Contacts of the helix formed by residues 354 - 375 (chain B) in PDB entry 3NJ4
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 PRO 354 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 4.4 1.3 - - - +
194B GLY 4.7 2.0 - - - +
197B GLU* 3.5 17.0 - - + +
198B SER* 5.1 1.6 - - - +
352B GLY 4.2 2.9 - - - +
353B HIS* 1.3 91.3 - - + +
355B SER* 1.3 65.4 + - - +
356B PHE 3.1 1.4 + - - -
357B VAL* 3.4 4.5 - - - +
358B MET* 3.4 15.6 + - - +
204D LYS* 3.5 28.3 - - - +
208D ASP* 3.2 24.7 - - + +
210D MET* 3.3 38.4 - - + +
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Residues in contact with SER 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 6.2 0.2 - - - +
25B ALA* 4.3 12.9 - - - -
28B GLU* 3.1 25.7 + - - +
29B MET* 3.1 32.6 - - - +
59B GLU* 3.5 32.5 + - - -
354B PRO* 1.3 72.1 - - - +
356B PHE* 1.3 61.9 + - - +
358B MET 3.8 0.4 - - - -
359B SER 3.0 17.0 + - - -
208D ASP* 4.5 4.0 + - - +
209D VAL* 5.7 1.6 - - - -
210D MET 5.8 0.2 + - - -
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Residues in contact with PHE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 4.4 6.1 - - + -
254A MET* 3.9 23.8 - - - -
28B GLU* 3.2 42.8 + - - +
30B PRO* 4.2 3.1 - - + -
354B PRO* 3.1 2.4 + - - +
355B SER* 1.3 80.1 + - - +
357B VAL* 1.3 68.0 + - - +
359B SER* 3.0 19.9 + - - -
360B ASN* 3.7 4.3 + - - +
398B HIS* 3.7 38.6 - + + -
401B LYS* 4.1 24.9 - - + -
402B LEU* 3.8 31.9 - - + -
210D MET* 3.9 23.3 - - + -
212D ALA 4.6 5.8 - - - -
214D LYS* 5.3 3.1 - - - -
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A MET* 4.5 7.6 - - + -
189B PHE* 3.3 44.2 - - + +
190B ASP* 3.7 4.3 - - - +
194B GLY* 4.2 5.2 - - - +
353B HIS* 3.7 23.8 - - + +
354B PRO* 3.4 12.1 + - + +
356B PHE* 1.3 83.3 - - - +
358B MET* 1.3 66.3 + - - +
360B ASN* 3.1 24.4 + - + +
361B SER* 3.5 6.8 + - - -
210D MET* 3.4 30.0 - - + -
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Residues in contact with MET 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 3.8 5.6 - - + -
59B GLU* 3.7 25.6 - - + -
190B ASP* 3.4 19.5 - - - +
353B HIS* 3.8 19.7 - - + +
354B PRO 3.4 12.5 + - - +
355B SER 3.4 8.0 + - - +
356B PHE 3.2 0.6 - - - -
357B VAL* 1.3 80.0 - - - +
359B SER* 1.3 60.2 + - - +
361B SER* 3.2 6.3 + - - -
362B PHE* 2.9 68.9 + - + +
602B AFX 3.4 44.0 - - + +
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Residues in contact with SER 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 3.2 41.0 + - - +
31B GLY* 3.1 16.6 + - - -
32B LEU* 3.6 5.0 + - - +
355B SER 3.0 6.0 + - - -
356B PHE 3.0 14.8 + - - -
358B MET* 1.3 77.1 - - - +
360B ASN* 1.3 54.5 + - - +
362B PHE* 4.3 0.2 - - - +
363B THR* 2.8 37.9 + - - -
398B HIS* 2.7 24.6 + - - -
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Residues in contact with ASN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 3.6 26.7 - - - +
185B THR* 2.9 30.7 + - - +
189B PHE* 3.7 16.9 - - + -
190B ASP 5.9 0.2 - - - +
356B PHE* 3.7 3.8 + - - +
357B VAL* 3.1 16.1 + - - +
359B SER* 1.3 76.3 - - - +
361B SER* 1.3 67.2 + - - +
363B THR* 3.2 10.0 + - - -
364B ASN* 2.8 22.9 + - - -
394B VAL* 3.8 7.2 - - - +
398B HIS* 3.1 35.8 + - - -
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Residues in contact with SER 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU* 3.5 21.7 - - - +
180B VAL* 4.1 4.2 - - - +
185B THR 4.3 0.2 + - - -
186B LYS* 4.2 16.3 - - - +
190B ASP* 2.7 36.4 + - - +
357B VAL 3.6 7.8 + - - -
358B MET* 3.2 12.6 + - - +
360B ASN* 1.3 77.9 - - - +
362B PHE* 1.3 63.9 + - - +
364B ASN* 3.1 16.8 + - - +
365B GLN* 3.1 11.3 + - - +
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Residues in contact with PHE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 4.1 8.1 - - + -
32B LEU* 3.6 19.7 - - + -
54B LEU* 3.8 29.4 - - + -
59B GLU* 3.5 42.6 - - + -
60B THR* 3.5 21.1 - - - -
63B LEU* 3.7 25.4 - - + -
156B GLU* 3.9 8.5 - - - -
358B MET* 2.9 45.1 + - + +
361B SER* 1.3 73.8 - - - +
363B THR* 1.3 65.5 + - - +
365B GLN* 3.2 8.8 + - + +
366B VAL* 3.0 27.5 + - - +
602B AFX 3.9 1.6 - + - -
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Residues in contact with THR 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY* 3.1 34.0 - - - +
32B LEU* 3.2 4.7 + - - +
35B MET* 3.3 25.0 - - + +
359B SER 2.8 25.0 + - - -
360B ASN 3.2 5.1 + - - -
362B PHE* 1.3 76.3 - - - +
364B ASN* 1.3 60.4 + - - +
366B VAL 3.6 0.2 + - - -
367B MET* 2.9 33.4 + - + +
394B VAL* 3.4 33.0 - - + -
397B ALA* 5.8 1.6 - - + -
398B HIS* 4.0 0.2 - - - -
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Residues in contact with ASN 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL* 3.7 18.1 - - + +
183B SER* 3.1 22.7 + - - +
185B THR* 2.8 30.6 + - - -
186B LYS* 4.5 2.2 - - - +
360B ASN 2.8 24.7 + - - -
361B SER* 3.1 9.7 + - - +
363B THR* 1.3 76.9 - - - +
365B GLN* 1.3 54.5 + - - +
367B MET* 3.2 8.1 + - - +
368B ALA* 2.8 35.0 + - - +
386B LEU* 3.9 15.9 - - + +
391B ASP* 4.3 2.9 - - - +
394B VAL* 3.6 15.7 - - - +
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Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 4.6 9.0 - - + -
129B LEU* 3.4 37.8 - - + +
154B SER* 2.6 47.4 + - - -
155B GLU 3.3 8.0 + - - +
156B GLU* 3.0 32.1 - - + +
180B VAL* 3.8 8.9 - - - +
361B SER 3.1 6.3 + - - +
362B PHE* 3.2 20.6 + - + +
364B ASN* 1.3 77.3 - - - +
366B VAL* 1.3 63.2 + - - +
368B ALA* 3.1 6.2 + - - +
369B GLN* 2.9 25.8 + - - +
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.0 11.9 - - + -
35B MET* 3.6 28.7 - - + -
45B LEU* 5.1 0.2 - - + -
63B LEU* 3.8 20.4 - - + -
66B THR* 4.2 10.3 - - + -
67B LEU* 4.2 15.7 - - + -
70B LEU* 3.6 24.0 - - + -
362B PHE 3.0 17.2 + - - +
363B THR 3.8 4.3 - - - +
365B GLN* 1.3 74.4 - - - +
367B MET* 1.3 63.4 + - - +
369B GLN* 3.1 7.8 + - - +
370B ILE* 2.9 25.5 + - + +
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Residues in contact with MET 367 (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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35B MET* 3.6 23.3 - - + -
38B ARG* 5.8 6.1 - - - +
363B THR* 2.9 19.5 + - + +
364B ASN* 3.5 6.7 - - - +
366B VAL* 1.3 75.4 - - - +
368B ALA* 1.3 56.5 + - - +
370B ILE* 3.3 9.4 + - + +
371B GLU* 2.9 36.3 + - - +
386B LEU* 3.8 15.7 - - + -
390B LEU* 4.0 36.1 - - + +
393B ALA* 4.2 13.9 - - + -
394B VAL* 3.4 35.0 - - + +
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Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.8 23.3 - - - -
178B ILE* 3.9 26.0 - - + +
180B VAL* 3.8 13.2 - - + -
364B ASN 2.8 14.1 + - - +
365B GLN 3.3 9.0 - - - +
367B MET* 1.3 77.2 - - - +
369B GLN* 1.3 57.3 + - - +
371B GLU* 3.8 0.7 - - - +
372B LEU* 3.0 34.7 + - - +
386B LEU* 4.2 4.2 - - + +
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Residues in contact with GLN 369 (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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45B LEU* 3.8 18.3 - - + +
50B ILE* 3.2 24.1 - - + +
67B LEU* 4.3 4.5 - - + -
127B MET* 3.2 39.4 - - - +
128B ILE 3.7 11.1 + - - -
129B LEU* 3.6 30.1 - - + +
154B SER* 3.0 24.0 + - - +
365B GLN 2.9 16.3 + - - +
366B VAL* 3.5 8.1 - - - +
368B ALA* 1.3 73.5 - - - +
370B ILE* 1.3 65.3 + - - +
373B TRP* 2.9 28.4 + - - +
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Residues in contact with ILE 370 (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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35B MET* 5.1 2.7 - - + -
39B TYR* 4.5 23.8 - - + -
44B PRO* 4.4 17.0 - - + -
45B LEU* 3.8 24.5 - - + -
70B LEU* 3.8 22.2 - - + -
366B VAL* 2.9 26.5 + - + +
367B MET* 3.7 7.9 - - + +
369B GLN* 1.3 75.7 - - - +
371B GLU* 1.3 61.0 + - + +
374B THR* 2.6 57.6 + - + +
375B HIS* 5.7 2.5 - - + -
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Residues in contact with GLU 371 (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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178B ILE* 4.1 5.2 - - + -
367B MET 2.9 25.2 + - - +
368B ALA 3.8 3.6 - - - +
370B ILE* 1.3 76.0 - - + +
372B LEU* 1.3 58.2 + - - +
375B HIS* 2.9 60.2 + - - +
378B LYS* 3.5 11.6 + - - -
379B TYR* 2.5 42.6 + - + +
386B LEU* 4.8 4.7 - - + -
387B PRO* 5.4 1.6 - - - -
390B LEU* 4.2 26.4 - - + +
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Residues in contact with LEU 372 (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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127B MET* 3.4 16.6 - - + -
151B ARG* 3.4 20.5 - - - +
152B GLY* 3.9 11.4 - - - -
153B ILE 2.9 43.1 - - - +
154B SER* 4.7 2.7 - - - -
176B PRO* 3.8 8.3 - - + +
177B ALA 5.0 1.3 - - - -
178B ILE* 3.4 37.0 - - + -
368B ALA 3.0 16.4 + - - +
371B GLU* 1.3 77.5 - - - +
373B TRP* 1.3 59.2 + - - +
376B PRO* 3.6 14.4 - - - +
379B TYR* 3.6 29.6 - - + -
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Residues in contact with TRP 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PRO 3.6 20.2 + - - -
45B LEU* 3.9 16.4 - - + -
46B LYS 3.1 19.7 + - - -
47B GLY* 3.4 21.8 - - - -
48B ALA* 3.5 11.9 - - + +
126B ASN* 3.5 39.9 - - + -
127B MET* 4.1 16.8 - - + -
151B ARG* 3.2 79.9 + - + +
369B GLN 2.9 18.6 + - - +
370B ILE 4.0 0.7 - - - +
372B LEU* 1.3 78.1 - - - +
374B THR* 1.3 64.8 + - - +
376B PRO* 3.7 3.6 - - - +
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Residues in contact with THR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PRO* 4.3 17.9 + - + +
370B ILE* 2.6 46.0 + - + +
373B TRP* 1.3 75.2 - - - +
375B HIS* 1.3 84.9 + - + +
376B PRO* 3.3 8.0 - - - +
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Residues in contact with HIS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ILE* 5.7 2.7 - - + -
371B GLU* 2.9 44.3 + - - +
374B THR* 1.3 107.4 - - + +
376B PRO* 1.3 66.9 - - - +
377B ASP* 3.3 2.7 - - - -
378B LYS* 3.2 33.6 + - + +
379B TYR* 3.4 14.8 - - + -
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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
------------------------------------------------------------
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