Contacts of the helix formed by residues 376 - 396 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F GLU* 3.6 34.8 - - + +
354F ASP* 3.9 8.0 - - + +
375F GLY* 1.3 68.9 - - - -
377F TRP* 1.3 66.2 + - - +
379F HIS* 2.9 15.2 + - - +
380F TYR* 3.0 30.0 + - + +
434F SO4 2.9 28.1 + - - +
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Residues in contact with TRP 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E PHE* 4.6 9.1 - - + -
357F PHE* 3.6 43.3 - + + -
373F LYS* 3.8 24.8 - - + +
374F MET 4.1 3.0 + - - -
375F GLY* 3.8 15.3 - - - -
376F LYS* 1.3 77.1 - - - +
378F ALA* 1.3 77.8 + - + +
380F TYR* 3.2 12.2 + - - +
381F PHE* 2.9 41.6 + + + +
434F SO4 3.1 29.7 + - - +
600F LMT 3.7 80.7 + - + +
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Residues in contact with ALA 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348F ILE* 3.5 15.6 - - + +
355F ALA* 3.6 31.2 - - + +
357F PHE* 4.2 19.1 - - + -
374F MET 5.5 0.2 - - - -
375F GLY 3.4 3.5 + - - +
376F LYS 3.1 0.8 + - - -
377F TRP* 1.3 103.0 - - + +
379F HIS* 1.3 58.4 + - - +
381F PHE* 3.5 4.2 - - - +
382F LYS 2.9 22.9 + - - -
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Residues in contact with HIS 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F ASP* 2.9 30.4 + - - +
352F GLY 3.2 19.2 + - - -
353F GLU* 3.6 24.2 + - + +
354F ASP 3.8 13.7 - - - -
355F ALA* 3.5 9.1 - - - +
375F GLY 3.8 0.2 + - - -
376F LYS 2.9 10.3 + - - +
378F ALA* 1.3 77.0 - - - +
380F TYR* 1.3 93.3 + + - +
382F LYS* 3.4 3.9 + - - +
383F THR* 3.2 35.1 + - - -
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Residues in contact with TYR 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E ILE* 4.0 29.4 - - + +
410E PHE* 3.8 25.1 - + + -
353F GLU* 4.6 16.5 + - - +
376F LYS* 3.0 43.1 + - + +
377F TRP* 3.2 9.0 + - - +
379F HIS* 1.3 95.7 + + - +
381F PHE* 1.3 59.4 + - - +
383F THR* 3.4 6.2 + - - -
384F ALA* 2.9 30.5 + - - +
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Residues in contact with PHE 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410E PHE* 3.8 10.0 - + + -
500E DCQ 4.8 4.7 - - + -
600E LMT 3.7 30.3 - - + -
346F ILE* 5.4 2.5 - - + -
348F ILE* 3.5 20.4 - - + -
357F PHE* 5.5 3.4 - + - -
377F TRP* 2.9 26.2 + + + +
378F ALA* 3.5 12.3 - - - +
379F HIS 3.2 0.2 - - - -
380F TYR* 1.3 74.7 - - - +
382F LYS* 1.3 55.4 + - - +
384F ALA* 3.3 2.7 + - - +
385F PHE* 2.8 41.7 + - + +
500F DCQ 3.3 31.2 - - + -
600F LMT 3.6 47.3 - - + -
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Residues in contact with LYS 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE* 5.7 0.8 - - - -
43F PRO* 4.1 11.3 + - - +
47F HIS* 4.1 15.7 - - + +
53F ARG* 6.0 0.9 - - - +
162F GLU* 3.1 21.1 + - - -
348F ILE* 2.7 45.4 + - + +
350F ASP* 3.9 21.5 - - + +
378F ALA 2.9 14.0 + - - +
379F HIS* 3.4 12.8 - - - +
381F PHE* 1.3 76.4 - - - +
383F THR* 1.3 62.6 + - - +
385F PHE* 3.3 8.0 + - + +
386F GLU* 3.1 23.4 + - - +
441F FAD 2.4 32.1 + - - -
500F DCQ 5.6 4.5 - - - -
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Residues in contact with THR 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E ILE* 4.3 19.7 - - + -
53F ARG* 4.2 23.0 + - - +
350F ASP* 4.9 1.7 + - - -
379F HIS* 3.2 29.1 + - - -
380F TYR* 3.7 10.8 - - - -
382F LYS* 1.3 77.5 - - - +
384F ALA* 1.3 63.4 + - - +
386F GLU* 3.3 10.2 + - - +
387F LYS* 3.2 35.0 + - - +
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Residues in contact with ALA 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406E VAL* 3.8 18.4 - - + +
409E ILE* 3.7 15.0 - - + +
410E PHE* 3.7 22.0 - - + -
500E DCQ 4.3 11.2 - - + -
600E LMT 5.1 0.4 - - + -
380F TYR 2.9 18.2 + - - +
381F PHE* 3.3 6.0 + - - +
383F THR* 1.3 74.3 - - - +
385F PHE* 1.3 58.1 + - - +
387F LYS* 3.3 6.9 + - - +
388F TYR* 3.0 26.7 + - - +
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Residues in contact with PHE 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500E DCQ 4.5 4.4 - - + +
41F PHE* 4.2 18.2 - + - -
43F PRO* 6.1 0.2 - - + -
318F GLU* 4.2 2.0 - - - -
381F PHE* 2.8 25.9 + - + +
382F LYS* 3.6 7.0 - - + +
384F ALA* 1.3 69.2 - - - +
386F GLU* 1.3 58.7 + - - +
388F TYR* 3.3 19.2 + + - -
389F PHE* 2.8 58.8 + + + +
392F LYS* 5.1 0.2 - - - -
403F GLU* 5.1 1.1 - - - -
500F DCQ 3.1 101.9 - + + +
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Residues in contact with GLU 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE* 3.6 31.4 - - + -
44F ALA* 3.6 17.3 - - - +
47F HIS* 5.3 1.6 + - - -
53F ARG* 2.8 46.7 + - - -
57F ASP* 4.5 3.1 - - - +
58F ILE* 3.4 13.5 - - - +
382F LYS* 3.1 13.2 + - + +
383F THR* 3.3 12.3 + - - +
385F PHE* 1.3 77.9 - - - +
387F LYS* 1.3 78.1 + - - +
389F PHE* 3.5 1.0 + - - +
390F LEU* 3.2 34.3 + - + +
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Residues in contact with LYS 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402E PHE* 3.8 12.2 - - + +
405E LYS* 3.7 52.9 - - + +
406E VAL* 5.2 0.9 - - + -
409E ILE* 5.1 3.8 - - + -
53F ARG* 6.3 0.8 - - - +
57F ASP* 5.1 14.8 + - - +
383F THR* 3.2 27.0 + - + +
384F ALA* 3.5 9.2 - - - +
386F GLU* 1.3 92.2 + - + +
388F TYR* 1.3 63.3 + - - +
390F LEU* 3.6 7.0 + - + +
391F TRP* 3.1 23.7 + - - +
394F ARG* 4.8 2.8 + - - -
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Residues in contact with TYR 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402E PHE* 3.7 40.9 - + + +
500E DCQ 4.0 18.4 - - + -
384F ALA 3.0 14.3 + - - +
385F PHE* 3.6 23.6 - + - +
387F LYS* 1.3 76.3 - - - +
389F PHE* 1.3 58.7 + - - +
391F TRP* 3.2 8.3 + + - +
392F LYS* 3.0 50.7 + - + +
400F PRO* 3.6 7.1 - - - +
402F PHE* 3.5 32.5 - + - -
403F GLU* 2.4 41.8 + - - +
500F DCQ 4.1 16.6 - - + -
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Residues in contact with PHE 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F VAL* 4.1 26.0 - - + -
15F ILE* 6.3 0.4 - - + -
39F PHE* 3.6 24.9 - + - -
41F PHE* 3.7 33.4 - + + -
318F GLU* 3.5 26.5 - - - -
385F PHE* 2.8 40.9 + + + +
386F GLU 4.1 0.2 - - - +
388F TYR* 1.3 73.1 - - - +
390F LEU* 1.3 57.7 + - - +
392F LYS* 3.2 22.0 + - - +
393F VAL* 3.0 37.1 + - + +
398F ILE* 3.8 24.9 - - + -
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Residues in contact with LEU 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F PHE* 4.1 10.1 - - + -
41F PHE* 3.8 25.4 - - + -
57F ASP 3.3 25.8 - - - +
58F ILE* 4.0 15.0 - - - -
59F SER 4.3 0.7 - - - +
60F VAL* 3.9 23.9 - - + +
386F GLU* 3.2 33.5 + - + +
387F LYS* 4.0 8.5 - - + +
389F PHE* 1.3 70.8 - - - +
391F TRP* 1.3 61.1 + - - +
393F VAL* 3.3 5.3 + - - +
394F ARG* 3.0 50.2 + - - +
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Residues in contact with TRP 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391E TRP* 3.6 35.9 - + - -
397E ASN* 4.6 9.7 - - + +
400E PRO* 3.5 27.4 - - + +
401E SER* 3.3 20.7 - - - +
402E PHE* 3.5 32.3 - + + -
387F LYS 3.1 15.4 + - - +
388F TYR* 3.4 11.9 - + - +
389F PHE 3.2 0.2 - - - -
390F LEU* 1.3 77.2 - - - +
392F LYS* 1.3 89.8 + - + +
394F ARG* 3.2 12.0 + - - +
395F ASN* 2.7 74.0 + - + +
397F ASN* 5.2 2.2 - - + -
400F PRO* 5.1 3.8 - - + -
402F PHE* 5.9 0.2 - + - -
432F SO4 3.2 18.1 + - - -
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Residues in contact with LYS 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F TYR* 3.7 2.4 - - - -
318F GLU* 3.5 10.7 + - - -
385F PHE* 5.1 1.2 - - - -
388F TYR* 3.0 44.5 + - + +
389F PHE* 3.2 32.6 + - - +
391F TRP* 1.3 93.2 - - + +
393F VAL* 1.3 60.9 + - - +
395F ASN* 4.4 1.3 - - - +
396F GLY 3.0 20.8 + - - -
397F ASN 3.4 29.4 + - - +
398F ILE* 2.8 29.4 + - + +
400F PRO* 3.7 4.3 - - + -
403F GLU* 2.7 30.8 + - - +
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Residues in contact with VAL 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ILE* 4.5 10.8 - - + -
19F TYR* 2.6 39.2 + - - +
39F PHE* 3.7 44.9 - - + -
60F VAL* 4.1 12.1 - - + -
62F LEU* 5.1 1.8 - - + -
65F LEU* 3.4 17.5 - - + +
69F PHE* 4.0 0.5 - - - -
389F PHE* 3.0 31.7 + - + +
390F LEU* 3.6 9.2 - - - +
391F TRP 3.3 0.2 - - - -
392F LYS* 1.3 73.8 - - - +
394F ARG* 1.3 62.5 + - - +
395F ASN 3.2 0.2 + - - -
396F GLY 3.7 0.3 + - - -
398F ILE* 3.9 9.2 - - + -
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Residues in contact with ARG 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E SER* 4.1 5.1 + - - -
405E LYS* 5.8 4.8 - - - +
57F ASP 5.6 1.2 + - - -
59F SER 5.3 1.6 + - - -
60F VAL* 3.8 32.5 - - + +
65F LEU* 3.6 17.2 - - + +
68F LYS* 5.7 1.0 - - - +
69F PHE* 3.5 13.0 - - - -
387F LYS 4.8 2.4 + - - -
390F LEU* 3.0 42.5 + - - +
391F TRP* 3.8 18.1 - - - +
393F VAL* 1.3 74.2 - - - +
395F ASN* 1.3 62.4 + - - +
396F GLY 3.7 0.2 - - - -
432F SO4 2.9 47.0 + - - +
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Residues in contact with ASN 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E ASN* 4.8 6.9 - - - +
69F PHE* 3.6 11.0 - - - -
391F TRP* 2.7 75.7 + - + +
392F LYS* 3.7 1.6 - - - +
393F VAL 3.2 0.2 - - - -
394F ARG* 1.3 80.1 + - - +
396F GLY* 1.3 59.5 + - - +
397F ASN* 3.5 5.2 + - - +
432F SO4 3.2 20.0 + - - -
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Residues in contact with GLY 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F TYR* 3.5 26.1 - - - +
22F ARG* 5.8 1.0 - - - +
23F ASN* 3.0 22.2 + - - +
69F PHE* 3.4 30.1 - - - +
392F LYS 3.0 5.1 + - - -
393F VAL 3.7 1.0 + - - -
395F ASN* 1.3 77.0 - - - +
397F ASN* 1.3 59.8 + - - +
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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