Contacts of the helix formed by residues 376 - 396 (chain E) in PDB entry 3HYW
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 LYS 376 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E GLU* 3.4 51.1 + - + +
354E ASP* 3.8 14.6 + - + +
375E GLY* 1.3 70.7 - - - -
377E TRP* 1.3 64.9 + - - +
379E HIS* 3.1 14.0 + - - +
380E TYR* 3.0 30.5 + - + -
434E SO4 2.8 28.3 + - - +
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Residues in contact with TRP 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E PHE* 3.6 44.6 - + + -
373E LYS* 4.0 24.4 - - + +
374E MET 4.2 6.1 + - - +
375E GLY* 4.0 12.8 - - - -
376E LYS* 1.3 77.6 - - - +
378E ALA* 1.3 77.5 + - + +
380E TYR* 3.2 12.3 + - - +
381E PHE* 2.8 42.2 + + + +
434E SO4 3.1 31.6 + - - +
600E LMT 3.2 85.8 + - + +
410F PHE* 4.4 10.9 - - + -
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Residues in contact with ALA 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E ILE* 3.4 18.0 - - + +
355E ALA* 3.6 30.5 - - + +
357E PHE* 4.2 15.3 - - + -
375E GLY 3.4 3.7 + - - +
376E LYS 3.2 1.2 - - - -
377E TRP* 1.3 102.7 - - + +
379E HIS* 1.3 59.6 - - - +
381E PHE* 3.6 3.9 - - - +
382E LYS 3.0 21.8 + - - -
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Residues in contact with HIS 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E HIS* 6.3 0.2 - - - -
350E ASP* 2.9 35.4 + - - +
352E GLY 3.1 21.9 + - - -
353E GLU* 3.7 20.2 + - + +
354E ASP 3.8 10.1 - - - -
355E ALA* 3.4 8.7 - - - +
376E LYS 3.1 10.1 + - - +
378E ALA* 1.3 79.4 - - - +
380E TYR* 1.3 90.1 + + - +
382E LYS* 3.3 4.9 + - - +
383E THR* 3.2 33.4 + - - -
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Residues in contact with TYR 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353E GLU* 4.6 10.5 + - - +
376E LYS* 3.0 42.3 + - + +
377E TRP* 3.2 10.1 + - - +
379E HIS* 1.3 98.8 + + - +
381E PHE* 1.3 60.3 + - - +
383E THR* 3.5 5.0 + - - -
384E ALA* 2.9 29.5 + - - +
409F ILE* 3.7 33.0 - - + +
410F PHE* 3.8 24.9 - + + -
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Residues in contact with PHE 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E ILE* 5.8 0.2 - - + -
348E ILE* 3.4 20.4 - - + -
357E PHE* 5.3 4.3 - + - -
377E TRP* 2.8 31.0 + + + +
378E ALA* 3.6 10.5 - - - +
379E HIS 3.3 0.2 - - - -
380E TYR* 1.3 76.9 - - - +
382E LYS* 1.3 57.1 + - - +
384E ALA* 3.3 3.0 + - + +
385E PHE* 2.8 32.4 + - + +
500E DCQ 2.9 44.0 - + + -
600E LMT 3.6 40.6 - - + -
410F PHE* 3.9 8.0 - + + -
500F DCQ 5.7 2.9 - - + -
600F LMT 3.7 29.6 - - + -
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Residues in contact with LYS 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PHE* 5.5 1.5 - - + -
43E PRO* 3.8 24.0 - - + +
47E HIS* 3.9 8.3 - - + -
53E ARG* 6.0 0.4 - - - -
162E GLU* 3.2 15.5 + - - -
348E ILE* 2.9 37.1 + - + +
350E ASP* 3.5 28.9 - - + +
378E ALA 3.0 17.1 + - - +
379E HIS* 3.3 6.9 + - - +
380E TYR 3.3 0.2 - - - -
381E PHE* 1.3 77.2 - - - +
383E THR* 1.3 56.9 + - - +
385E PHE* 3.4 6.8 + - + +
386E GLU* 3.0 30.5 + - + +
441E FAD 2.5 33.5 + - - -
500E DCQ 4.8 9.0 - - - -
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Residues in contact with THR 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ARG* 4.2 23.8 + - - +
350E ASP* 4.9 1.7 + - - -
379E HIS* 3.2 28.9 + - - -
380E TYR* 3.9 10.1 - - - -
382E LYS* 1.3 74.8 - - - +
384E ALA* 1.3 65.7 + - - +
386E GLU* 3.4 7.4 + - - +
387E LYS* 3.2 34.7 + - - +
409F ILE* 3.8 22.0 - - + -
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Residues in contact with ALA 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380E TYR 2.9 20.1 + - - +
381E PHE* 3.6 5.8 - - + +
383E THR* 1.3 76.1 - - - +
385E PHE* 1.3 61.7 + - - +
387E LYS* 3.2 6.7 + - - +
388E TYR* 3.0 22.2 + - - +
406F VAL* 3.7 28.5 - - + +
409F ILE* 4.3 8.7 - - + +
410F PHE* 3.8 17.5 - - + -
500F DCQ 4.7 7.4 - - + -
600F LMT 4.9 3.1 - - + -
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Residues in contact with PHE 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PHE* 4.0 21.1 - + - -
43E PRO* 6.1 0.2 - - + -
318E GLU* 4.1 1.8 - - - -
381E PHE* 2.8 22.3 + + + +
382E LYS* 3.8 5.2 - - + +
384E ALA* 1.3 72.3 - - - +
386E GLU* 1.3 61.3 + - - +
388E TYR* 3.2 22.3 + + - +
389E PHE* 2.8 53.5 + + + +
392E LYS* 5.1 0.2 - - - -
403E GLU* 5.0 0.9 - - - -
500E DCQ 3.3 104.1 - + + -
500F DCQ 4.8 3.8 - - + +
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Residues in contact with GLU 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PHE* 3.6 32.5 - - + -
43E PRO 5.6 0.2 - - - -
44E ALA* 3.4 19.0 - - - +
47E HIS* 5.1 2.4 + - - -
53E ARG* 2.8 45.9 + - - -
57E ASP* 4.9 0.5 - - - +
58E ILE* 3.5 11.6 - - - +
382E LYS* 3.0 15.6 + - + +
383E THR* 3.4 10.9 - - - +
384E ALA 3.3 0.2 - - - -
385E PHE* 1.3 76.5 - - - +
387E LYS* 1.3 77.8 + - + +
389E PHE* 4.1 0.7 - - - +
390E LEU* 3.1 40.1 + - + +
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Residues in contact with LYS 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ARG* 5.6 3.0 - - - +
57E ASP* 5.2 15.2 + - - +
383E THR* 3.4 28.0 - - - +
384E ALA* 3.2 7.3 + - - +
386E GLU* 1.3 92.5 + - + +
388E TYR* 1.3 57.4 + - - +
390E LEU* 3.8 9.1 - - + +
391E TRP* 3.0 28.9 + - - +
394E ARG* 4.7 2.6 + - - -
402F PHE* 3.7 13.9 - - + +
405F LYS* 3.8 42.8 - - + +
406F VAL* 5.3 0.9 - - + -
409F ILE* 4.5 10.1 - - + -
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Residues in contact with TYR 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E ALA 3.0 13.7 + - - +
385E PHE* 3.2 24.0 + + - +
387E LYS* 1.3 74.7 - - - +
389E PHE* 1.3 61.7 + - - +
391E TRP* 3.2 7.2 + + - +
392E LYS* 2.9 51.4 + - + +
400E PRO* 3.4 8.7 - - + +
402E PHE* 3.2 36.9 - + - -
403E GLU* 2.6 38.9 + - + +
500E DCQ 4.1 13.0 - - + -
402F PHE* 3.6 39.9 - + + +
500F DCQ 3.8 19.3 - - + -
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Residues in contact with PHE 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E VAL* 4.3 25.6 - - + -
15E ILE* 5.9 1.1 - - + -
16E ALA 6.3 0.2 - - - -
39E PHE* 3.6 23.8 - + - -
41E PHE* 3.7 31.2 - + + -
318E GLU* 3.4 21.3 - - + -
385E PHE* 2.8 42.7 + + + +
388E TYR* 1.3 73.9 - - - +
390E LEU* 1.3 61.6 + - - +
392E LYS* 3.1 19.8 + - - +
393E VAL* 3.0 34.3 + - + +
398E ILE* 3.8 30.3 - - + -
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Residues in contact with LEU 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E PHE* 3.9 15.9 - - + -
41E PHE* 3.5 34.1 - - + -
57E ASP 3.5 24.7 - - - +
58E ILE* 4.1 12.6 - - - +
59E SER 5.1 0.7 - - - +
60E VAL* 4.5 7.2 - - + +
386E GLU* 3.1 38.8 + - + +
387E LYS* 3.8 9.9 - - + +
389E PHE* 1.3 77.2 - - - +
391E TRP* 1.3 61.6 + - - +
393E VAL* 3.3 7.0 + - - +
394E ARG* 3.1 46.0 + - - +
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Residues in contact with TRP 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E LYS 3.0 14.3 + - - +
388E TYR* 3.3 11.0 - + - +
390E LEU* 1.3 77.2 - - - +
392E LYS* 1.3 76.5 + - + +
394E ARG* 3.2 13.0 + - - +
395E ASN* 2.9 70.2 + - + +
397E ASN* 5.3 4.3 - - + -
400E PRO* 5.6 2.0 - - + -
402E PHE* 5.8 0.2 - + - -
432E SO4 3.3 16.3 + - - -
391F TRP* 3.6 34.3 - + - -
397F ASN* 4.4 11.9 - - + +
400F PRO* 3.6 28.5 - - + +
401F SER* 3.3 30.3 - - - +
402F PHE* 3.5 28.9 - + + -
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Residues in contact with LYS 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TYR* 3.7 2.3 - - - -
318E GLU* 3.8 8.9 + - - -
385E PHE* 5.1 1.0 - - - -
388E TYR* 2.9 50.7 + - + +
389E PHE* 3.1 31.4 + - - +
391E TRP* 1.3 92.4 - - + +
393E VAL* 1.3 62.7 + - - +
395E ASN* 4.5 0.9 - - - +
396E GLY 3.0 21.0 + - - -
397E ASN 3.3 29.6 + - - +
398E ILE* 2.7 34.4 + - + +
400E PRO* 3.7 4.9 - - + -
403E GLU* 2.8 23.2 + - - +
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Residues in contact with VAL 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ILE* 4.5 9.2 - - + -
19E TYR* 2.6 42.0 + - - +
39E PHE* 3.9 31.2 - - + -
60E VAL* 4.1 29.8 - - + -
62E LEU* 4.8 2.5 - - + -
65E LEU* 3.4 5.3 - - + +
69E PHE* 3.9 0.3 - - - -
389E PHE* 3.0 36.8 + - + +
390E LEU* 3.5 7.9 - - - +
391E TRP 3.3 0.2 - - - -
392E LYS* 1.3 75.3 - - - +
394E ARG* 1.3 60.4 + - - +
395E ASN 3.4 0.2 + - - -
396E GLY 3.7 0.7 + - - -
398E ILE* 3.9 7.9 - - + -
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Residues in contact with ARG 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ASP 5.5 2.4 + - - -
59E SER 5.4 1.4 + - - -
60E VAL* 3.8 31.1 - - + +
65E LEU* 3.4 25.1 - - + +
68E LYS* 5.9 0.2 - - - +
69E PHE* 3.5 4.9 - - - -
387E LYS 4.7 2.2 + - - -
390E LEU* 3.1 37.7 + - - +
391E TRP* 3.7 19.6 - - - +
393E VAL* 1.3 75.4 - - - +
395E ASN* 1.3 61.7 + - - +
396E GLY 3.6 0.2 - - - -
432E SO4 2.7 48.2 + - - +
401F SER* 4.0 4.8 + - - -
405F LYS* 5.5 7.3 - - - +
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Residues in contact with ASN 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E PHE* 3.6 10.7 - - - -
391E TRP* 2.9 61.9 + - + +
392E LYS* 3.7 1.6 - - - +
393E VAL 3.2 0.2 - - - -
394E ARG* 1.3 82.6 + - - +
396E GLY* 1.3 60.5 + - - +
397E ASN* 3.5 6.3 + - + +
432E SO4 2.8 29.0 + - - -
397F ASN* 4.7 7.5 - - - +
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Residues in contact with GLY 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TYR* 3.4 25.5 - - - +
22E ARG* 5.7 2.3 - - - +
23E ASN* 3.1 19.9 + - - +
69E PHE* 3.3 32.2 - - - +
392E LYS 3.0 4.9 + - - -
393E VAL 3.7 0.8 + - - -
394E ARG 3.6 0.2 - - - -
395E ASN* 1.3 76.9 - - - +
397E ASN* 1.3 59.2 + - - +
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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
------------------------------------------------------------
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