3 - - - +
406A ALA* 1.3 56.3 + - - +
408A GLU* 3.0 8.0 + - - +
409A VAL* 2.9 30.0 + - - +
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Residues in contact with ALA 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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87A ILE* 4.5 10.9 - - + +
90A ASN* 3.5 31.2 - - + +
91A ILE* 4.8 2.7 - - + +
402A GLY 3.2 19.4 + - - +
403A GLY 3.2 5.4 + - - +
405A ALA* 1.3 72.9 - - - +
407A GLN* 1.3 60.2 + - - +
409A VAL* 3.2 10.9 + - - +
410A MET* 2.8 34.9 + - + +
396B PRO* 3.9 9.0 - - + -
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Residues in contact with GLN 407 (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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403A GLY 3.2 17.3 + - - +
404A LEU* 3.3 20.1 + - - +
406A ALA* 1.3 72.8 - - - +
408A GLU* 1.3 70.1 + - - +
410A MET* 3.7 9.6 - - - +
411A LYS* 3.0 39.9 + - + +
396B PRO* 3.5 22.8 + - + -
397B ILE* 4.3 14.3 - - + +
400B PHE* 3.7 29.1 - - - -
426B PHE* 4.6 3.7 - - - -
428B ALA* 3.9 22.5 - - - +
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Residues in contact with GLU 408 (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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187A VAL* 4.0 9.4 - - + -
198A LEU* 4.4 3.6 - - + -
200A CYS* 3.3 27.3 - - - -
202A PHE* 3.4 11.2 - - - -
404A LEU* 3.1 17.0 + - - +
405A ALA* 3.0 14.2 + - - +
407A GLN* 1.3 76.8 - - - +
409A VAL* 1.3 63.6 + - - +
411A LYS* 2.9 34.1 + - - +
412A ALA 2.9 19.1 + - - -
419A PRO* 3.8 3.6 - - - +
420A ILE* 3.3 46.4 + - + +
430B GLU* 5.1 0.2 - - - +
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Residues in contact with VAL 409 (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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75A VAL* 4.0 19.1 - - + -
87A ILE* 4.5 3.6 - - + -
91A ILE* 3.3 36.1 - - + -
96A VAL* 4.9 0.7 - - + -
161A VAL* 4.3 5.4 - - + -
163A VAL* 3.5 30.7 - - + -
187A VAL* 4.6 9.9 - - + -
405A ALA 2.9 18.8 + - - +
406A ALA* 3.2 8.9 + - - +
408A GLU* 1.3 76.7 - - - +
410A MET* 1.3 57.5 + - - +
412A ALA* 3.1 8.5 + - - +
413A CYS* 2.9 31.9 + - - +
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Residues in contact with MET 410 (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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62A LEU* 3.3 39.9 - - + +
63A GLY* 4.9 5.2 - - - -
64A HIS* 4.5 6.3 - - - -
90A ASN 3.7 4.9 - - - +
91A ILE* 3.5 41.5 - - + +
94A GLY* 3.6 26.9 - - - +
96A VAL* 4.0 15.3 - - + -
406A ALA 2.8 21.1 + - - +
407A GLN* 3.7 7.4 - - - +
408A GLU 3.2 0.2 - - - -
409A VAL* 1.3 75.6 - - - +
411A LYS* 1.3 60.9 + - - +
413A CYS* 3.2 15.6 + - - +
414A SER* 3.3 8.7 + - - -
396B PRO* 4.1 17.7 - - + -
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Residues in contact with LYS 411 (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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62A LEU* 4.0 11.0 - - + -
185A LYS* 4.5 3.6 + - - -
202A PHE* 4.0 11.4 - - + -
206A MET* 5.2 0.7 - - - +
407A GLN* 3.0 32.5 + - + +
408A GLU* 2.9 36.6 + - - +
410A MET* 1.3 77.0 - - - +
412A ALA* 1.3 58.9 + - - +
414A SER 2.9 22.6 + - - +
416A LYS* 4.1 9.4 + - - -
417A PHE* 4.5 22.4 - - + +
418A MET 3.0 28.1 + - - +
419A PRO* 4.1 3.5 - - + +
428B ALA 5.3 8.8 + - - -
429B LEU* 5.7 1.5 - - - +
430B GLU* 3.8 18.2 - - - +
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Residues in contact with ALA 412 (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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73A SER* 4.4 2.4 + - - -
160A GLN* 5.2 0.5 - - - +
161A VAL* 4.1 21.0 - - + +
185A LYS* 3.1 45.8 + - + +
187A VAL* 5.1 0.4 - - + -
202A PHE* 3.5 31.1 - - + -
408A GLU 2.9 7.0 + - - +
409A VAL* 3.5 9.0 - - - +
411A LYS* 1.3 76.2 - - - +
413A CYS* 1.3 59.1 + - - +
414A SER 3.5 0.2 - - - -
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Residues in contact with CYS 413 (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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72A THR* 5.2 4.7 + - - -
73A SER* 3.0 43.4 + - - -
75A VAL* 3.7 26.0 - - - -
96A VAL* 3.8 22.0 - - + -
161A VAL* 3.8 5.4 - - - -
409A VAL* 2.9 17.9 + - - +
410A MET* 3.5 10.1 - - - +
411A LYS 3.1 0.8 - - - -
412A ALA* 1.3 79.2 - - - +
414A SER* 1.3 63.9 + - - +
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 5.9 1.7 - - - +
62A LEU* 3.3 34.5 + - - +
72A THR* 6.5 0.7 - - - -
185A LYS* 6.1 0.9 - - - +
410A MET 3.3 2.6 + - - +
411A LYS 2.9 16.1 - - - +
412A ALA 3.5 1.4 - - - -
413A CYS* 1.3 81.7 - - - +
415A GLY* 1.3 59.5 + - - +
416A LYS* 3.3 5.2 - - - -
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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