Contacts of the helix formed by residues 354 - 375 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B LYS* 3.4 29.6 - - + +
208B ASP* 3.4 22.7 - - + +
210B MET* 3.4 43.7 - - + +
59D GLU* 4.9 0.9 - - - +
194D GLY 4.4 6.1 - - - +
197D GLU* 3.8 7.2 - - + +
198D SER* 4.9 2.0 - - - +
352D GLY 4.1 3.8 - - - +
353D HIS* 1.3 90.8 - - + +
355D SER* 1.3 65.1 + - - +
356D PHE 3.3 1.3 + - - -
357D VAL* 3.5 15.2 - - - +
358D MET* 3.5 4.7 + - - +
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Residues in contact with SER 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASP 4.3 4.7 + - - -
209B VAL* 5.7 2.1 - - - -
210B MET 5.4 0.2 - - - +
25D ALA* 4.0 13.2 - - - -
28D GLU* 3.3 24.8 + - - +
29D MET* 3.2 33.2 - - - +
59D GLU* 3.4 29.7 + - - -
354D PRO* 1.3 70.4 - - - +
356D PHE* 1.3 64.3 + - - +
358D MET* 3.3 1.6 + - - +
359D SER 3.0 18.4 + - - -
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Residues in contact with PHE 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 3.8 17.9 - - + -
212B ALA 4.8 2.7 - - - -
214B LYS* 5.0 3.4 - - - -
250C LEU* 4.8 3.6 - - + -
254C MET* 4.1 25.6 - - + -
28D GLU* 3.2 43.6 + - - +
30D PRO* 4.3 2.7 - - + -
354D PRO* 3.3 2.4 + - - +
355D SER* 1.3 80.6 + - - +
357D VAL* 1.3 64.8 + - - +
359D SER* 3.2 18.2 - - - -
360D ASN* 3.8 5.3 + - - +
398D HIS* 3.7 37.1 - + + -
401D LYS* 4.1 19.3 - - + -
402D LEU* 3.6 44.0 - - + -
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Residues in contact with VAL 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 3.5 23.8 - - - -
254C MET* 4.8 4.5 - - + -
189D PHE* 3.5 44.0 - - + +
190D ASP* 3.5 5.6 - - - +
193D TYR* 4.7 3.6 - - + -
194D GLY* 4.0 9.4 - - - +
353D HIS* 3.7 11.2 - - + -
354D PRO 3.5 12.3 + - - +
356D PHE* 1.3 80.4 - - - +
358D MET* 1.3 80.4 + - + +
360D ASN* 2.9 30.5 + - + +
361D SER* 3.5 5.4 + - - -
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Residues in contact with MET 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D MET* 4.2 3.6 - - + -
59D GLU* 3.6 31.0 - - + -
190D ASP* 3.1 21.8 - - + +
353D HIS* 3.1 37.7 - - + +
354D PRO 3.5 12.3 + - - +
355D SER 3.3 8.0 + - - +
356D PHE 3.2 0.4 - - - -
357D VAL* 1.3 88.7 - - + +
359D SER* 1.3 55.6 + - - +
361D SER* 3.1 5.2 + - - +
362D PHE* 2.8 44.6 + - + +
604D AFX 3.4 42.6 - - + -
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Residues in contact with SER 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D MET* 3.3 38.5 + - - +
31D GLY 3.2 15.8 + - - -
32D LEU* 3.5 6.9 + - - -
355D SER 3.0 7.1 + - - -
356D PHE 3.2 10.5 - - - -
357D VAL 3.1 0.2 - - - -
358D MET* 1.3 75.5 - - - +
360D ASN* 1.3 58.7 + - - +
362D PHE* 4.3 0.2 - - - +
363D THR* 2.7 33.1 + - - -
398D HIS* 2.5 28.3 + - - -
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Residues in contact with ASN 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C LEU* 3.4 26.1 - - - +
185D THR* 3.1 31.4 + - - +
189D PHE* 3.9 15.3 - - + -
190D ASP 5.9 0.2 - - - +
356D PHE* 4.4 5.2 - - - +
357D VAL* 2.9 16.1 + - + +
359D SER* 1.3 80.4 - - - +
361D SER* 1.3 66.3 + - - +
364D ASN* 3.1 26.3 + - - -
394D VAL* 3.6 9.7 - - - +
398D HIS* 3.1 38.9 + - - +
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Residues in contact with SER 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D GLU* 3.5 24.0 - - - -
180D VAL* 4.2 2.3 - - - +
186D LYS* 3.6 16.9 - - - +
190D ASP* 2.9 36.4 + - - +
357D VAL 3.5 3.9 + - - -
358D MET* 3.1 9.3 + - - +
360D ASN* 1.3 79.0 - - - +
362D PHE* 1.3 62.4 + - - +
364D ASN* 2.9 23.0 + - - +
365D GLN* 2.9 12.2 + - - +
604D AFX 4.5 0.9 - - - -
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Residues in contact with PHE 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D MET* 3.9 8.7 - - + -
32D LEU* 3.5 19.1 - - + -
54D LEU* 3.6 18.2 - - + -
59D GLU* 3.3 43.3 - - + -
60D THR* 3.5 20.9 - - - -
63D LEU* 3.6 22.6 - - + +
156D GLU* 3.6 25.8 - - - -
358D MET* 2.8 26.6 + - + +
361D SER* 1.3 76.3 - - - +
363D THR* 1.3 57.2 + - - +
365D GLN* 3.4 6.6 - - + +
366D VAL* 3.0 33.4 + - - +
604D AFX 3.9 18.4 - + - -
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Residues in contact with THR 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLY* 3.3 32.9 - - - +
32D LEU* 3.3 8.0 + - - +
35D MET* 4.2 21.1 - - + -
359D SER 2.7 22.6 + - - -
360D ASN 3.8 4.0 - - - -
361D SER 3.2 0.2 - - - -
362D PHE* 1.3 74.9 - - - +
364D ASN* 1.3 60.5 + - - +
366D VAL* 3.4 3.4 + - - +
367D MET* 3.0 35.4 + - + +
394D VAL* 4.1 25.8 - - + -
397D ALA* 5.9 2.0 - - + -
398D HIS* 4.1 0.2 - - - -
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Residues in contact with ASN 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D VAL* 3.7 17.3 - - + +
183D SER* 2.8 31.2 + - - -
185D THR* 2.8 31.0 + - - -
186D LYS* 4.5 2.2 - - + +
360D ASN 3.1 20.6 + - - -
361D SER* 2.9 12.3 + - - +
363D THR* 1.3 77.3 - - - +
365D GLN* 1.3 56.6 + - - +
367D MET* 3.5 7.7 + - - +
368D ALA* 2.9 30.3 + - - +
386D LEU* 3.5 18.6 - - - +
391D ASP* 4.8 2.1 - - - +
394D VAL* 3.8 11.2 - - - +
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Residues in contact with GLN 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D LEU* 4.3 9.4 - - + -
129D LEU* 3.5 35.2 - - + +
154D SER* 2.5 52.9 + - - -
156D GLU* 3.0 26.1 - - - +
180D VAL* 3.3 21.8 - - - +
361D SER 2.9 9.6 + - - +
362D PHE* 3.4 15.9 - - + +
364D ASN* 1.3 77.5 - - - +
366D VAL* 1.3 57.4 + - - +
368D ALA* 3.2 5.2 + - - +
369D GLN* 2.9 32.8 + - - +
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Residues in contact with VAL 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.6 14.8 - - + -
35D MET* 3.7 26.9 - - + -
63D LEU* 3.5 21.5 - - + -
66D THR* 4.2 9.6 - - + -
67D LEU* 4.4 11.4 - - + -
70D LEU* 3.8 22.9 - - + -
362D PHE 3.0 23.6 + - - +
363D THR 3.8 4.3 - - - +
364D ASN 3.4 0.2 - - - -
365D GLN* 1.3 72.4 - - - +
367D MET* 1.3 66.2 + - - +
369D GLN* 3.0 8.2 + - - +
370D ILE* 3.0 29.5 + - + +
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Residues in contact with MET 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D MET* 4.0 23.6 - - + -
363D THR* 3.0 32.4 + - + +
364D ASN 3.7 3.8 - - - +
366D VAL* 1.3 74.2 - - - +
368D ALA* 1.3 57.8 + - - +
370D ILE* 3.1 12.8 + - - +
371D GLU* 2.9 33.9 + - + +
386D LEU* 4.0 14.4 - - + -
390D LEU* 3.9 39.0 - - + +
393D ALA* 4.4 12.8 - - + -
394D VAL* 3.4 35.0 - - + +
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Residues in contact with ALA 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D SER* 3.8 22.4 - - - -
178D ILE* 3.9 30.1 - - + -
180D VAL* 4.0 4.3 - - + -
364D ASN 2.9 19.4 + - - +
365D GLN 3.3 5.6 - - - +
366D VAL 3.1 0.2 - - - -
367D MET* 1.3 76.6 - - - +
369D GLN* 1.3 62.3 + - - +
371D GLU* 3.0 2.6 + - - +
372D LEU* 2.9 30.9 + - - +
386D LEU* 4.3 4.4 - - + +
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Residues in contact with GLN 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 3.9 13.3 - - + +
50D ILE* 3.5 25.0 - - + +
67D LEU* 4.1 15.5 - - + -
127D MET* 3.0 30.3 - - - +
128D ILE 2.8 32.5 + - - -
129D LEU* 3.7 22.8 - - + +
154D SER* 2.9 17.4 + - - -
365D GLN 2.9 15.9 + - - +
366D VAL 3.0 7.6 + - - +
368D ALA* 1.3 75.2 - - - +
370D ILE* 1.3 62.6 + - - +
372D LEU 3.4 0.9 + - - -
373D TRP* 3.1 28.1 + - - +
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Residues in contact with ILE 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D MET* 5.0 2.0 - - - -
39D TYR* 4.3 22.2 - - + -
44D PRO* 4.1 19.1 - - + -
45D LEU* 3.8 22.9 - - + -
70D LEU* 3.9 23.1 - - + -
366D VAL* 3.0 26.2 + - + +
367D MET* 3.4 11.9 - - - +
369D GLN* 1.3 75.7 - - - +
371D GLU* 1.3 62.4 + - - +
373D TRP* 3.9 0.9 - - - -
374D THR* 3.0 39.4 + - + +
375D HIS* 4.4 3.9 + - + -
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Residues in contact with GLU 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ILE* 3.9 5.6 - - + -
367D MET 2.9 17.6 + - - +
368D ALA 3.0 7.6 + - - +
370D ILE* 1.3 78.9 - - - +
372D LEU* 1.3 59.3 + - - +
373D TRP 3.0 4.7 - - - -
375D HIS* 3.0 60.5 + - - +
378D LYS* 3.7 11.6 + - - -
379D TYR* 2.4 47.8 + - + +
386D LEU* 3.9 14.8 - - + -
390D LEU* 4.2 17.6 - - + +
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Residues in contact with LEU 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D MET* 3.8 19.5 - - + +
151D ARG* 2.9 30.2 - - - +
152D GLY* 3.8 7.9 - - - -
153D ILE 3.4 35.2 - - - +
154D SER* 4.7 0.7 - - - -
176D PRO* 4.6 10.1 - - + -
177D ALA 4.8 0.7 - - - +
178D ILE* 3.4 27.6 - - + +
368D ALA* 2.9 35.2 + - + +
369D GLN 4.6 0.2 - - - +
371D GLU* 1.3 75.4 - - - +
373D TRP* 1.3 57.4 + - - +
376D PRO* 3.9 7.7 - - + +
379D TYR* 3.5 39.0 - - + -
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Residues in contact with TRP 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D PRO 3.4 22.5 + - - -
45D LEU* 4.0 14.3 - - + -
46D LYS 3.4 18.1 + - - -
47D GLY* 3.4 7.9 - - - -
48D ALA* 3.4 26.2 - - + +
126D ASN* 3.1 43.3 - - + -
127D MET* 3.5 21.5 - - + -
151D ARG* 2.8 73.3 + - + +
369D GLN 3.1 17.7 + - - +
370D ILE 4.4 0.4 - - - +
371D GLU 3.0 0.8 - - - -
372D LEU* 1.3 81.4 - - - +
374D THR* 1.3 61.3 + - - +
375D HIS 3.6 0.4 - - - -
376D PRO* 3.9 2.8 - - - +
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Residues in contact with THR 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D PRO* 3.7 23.8 + - + +
370D ILE* 3.0 27.9 + - + +
373D TRP* 1.3 74.9 - - - +
375D HIS* 1.3 88.7 + - + +
376D PRO* 3.2 9.6 - - - +
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Residues in contact with HIS 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D ILE* 4.4 6.0 + - + -
371D GLU* 3.0 41.5 + - - +
374D THR* 1.3 114.5 - - + +
376D PRO* 1.3 64.2 - - - +
377D ASP* 3.1 4.7 - - + +
378D LYS* 2.9 37.4 + - + +
379D TYR* 3.2 12.8 - - - -
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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