Contacts of the helix formed by residues 490 - 511 (chain G) in PDB entry 1R4N
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 490 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G THR* 4.1 3.5 - - + +
157G GLY 3.0 22.7 - - - +
158G LEU* 4.5 4.5 - - + -
488G ALA 2.9 23.1 - - - +
489G GLU* 1.3 76.5 - - - +
491G HIS* 1.3 65.9 + - - +
492G THR* 4.7 5.4 - - - +
493G ILE* 3.2 17.0 + - + +
494G ALA* 3.0 18.7 + - - +
19H HIS* 4.2 15.2 - - + +
23H PHE* 3.3 33.7 - - + -
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Residues in contact with HIS 491 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ALA* 4.3 5.6 - - + +
43G THR* 5.8 0.2 - - + -
44G GLU* 3.1 29.2 - - + -
72G ASN* 2.8 32.8 + - + +
73G ASN* 4.8 0.4 - - - -
74G PHE 4.3 5.8 - - - -
489G GLU 3.3 4.4 + - - -
490G PRO* 1.3 65.7 - - - +
492G THR* 1.3 55.8 + - + +
493G ILE 2.8 5.4 + - - -
494G ALA* 3.0 4.8 + - - -
495G ALA* 2.6 36.5 + - + +
19H HIS* 5.4 0.6 - - - +
65H LYS* 2.6 25.5 + - + -
66H ASN* 3.3 28.3 - - - -
69H LEU* 3.5 42.4 - - + +
70H SER* 5.3 1.8 - - - +
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Residues in contact with THR 492 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G LEU* 5.3 1.4 - - - +
490G PRO* 4.7 5.5 - - - +
491G HIS* 1.3 75.7 - - - +
493G ILE* 1.3 64.2 + - - +
495G ALA* 3.9 6.7 - - - -
496G PHE* 3.4 16.3 + - - +
522G TYR* 5.3 0.7 + - - -
66H ASN* 4.0 7.2 - - + -
70H SER* 3.3 25.1 + - - +
301H ALA* 3.4 17.4 - - - +
304H ALA* 3.4 28.9 - - + -
305H THR* 2.8 34.9 + - - +
308H PHE* 5.6 2.3 - - + +
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Residues in contact with ILE 493 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G THR* 3.4 23.1 - - + +
157G GLY 3.5 11.4 - - - +
158G LEU* 3.3 45.1 - - + +
159G VAL 4.2 15.9 - - - +
160G GLY* 4.6 6.1 - - - -
490G PRO* 3.2 13.4 + - + +
491G HIS 2.8 1.0 + - - -
492G THR* 1.3 80.2 + - - +
494G ALA* 1.3 68.5 + - - +
495G ALA 2.8 2.1 + - - -
496G PHE* 2.9 14.6 + - - +
497G LEU* 3.0 11.1 + - + +
522G TYR* 3.7 26.9 - - + +
524G GLY* 4.1 6.3 - - - -
305H THR* 4.7 6.1 - - - +
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Residues in contact with ALA 494 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ALA* 3.6 17.5 - - + -
41G THR* 3.4 36.8 - - - +
44G GLU* 4.0 6.6 - - + +
155G THR* 3.4 14.1 + - - +
489G GLU* 4.0 2.7 - - + +
490G PRO 3.0 8.9 + - - +
491G HIS* 3.0 6.8 + - - +
493G ILE* 1.3 79.0 - - - +
495G ALA* 1.3 51.7 + - - +
497G LEU* 3.6 1.9 - - - +
498G GLY* 2.7 32.2 + - - -
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Residues in contact with ALA 495 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 3.9 14.6 - - - +
48G ASN* 4.8 0.2 + - - -
491G HIS* 2.6 21.5 + - + +
492G THR 3.8 1.3 - - - +
493G ILE 2.8 0.8 + - - -
494G ALA* 1.3 69.6 - - - +
496G PHE* 1.3 67.2 + - - +
498G GLY* 3.0 2.6 + - - -
499G GLY* 2.9 19.8 + - - -
62H GLU* 5.6 1.6 - - - +
65H LYS* 4.1 10.3 - - - +
66H ASN* 3.7 20.0 - - - +
297H ALA* 4.6 8.7 - - + +
301H ALA* 3.5 18.8 - - + -
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Residues in contact with PHE 496 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492G THR 3.4 9.4 + - - +
493G ILE 2.9 12.0 + - - +
495G ALA* 1.3 75.0 - - - +
497G LEU* 1.3 70.9 + - + +
499G GLY* 2.9 12.3 + - - -
500G ALA* 3.1 16.4 + - + -
520G TYR* 3.8 25.6 - + - -
522G TYR* 3.3 61.9 - + + +
298H VAL* 3.3 38.0 - - + +
301H ALA* 3.3 12.3 - - + +
302H VAL* 3.8 22.4 - - + -
322H LEU* 5.8 2.2 - - + -
324H PHE* 4.4 9.9 - + - -
332H THR* 5.0 5.4 - - + -
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Residues in contact with LEU 497 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G THR* 4.0 9.6 - - + -
45G ILE* 4.8 0.4 - - - -
153G CYS* 4.6 6.5 - - + -
154G ARG 3.1 35.2 - - - +
155G THR* 3.5 14.8 - - - +
160G GLY* 3.8 23.3 - - - +
161G TYR 3.5 8.5 - - - +
162G MET* 4.0 29.8 - - + -
493G ILE* 3.0 8.3 + - + +
494G ALA 3.6 8.1 - - - +
496G PHE* 1.3 89.8 - - + +
498G GLY* 1.3 64.7 + - - +
500G ALA* 3.3 2.3 + - + -
501G ALA* 2.9 28.6 + - - +
520G TYR* 5.0 5.6 - - + -
522G TYR* 6.0 0.2 - - + -
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Residues in contact with GLY 498 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G THR* 4.7 0.4 - - - +
44G GLU* 4.2 2.2 - - - -
45G ILE* 3.3 34.1 - - - +
48G ASN* 2.9 17.8 + - - -
494G ALA 2.7 20.5 + - - -
495G ALA 3.0 3.6 + - - -
497G LEU* 1.3 73.5 - - - +
499G GLY* 1.3 57.9 + - - +
502G ALA* 3.1 21.5 + - - +
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Residues in contact with GLY 499 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ASN* 3.5 11.9 - - - +
495G ALA 2.9 9.5 + - - -
496G PHE 2.9 4.6 + - - -
498G GLY* 1.3 77.0 - - - +
500G ALA* 1.3 64.2 + - - +
502G ALA* 3.4 4.7 + - - +
503G GLN* 3.4 16.1 + - - +
294H SER* 3.6 25.9 - - - +
297H ALA* 3.8 7.4 - - - -
298H VAL* 3.8 7.9 - - - -
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Residues in contact with ALA 500 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G MET* 4.3 4.5 - - + -
496G PHE* 3.1 24.0 + - + +
497G LEU* 4.1 2.7 - - - +
499G GLY* 1.3 75.7 - - - +
501G ALA* 1.3 63.3 + - - +
503G GLN* 3.3 6.9 + - - +
504G GLU* 3.2 29.1 + - - +
520G TYR* 4.9 0.7 - - + -
298H VAL* 3.6 11.8 - - + +
324H PHE* 4.5 6.3 - - + -
326H ASP* 4.8 2.5 - - - -
330H LEU* 3.7 32.8 - - + -
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Residues in contact with ALA 501 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ILE* 3.9 14.6 - - + -
151G LEU* 3.9 6.8 - - + +
153G CYS* 3.7 21.1 - - - -
162G MET* 3.6 22.1 - - - -
497G LEU 2.9 18.6 + - - +
500G ALA* 1.3 74.6 - - - +
502G ALA* 1.3 66.2 + - - +
504G GLU* 2.9 16.0 + - - +
505G VAL* 3.0 18.0 + - - +
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Residues in contact with ALA 502 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ILE* 3.9 16.5 - - - +
48G ASN* 3.3 29.4 - - + +
49G LEU* 3.3 23.9 - - + +
498G GLY 3.1 19.8 + - - +
499G GLY 3.6 4.7 - - - +
500G ALA 3.4 0.2 - - - -
501G ALA* 1.3 78.5 - - - +
503G GLN* 1.3 63.2 + - - +
505G VAL* 3.3 2.3 + - - -
506G ILE* 3.2 18.4 + - - +
294H SER* 5.0 2.7 - - - +
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Residues in contact with GLN 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G TRP* 4.3 0.9 - - - -
499G GLY 3.4 3.8 + - - +
500G ALA 3.3 9.8 + - - +
501G ALA 3.1 0.8 - - - -
502G ALA* 1.3 77.9 - - - +
504G GLU* 1.3 65.0 + - - +
506G ILE* 3.0 27.4 + - - +
507G LYS* 2.8 45.4 + - - +
513G PHE* 4.6 6.5 - - - -
185H PHE* 3.0 43.6 - - + -
294H SER* 3.4 16.7 + - - -
326H ASP* 3.6 28.9 - - + +
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Residues in contact with GLU 504 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G LEU* 4.4 8.7 - - + -
162G MET* 4.6 1.8 - - + -
164G ILE* 5.3 3.6 - - + -
500G ALA 3.3 13.7 - - - +
501G ALA* 2.9 9.4 + - - +
503G GLN* 1.3 74.4 - - - +
505G VAL* 1.3 65.3 + - - +
507G LYS* 2.9 46.6 + - - +
508G ILE* 2.8 32.2 + - + +
515G ILE* 3.6 3.0 - - + -
516G PHE* 3.3 49.1 + - + -
326H ASP* 3.3 16.3 - - - +
330H LEU* 3.3 7.7 - - - +
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Residues in contact with VAL 505 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G VAL* 3.9 18.6 - - + -
45G ILE* 4.9 2.5 - - + -
49G LEU* 4.0 14.1 - - + -
125G VAL* 4.3 13.7 - - + -
127G VAL* 3.7 26.2 - - + -
151G LEU* 3.7 12.1 - - + +
501G ALA 3.0 15.5 + - - +
502G ALA* 3.4 10.3 - - - +
503G GLN 3.2 0.2 - - - -
504G GLU* 1.3 76.5 - - - +
506G ILE* 1.3 57.9 + - - +
508G ILE* 3.3 11.4 + - + +
509G ILE* 2.9 43.6 + - + +
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Residues in contact with ILE 506 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G TRP* 3.7 39.3 - - + -
28G LEU* 4.4 16.8 - - + -
48G ASN 4.8 0.9 - - - +
49G LEU* 3.9 16.6 - - + -
52G PRO* 4.7 9.2 - - + -
502G ALA 3.2 12.8 + - - +
503G GLN* 3.0 28.1 + - - +
505G VAL* 1.3 71.8 - - - +
507G LYS* 1.3 61.3 - - - +
508G ILE 2.8 1.8 - - - -
509G ILE* 2.8 8.7 + - + +
510G THR* 2.6 57.4 + - + +
513G PHE* 6.1 0.7 - - + -
294H SER* 4.2 8.5 - - - +
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Residues in contact with LYS 507 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G HIS* 3.8 6.9 + - - -
503G GLN* 2.8 35.1 + - - +
504G GLU* 2.9 44.8 + - - +
506G ILE* 1.3 75.5 - - - +
508G ILE* 1.3 56.7 + - - +
510G THR* 3.8 5.6 - - - -
511G LYS* 2.9 27.0 + - - -
512G GLN 3.4 2.8 + - - -
513G PHE* 3.8 25.9 + - + +
514G VAL 3.1 28.6 + - - +
515G ILE* 4.0 10.3 - - + -
326H ASP 2.6 31.9 + - - -
327H VAL* 4.9 0.2 - - - +
329H GLY* 3.4 11.5 + - - +
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Residues in contact with ILE 508 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G THR* 5.2 0.9 - - + +
125G VAL* 3.5 33.9 - - + -
149G PRO* 4.4 8.5 - - + -
150G LEU 5.8 0.7 - - - +
151G LEU* 5.5 5.8 - - + -
164G ILE* 3.8 16.4 - - + -
166G ILE* 3.6 35.2 - - + -
169G HIS* 3.8 12.6 - - + +
504G GLU* 2.8 20.8 + - + +
505G VAL* 3.3 15.7 - - + +
507G LYS* 1.3 76.1 - - - +
509G ILE* 1.3 65.7 + - - +
511G LYS* 3.4 19.1 + - - +
515G ILE* 4.2 12.1 - - + -
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Residues in contact with ILE 509 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ALA* 3.7 23.3 - - - +
28G LEU* 3.8 26.5 - - + -
31G ALA* 3.5 33.7 - - + -
33G VAL* 4.1 12.6 - - + -
49G LEU* 5.8 0.9 - - + -
54G ILE* 4.7 1.8 - - + -
124G THR* 3.9 22.7 - - + -
125G VAL* 4.5 3.6 - - + -
505G VAL* 2.9 37.5 + - + +
506G ILE* 2.8 12.2 + - + +
508G ILE* 1.3 74.1 - - - +
510G THR* 1.3 59.2 + - + +
511G LYS* 4.4 4.9 - - - +
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Residues in contact with THR 510 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G TRP* 4.9 7.4 - - + +
24G GLY* 3.7 31.5 - - - +
27G ALA* 4.3 8.7 - - - +
28G LEU* 4.5 10.5 - - + +
506G ILE* 2.6 48.9 + - + +
507G LYS* 3.7 2.1 + - - -
509G ILE* 1.3 73.1 - - + +
511G LYS* 1.3 71.5 + - - +
512G GLN* 2.9 35.0 + - + +
513G PHE* 4.8 1.2 - - - -
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Residues in contact with LYS 511 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G HIS* 4.1 19.1 - - + -
170G PRO* 4.8 16.1 - - + +
171G VAL* 4.1 17.0 - - - +
172G ILE 4.7 2.6 + - - -
173G GLU* 4.3 5.2 + - - +
507G LYS 2.9 14.9 + - - -
508G ILE 3.4 13.4 + - - +
509G ILE 3.3 4.6 - - - +
510G THR* 1.3 80.6 - - - +
512G GLN* 1.3 60.3 + - - +
513G PHE 3.8 1.6 - - - -
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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