Contacts of the helix formed by residues 313 - 333 (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 THR 313 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E PRO* 4.3 9.2 - - + -
312E LYS* 1.3 75.0 - - - +
314E GLY* 1.3 60.4 + - - +
315E MET* 3.8 2.3 + - - +
316E MET* 3.1 25.0 + - - +
317E ILE* 2.8 31.3 + - - +
345E ALA* 3.3 23.5 - - + +
346E ILE 5.2 0.2 + - - -
347E CSS 3.5 24.9 - - - -
363E VAL* 5.4 2.0 - - + -
441E FAD 3.4 18.6 + - - -
800E PS9 4.1 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 4.4 7.8 - - - +
43E PRO* 6.4 0.4 - - - -
313E THR* 1.3 71.3 - - - +
315E MET* 1.3 55.3 + - - +
317E ILE* 3.2 8.0 + - - +
318E GLU* 2.9 35.7 + - - +
441E FAD 2.8 34.7 + - - -
500E DCQ 3.5 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 315 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E THR* 3.4 2.5 + - - +
314E GLY* 1.3 73.5 - - - +
316E MET* 1.3 63.8 + - - +
318E GLU* 3.3 7.2 + - + +
319E GLN* 3.0 41.5 + - + +
344E SER* 3.5 29.4 - - - +
345E ALA* 3.8 9.9 - - - -
346E ILE* 3.6 47.8 + - + +
359E PHE* 4.9 3.4 - - - -
407E LEU* 3.9 18.6 - - + -
413E VAL* 5.0 3.8 - - + -
441E FAD 4.3 1.0 + - - -
500E DCQ 2.9 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 316 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E ILE* 5.0 5.6 - - + -
310E VAL* 5.0 4.9 - - + -
311E PRO 3.4 22.0 - - - +
312E LYS* 4.1 7.2 - - + -
313E THR* 3.1 37.5 + - - +
315E MET* 1.3 77.7 - - - +
317E ILE* 1.3 55.8 + - - +
319E GLN* 3.2 7.7 + - - +
320E MET* 3.0 42.1 + - + +
343E LEU* 3.7 37.1 - - + +
344E SER 3.5 16.8 + - - +
363E VAL* 3.7 29.6 - - + -
364E ILE* 5.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 3.9 11.7 - - + +
13E GLY* 3.4 36.8 - - - +
292E VAL* 3.9 1.7 - - + +
293E GLY* 3.2 33.7 - - - +
294E VAL 3.8 1.8 - - - +
312E LYS* 3.5 32.1 - - + +
313E THR 2.8 32.3 + - - +
314E GLY* 3.5 7.6 - - - +
316E MET* 1.3 72.0 - - - +
318E GLU* 1.3 56.3 + - - +
320E MET* 3.2 11.4 + - - +
321E ALA* 2.9 27.4 + - - +
441E FAD 4.4 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 4.7 7.4 - - + -
16E ALA* 4.8 4.9 - - + +
20E ASN* 4.8 0.7 + - - -
314E GLY 2.9 18.4 + - - +
315E MET* 3.6 5.8 - - - +
317E ILE* 1.3 76.7 - - - +
319E GLN* 1.3 56.5 + - + +
321E ALA* 3.3 8.8 + - - +
322E MET* 3.0 45.2 + - + +
385E PHE* 4.1 0.7 - - - -
389E PHE* 3.4 33.5 - - + -
392E LYS* 3.8 7.0 + - - -
398E ILE* 4.1 13.7 - - + +
403E GLU* 3.8 11.1 - - - +
500E DCQ 3.2 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 319 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E MET* 3.0 29.9 + - + +
316E MET 3.2 5.6 + - - +
318E GLU* 1.3 75.7 - - + +
320E MET* 1.3 59.1 + - - +
322E MET* 3.3 10.9 + - + +
323E ALA* 2.9 30.3 + - - +
341E PRO* 3.5 10.8 - - + +
342E ARG* 4.3 1.3 - - - +
343E LEU* 2.7 33.2 + - - +
344E SER* 2.9 33.6 + - - +
407E LEU* 6.2 0.4 - - - +
413E VAL* 3.8 9.1 - - - +
415E PRO* 3.4 44.5 - - + +
416E ILE* 3.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 320 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E PHE* 3.5 49.4 - - + -
292E VAL* 4.0 9.6 - - + -
293E GLY* 3.3 29.6 - - - +
296E THR* 4.2 0.7 - - - +
298E ILE* 3.9 4.9 - - + -
312E LYS* 3.9 30.7 - - + -
316E MET* 3.0 21.9 + - + +
317E ILE* 3.3 11.0 - - + +
319E GLN* 1.3 76.5 - - - +
321E ALA* 1.3 52.7 + - - +
323E ALA* 3.4 1.4 + - - +
324E VAL* 2.8 40.1 + - - +
341E PRO* 3.6 9.5 - - - +
343E LEU* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLY 4.2 2.5 - - - +
16E ALA* 3.5 30.5 - - + -
17E THR* 3.4 30.0 - - - +
20E ASN* 4.0 4.5 + - - +
292E VAL* 4.0 4.5 - - + +
317E ILE 2.9 11.7 + - - +
318E GLU 3.5 7.4 - - - +
319E GLN 3.2 0.2 - - - -
320E MET* 1.3 73.1 - - - +
322E MET* 1.3 60.7 + - - +
324E VAL* 4.1 0.2 - - - -
325E ALA* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 322 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ASN* 4.0 24.2 - - - +
318E GLU* 3.0 37.8 + - + +
319E GLN* 3.3 8.7 + - + +
321E ALA* 1.3 76.4 - - - +
323E ALA* 1.3 61.5 + - - +
325E ALA* 3.7 1.2 - - - +
326E HIS* 3.0 39.8 + - + +
398E ILE 5.7 0.4 - - - +
399E ALA* 4.2 20.0 - - + -
403E GLU* 6.2 1.3 - - - +
404E GLU* 5.3 7.0 - - + +
407E LEU* 6.4 1.8 - - + -
415E PRO* 3.5 40.2 - - + -
416E ILE* 3.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E CYS 5.2 1.3 - - - +
281E PHE* 5.9 0.2 - - + -
319E GLN 2.9 16.8 + - - +
320E MET* 3.7 3.6 - - - +
322E MET* 1.3 75.7 - - - +
324E VAL* 1.3 59.0 + - + +
326E HIS* 3.3 3.6 + - - +
327E ASN* 2.9 36.5 + - - +
339E TYR* 3.9 18.8 - - - +
340E ALA 4.1 0.4 - - - -
341E PRO* 3.7 30.3 - - + -
416E ILE* 3.7 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 324 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E THR* 3.9 6.5 - - + -
102E VAL* 3.9 20.0 - - + -
280E CYS 4.1 1.8 - - - +
281E PHE* 3.7 37.2 - - + +
290E PHE* 3.5 30.7 - - + -
292E VAL* 3.7 17.3 - - + -
320E MET 2.8 24.8 + - - +
321E ALA 4.2 1.8 - - - +
323E ALA* 1.3 70.2 - - + +
325E ALA* 1.3 60.7 + - - +
327E ASN* 3.4 6.6 + - - +
328E ILE* 3.0 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E THR* 4.3 4.0 - - + +
20E ASN* 3.5 26.5 - - + -
21E LEU* 3.6 26.9 - - + +
24E LEU* 4.0 9.2 - - + -
321E ALA 2.9 20.3 + - - +
322E MET 3.7 3.1 - - - +
324E VAL* 1.3 79.3 - - - +
326E HIS* 1.3 61.2 + - - +
328E ILE 3.5 0.2 + - - -
329E VAL* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 326 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ASN* 5.8 2.7 - - - -
24E LEU* 4.0 34.3 - - + +
322E MET* 3.0 32.2 + - + +
323E ALA 3.7 4.3 - - - +
325E ALA* 1.3 75.7 - - - +
327E ASN* 1.3 55.0 + - - +
329E VAL* 3.9 3.3 - - + +
330E ASN* 2.8 45.4 + - - +
339E TYR* 3.7 27.8 - + + -
416E ILE* 3.7 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 327 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E CYS* 3.2 20.3 - - - +
290E PHE* 3.8 24.4 - - + -
323E ALA 2.9 23.1 + - - +
324E VAL 3.8 1.6 - - - +
326E HIS* 1.3 74.6 - - - +
328E ILE* 1.3 63.6 + - - +
330E ASN* 4.0 4.0 - - - +
331E ASP* 3.1 23.4 + - - +
337E ASP 4.5 0.6 + - - -
338E LYS* 3.4 28.3 - - + +
339E TYR* 2.7 51.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E VAL* 4.0 7.0 - - + -
21E LEU* 4.0 24.9 - - + -
100E TYR* 3.7 39.6 + - + -
102E VAL* 3.6 30.3 - - + -
290E PHE* 3.4 27.6 - - + -
324E VAL* 3.0 26.3 + - + +
325E ALA 3.9 3.8 - - - +
327E ASN* 1.3 73.0 - - - +
329E VAL* 1.3 65.8 + - - +
331E ASP* 3.1 6.4 + - - +
332E ILE* 3.0 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 4.0 15.3 - - + -
24E LEU* 4.0 29.6 - - + -
25E MET* 3.6 25.6 - - + -
28E LEU* 5.0 0.7 - - + -
325E ALA 3.1 17.8 + - - +
326E HIS* 3.9 5.4 - - + +
328E ILE* 1.3 74.1 - - - +
330E ASN* 1.3 64.3 + - - +
332E ILE* 3.1 10.4 + - - +
333E ARG* 2.8 63.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 330 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E HIS* 2.8 30.1 + - - +
327E ASN* 4.1 3.8 - - - +
329E VAL* 1.3 77.8 - - - +
331E ASP* 1.3 60.8 + - - +
333E ARG* 3.3 4.3 + - - +
334E ASN 3.1 3.8 + - - -
335E ASN* 2.8 56.3 + - + +
337E ASP* 2.8 45.1 + - - +
339E TYR* 3.7 16.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 331 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E TYR* 2.4 34.2 + - + +
287E LYS 6.1 0.7 - - - -
290E PHE* 6.1 1.8 - - + -
327E ASN 3.1 15.0 + - - +
328E ILE 3.1 9.6 + - - +
330E ASN* 1.3 75.0 - - - +
332E ILE* 1.3 61.7 + - - +
334E ASN* 3.4 15.7 + - - +
335E ASN 4.8 2.5 - - - +
338E LYS* 6.1 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 332 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LYS* 4.1 36.1 + - + +
25E MET* 3.9 35.9 - - + -
28E LEU* 4.5 7.6 - - + -
100E TYR* 3.4 31.0 - - + +
328E ILE* 3.0 30.0 + - + +
329E VAL* 3.4 6.7 - - - +
331E ASP* 1.3 78.5 - - - +
333E ARG* 1.3 57.9 + - + +
334E ASN* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E LEU* 3.8 20.0 + - - +
25E MET* 3.5 31.4 - - + +
26E PRO* 5.9 0.6 - - - +
27E ASP* 5.2 2.0 + - - -
329E VAL* 2.8 38.1 + - + +
330E ASN* 3.3 8.5 + - - +
331E ASP 3.3 0.2 - - - -
332E ILE* 1.3 74.6 - - + +
334E ASN* 1.3 71.4 + - - +
335E ASN* 3.2 9.2 + - + +
----------------------------------------------------------
Back to top of page
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