Contacts of the helix formed by residues 354 - 375 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LYS* 3.5 28.9 - - + +
208A ASP* 3.5 16.8 - - + +
209A VAL 4.0 1.1 - - - +
210A MET* 3.5 45.5 - - + +
59C GLU* 4.4 0.7 - - - +
194C GLY 4.5 9.9 - - - +
197C GLU* 3.9 5.4 - - + +
198C SER* 5.2 2.0 - - - -
352C GLY 4.1 4.0 - - - +
353C HIS* 1.3 93.1 - - + +
355C SER* 1.3 66.4 + - - +
356C PHE 3.4 0.2 - - - -
357C VAL* 3.1 15.6 - - + +
358C MET* 3.4 5.9 + - - +
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Residues in contact with SER 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ASP 4.3 7.5 + - - -
209A VAL* 5.4 1.4 - - - -
25C ALA* 4.0 11.5 - - - -
28C GLU* 3.5 20.9 + - - +
29C MET* 3.2 36.0 - - - +
59C GLU* 3.5 28.4 + - - -
354C PRO* 1.3 72.4 - - - +
356C PHE* 1.3 65.0 + - - +
358C MET* 3.3 1.6 + - - +
359C SER 3.1 17.3 + - - -
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Residues in contact with PHE 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 3.6 23.3 - - + -
212A ALA 4.7 2.5 - - - -
214A LYS* 4.1 9.0 - - - +
28C GLU* 3.1 43.5 + - - +
30C PRO* 4.4 1.3 - - + -
354C PRO* 3.4 1.4 - - - +
355C SER* 1.3 79.8 + - - +
357C VAL* 1.3 68.3 + - - +
359C SER* 3.1 18.9 - - - -
360C ASN* 3.9 3.5 + - - +
398C HIS* 3.9 33.0 - + + -
401C LYS* 4.0 22.4 - - + -
402C LEU* 3.5 45.5 - - + -
250D LEU* 4.6 5.2 - - + -
254D MET* 4.1 17.3 - - - -
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Residues in contact with VAL 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 3.5 30.0 - - + -
189C PHE* 3.7 32.3 - - + +
190C ASP* 3.8 14.6 - - - +
194C GLY* 4.3 6.5 - - - +
353C HIS* 3.7 21.5 - - + +
354C PRO* 3.1 15.9 - - + +
356C PHE* 1.3 83.3 - - - +
358C MET* 1.3 68.2 + - - +
360C ASN* 2.9 34.0 + - + +
361C SER* 3.8 2.3 + - - -
254D MET* 4.9 7.2 - - + -
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Residues in contact with MET 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 5.2 0.4 - - - -
59C GLU* 3.9 16.6 - - + -
190C ASP* 3.2 18.2 - - - +
353C HIS* 3.7 21.1 - - + +
354C PRO 3.6 15.5 - - - +
355C SER 3.3 5.7 + - - +
357C VAL* 1.3 77.2 - - - +
359C SER* 1.3 59.3 + - - +
361C SER* 3.0 12.5 + - - +
362C PHE* 2.8 61.7 + - + +
603C AFX 3.1 67.3 - - + +
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Residues in contact with SER 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 3.4 35.6 - - - +
31C GLY* 3.4 16.6 + - - -
32C LEU* 3.7 4.4 + - - -
355C SER 3.1 5.8 + - - -
356C PHE 3.1 11.7 - - - -
358C MET* 1.3 75.7 - - - +
360C ASN* 1.3 55.3 + - - +
362C PHE* 4.6 3.6 - - - -
363C THR* 2.8 35.9 + - - -
398C HIS* 2.6 28.8 + - - -
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Residues in contact with ASN 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C THR* 2.9 29.9 + - - +
189C PHE* 3.7 24.1 - - + +
190C ASP 5.8 0.7 - - - +
356C PHE* 4.8 2.3 - - - +
357C VAL* 2.9 17.2 + - - +
359C SER* 1.3 81.6 - - - +
361C SER* 1.3 61.3 + - - +
364C ASN* 3.0 26.8 + - - -
394C VAL* 3.3 15.9 - - - +
398C HIS* 3.3 31.7 + - - -
250D LEU* 3.8 18.9 - - - +
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Residues in contact with SER 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C GLU* 3.4 21.6 - - - +
180C VAL* 3.8 5.0 - - - +
185C THR 4.3 0.4 + - - -
186C LYS* 3.5 27.1 - - - -
190C ASP* 3.1 21.9 + - - -
357C VAL 4.2 0.3 + - - -
358C MET* 3.0 27.4 + - - +
360C ASN* 1.3 78.8 - - - +
362C PHE* 1.3 57.6 + - - +
364C ASN* 3.3 7.2 + - - +
365C GLN* 3.0 25.1 + - - +
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Residues in contact with PHE 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 5.3 1.1 - - - -
32C LEU* 3.8 20.9 - - + -
54C LEU* 3.8 15.0 - - + -
59C GLU* 3.2 46.2 - - + -
60C THR* 3.5 21.1 - - - -
63C LEU* 3.6 21.9 - - + +
156C GLU* 3.6 22.0 - - - -
358C MET* 2.8 50.5 + - + +
359C SER 4.1 1.1 - - - +
361C SER* 1.3 71.3 - - - +
363C THR* 1.3 60.8 + - - +
365C GLN* 3.2 6.0 - - + +
366C VAL* 2.9 32.1 + - - +
603C AFX 3.8 6.3 - + - -
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Residues in contact with THR 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLY* 3.3 12.0 - - - -
32C LEU* 3.2 31.0 + - - +
35C MET* 4.3 20.2 - - + -
359C SER 2.8 23.3 + - - -
360C ASN 3.6 4.5 - - - -
361C SER 3.3 0.2 - - - -
362C PHE* 1.3 77.0 - - - +
364C ASN* 1.3 55.8 - - - +
366C VAL* 3.3 4.3 + - - +
367C MET* 3.0 32.3 + - + +
394C VAL* 3.9 29.4 - - + -
397C ALA* 5.9 1.3 - - + -
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Residues in contact with ASN 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL* 3.5 18.1 - - + +
183C SER* 3.5 24.5 + - - +
185C THR* 2.9 32.1 + - - -
186C LYS* 4.2 1.4 - - - +
360C ASN 3.0 26.1 + - - -
361C SER* 3.4 10.1 - - - +
362C PHE 3.2 0.2 - - - -
363C THR* 1.3 73.6 - - - +
365C GLN* 1.3 61.0 + - - +
367C MET* 3.5 8.0 + - - +
368C ALA* 3.0 28.2 + - - +
386C LEU* 4.5 12.5 - - + +
391C ASP* 4.5 5.5 - - - +
394C VAL* 3.5 16.8 - - - +
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Residues in contact with GLN 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 4.1 0.6 - - - +
63C LEU* 4.2 9.4 - - + -
129C LEU* 3.2 45.6 - - + +
130C ASP 4.0 0.2 + - - -
154C SER* 3.8 17.9 + - - +
156C GLU* 3.2 35.5 + - - +
180C VAL* 3.0 35.7 - - - +
361C SER 3.0 12.4 + - - +
362C PHE* 3.2 15.0 - - - +
364C ASN* 1.3 77.9 - - - +
366C VAL* 1.3 62.1 + - - +
368C ALA* 3.2 5.4 + - - +
369C GLN* 3.1 26.8 + - - +
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Residues in contact with VAL 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.7 15.5 - - + -
35C MET* 3.8 26.2 - - + -
63C LEU* 3.4 23.3 - - + -
66C THR* 4.1 10.5 - - + -
67C LEU* 4.4 15.7 - - + -
70C LEU* 4.1 11.9 - - + -
362C PHE 2.9 20.3 + - - +
363C THR 3.3 6.5 + - - +
365C GLN* 1.3 77.2 - - - +
367C MET* 1.3 61.8 + - - +
368C ALA 3.2 0.3 + - - -
369C GLN* 3.2 2.1 + - - +
370C ILE* 3.0 36.7 + - + +
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Residues in contact with MET 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C MET* 4.2 24.9 - - + -
363C THR* 3.0 21.8 + - + +
364C ASN* 3.9 7.4 - - - +
366C VAL* 1.3 75.7 - - - +
368C ALA* 1.3 58.1 + - - +
370C ILE* 3.9 8.7 - - + +
371C GLU* 2.9 34.2 + - - +
386C LEU* 4.3 6.2 - - + +
390C LEU* 3.7 56.3 - - + +
393C ALA* 3.9 14.1 - - + -
394C VAL* 3.4 29.6 - - + +
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Residues in contact with ALA 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C SER* 3.9 17.9 - - - -
178C ILE* 3.7 33.9 - - + +
180C VAL* 3.9 3.6 - - + -
364C ASN 3.0 19.5 + - - +
365C GLN 3.3 6.3 - - - +
366C VAL 3.1 0.2 - - - -
367C MET* 1.3 75.6 - - - +
369C GLN* 1.3 57.2 + - - +
371C GLU* 3.5 0.3 - - - +
372C LEU* 2.7 40.6 + - - +
386C LEU* 4.1 3.6 - - + +
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Residues in contact with GLN 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 4.0 12.6 - - + -
50C ILE* 3.3 34.4 - - + +
67C LEU* 4.2 9.4 - - + -
127C MET* 3.2 33.1 - - - +
128C ILE 3.9 12.1 + - - +
129C LEU* 3.9 13.1 - - + +
152C GLY 5.5 0.4 + - - -
153C ILE 5.0 0.8 - - - -
154C SER* 2.6 34.1 + - - +
365C GLN 3.1 13.1 + - - +
366C VAL 3.7 5.8 - - - +
368C ALA* 1.3 76.2 - - - +
370C ILE* 1.3 58.6 + - - +
372C LEU* 3.6 4.3 - - - +
373C TRP* 2.8 34.5 + - - +
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C MET* 4.7 2.0 - - + -
39C TYR* 4.3 28.3 - - + -
44C PRO* 4.1 20.9 - - + -
45C LEU* 3.5 27.1 - - + +
70C LEU* 3.8 14.6 - - + -
366C VAL* 3.0 34.0 + - + +
367C MET* 3.9 7.9 - - - +
369C GLN* 1.3 77.0 - - - +
371C GLU* 1.3 56.8 + - - +
374C THR* 2.6 46.4 + - - +
375C HIS* 6.3 0.9 - - + -
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Residues in contact with GLU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ILE* 4.2 4.5 - - + -
367C MET 2.9 22.1 + - - +
368C ALA* 3.5 3.4 - - - +
370C ILE* 1.3 76.7 - - - +
372C LEU* 1.3 58.6 + - - +
373C TRP 3.0 4.3 - - - -
374C THR* 4.4 1.6 - - - -
375C HIS* 3.0 53.8 + - - +
378C LYS* 3.1 29.5 + - - -
379C TYR* 2.9 33.4 + - + +
386C LEU* 4.4 7.4 - - + -
387C PRO* 5.3 2.1 - - - +
390C LEU* 4.1 19.1 - - - +
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Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C MET* 4.1 9.0 - - + +
151C ARG* 3.3 24.6 - - - +
152C GLY* 3.5 12.8 - - - -
153C ILE 3.1 46.4 - - - +
154C SER* 5.1 2.2 - - - -
176C PRO* 4.6 8.3 - - + -
177C ALA* 4.3 2.9 - - - -
178C ILE* 3.6 31.9 - - + +
368C ALA 2.7 20.9 + - - +
369C GLN* 3.6 4.9 - - - +
371C GLU* 1.3 72.7 - - - +
373C TRP* 1.3 57.4 + - - +
375C HIS 5.2 0.2 - - - -
376C PRO* 4.1 7.0 - - + +
379C TYR* 3.6 31.0 - - + -
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Residues in contact with TRP 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PRO 3.4 22.4 + - - -
45C LEU* 4.2 10.5 - - + -
46C LYS 3.5 16.9 + - - -
47C GLY* 3.7 5.8 - - - -
48C ALA* 3.3 35.7 - - + +
126C ASN* 3.4 33.7 - - + -
127C MET* 3.3 24.2 - - + -
151C ARG* 3.1 67.0 + - + +
369C GLN 2.8 19.0 + - - +
370C ILE 4.1 2.2 - - - +
371C GLU 3.0 0.2 - - - -
372C LEU* 1.3 79.2 - - - +
374C THR* 1.3 65.8 + - + +
375C HIS 3.4 0.2 - - - -
376C PRO* 3.3 7.1 - - - +
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Residues in contact with THR 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PRO* 3.5 37.5 - - + +
370C ILE* 2.6 28.2 + - + +
373C TRP* 1.3 77.2 - - + +
375C HIS* 1.3 86.5 + - - +
376C PRO* 3.1 11.5 - - - +
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Residues in contact with HIS 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ILE* 6.3 0.7 - - + -
371C GLU* 3.0 42.4 + - - +
374C THR* 1.3 106.6 + - - +
376C PRO* 1.3 62.7 - - - +
377C ASP* 3.1 4.5 + - - +
378C LYS* 3.2 39.8 + - + +
379C TYR* 3.4 9.6 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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