Contacts of the helix formed by residues 366 - 385 (chain E) in PDB entry 4RYD
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 GLY 366 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E ASN* 3.8 2.5 - - - -
329E TYR* 3.5 21.3 - - - -
342E SER* 2.7 24.5 + - - -
343E SER* 3.1 9.3 + - - -
365E THR* 1.3 75.0 - - - +
367E THR* 1.3 67.4 + - - -
368E SER 3.0 4.2 + - - -
369E ALA 3.1 7.4 + - - -
601E FMT 3.6 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 367 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E ALA* 3.4 18.8 - - - +
293E SER* 3.4 7.6 + - - -
294E GLY 3.1 32.1 + - - -
295E ASN* 2.8 40.8 + - - +
317E ILE 4.3 2.3 + - - -
318E SER* 5.5 0.2 - - - -
319E SER* 3.8 13.5 + - - -
329E TYR* 3.5 4.8 - - - -
366E GLY* 1.3 70.5 - - - -
368E SER* 1.3 66.2 + - - +
370E SER* 3.1 15.4 + - - -
371E ALA 3.8 0.7 + - - -
5L 00S 3.4 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 368 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E HIS* 2.6 37.4 + - - -
198E CYS* 3.7 3.2 - - - -
253E SER* 2.9 16.7 + - - -
295E ASN* 4.7 1.4 + - - +
364E HIS* 4.0 10.3 - - - -
365E THR 3.9 11.9 - - - -
366E GLY 3.0 0.6 - - - -
367E THR* 1.3 81.7 - - - +
369E ALA* 1.3 55.9 + - - +
372E PRO* 2.9 26.0 - - - +
5L 00S 3.1 19.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 369 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E GLU* 2.6 30.0 - - - +
341E TYR 4.7 0.2 - - - -
342E SER* 3.5 13.5 - - - +
351E ILE* 3.5 25.6 - - + -
364E HIS* 3.5 23.1 - - + -
365E THR 3.9 5.1 + - - +
366E GLY 3.1 3.5 + - - +
368E SER* 1.3 78.3 - - - +
370E SER* 1.3 63.8 + - - +
372E PRO* 3.6 2.4 - - - +
373E LEU* 3.4 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 370 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E ILE* 4.1 8.3 - - - -
318E SER 3.7 11.2 - - - -
319E SER* 2.7 29.3 + - - -
340E THR* 2.8 40.0 + - - -
341E TYR 3.5 6.8 + - - -
342E SER* 3.6 1.9 - - - -
366E GLY 4.0 0.4 + - - -
367E THR* 3.1 8.6 + - - -
369E ALA* 1.3 78.9 - - - +
371E ALA* 1.3 67.4 + - - +
373E LEU 3.2 3.1 + - - -
374E ALA* 3.1 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E SER* 4.0 8.5 - - - +
252E ALA 4.4 2.7 - - - +
253E SER* 3.9 9.9 - - - +
290E VAL* 3.5 16.2 - - + +
291E TRP* 3.9 7.4 - - - -
292E ALA* 3.7 30.7 - - + +
317E ILE* 4.4 8.2 - - - +
367E THR 3.8 3.0 + - - -
370E SER* 1.3 75.1 - - - +
372E PRO* 1.4 66.5 - - + +
374E ALA* 3.0 6.1 + - - +
375E ALA* 2.8 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 372 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E ILE* 5.4 0.4 - - + -
198E CYS* 3.5 34.3 - - + +
201E GLU* 3.4 24.7 - - + +
202E VAL* 3.4 17.2 - - + +
251E SER* 3.8 13.0 - - - +
253E SER* 3.6 4.5 - - - +
368E SER 2.9 28.9 - - - +
369E ALA 3.6 2.7 - - - +
370E SER 3.5 3.1 - - - -
371E ALA* 1.4 90.1 - - + +
373E LEU* 1.3 55.1 + - - +
375E ALA* 3.2 1.6 + - + -
376E GLY* 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E TYR* 3.9 36.8 - - + -
124E LEU* 4.6 1.1 - - + -
132E LEU* 4.1 16.4 - - + -
201E GLU* 3.4 29.8 - - + +
215E VAL* 3.8 25.5 - - + +
340E THR* 4.1 10.8 - - - +
341E TYR 3.4 25.4 - - - +
351E ILE* 4.3 5.2 - - + -
369E ALA 3.4 8.7 - - - +
370E SER 3.2 7.2 + - - +
372E PRO* 1.3 76.6 - - - +
374E ALA* 1.3 63.7 + - - +
376E GLY* 3.3 1.9 + - - -
377E ILE* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E VAL* 4.0 4.0 - - + -
317E ILE* 3.6 29.2 - - + -
340E THR* 3.9 2.4 - - + +
370E SER 3.1 8.4 + - - +
371E ALA 3.0 9.3 + - - +
373E LEU* 1.3 78.6 - - - +
375E ALA* 1.3 61.7 + - - +
377E ILE* 3.2 3.0 + - - +
378E ILE* 2.9 32.7 + - + +
429E LEU* 3.6 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E VAL* 4.5 5.4 - - + +
202E VAL* 4.4 8.3 - - + -
249E ILE* 3.9 19.5 - - + +
251E SER* 4.0 24.5 - - - -
290E VAL* 4.1 14.5 - - + +
371E ALA 2.8 16.0 + - - +
372E PRO* 3.5 8.5 - - + +
374E ALA* 1.3 71.1 - - - +
376E GLY* 1.3 58.1 + - - +
378E ILE* 3.3 5.7 + - - +
379E ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 376 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E VAL* 4.0 17.4 - - - +
215E VAL* 3.5 20.5 - - - +
216E ALA* 3.8 3.8 - - - +
372E PRO 2.9 13.6 + - - -
373E LEU 3.3 3.3 + - - -
374E ALA 3.2 0.4 - - - -
375E ALA* 1.3 77.8 - - - +
377E ILE* 1.3 59.3 + - - +
379E ALA* 3.1 16.0 + - - +
380E LEU* 3.1 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 377 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LEU* 4.1 30.7 - - + -
134E VAL* 4.4 1.8 - - + -
215E VAL* 3.9 16.4 - - + -
373E LEU 3.0 13.9 + - - +
374E ALA* 3.7 7.2 - - - +
376E GLY* 1.3 74.8 - - - +
378E ILE* 1.3 62.6 + - + +
380E LEU* 3.2 8.0 + - - +
381E THR* 2.8 27.8 + - - +
429E LEU* 3.9 31.9 - - + -
431E ALA* 3.9 35.9 - - + +
434E MET* 4.1 20.6 - - + -
435E VAL* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 378 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E ILE* 3.7 16.6 - - + -
288E ILE* 4.0 13.7 - - + -
290E VAL* 3.7 26.9 - - + -
315E LEU* 4.1 24.7 - - + -
317E ILE* 6.1 0.9 - - + -
374E ALA* 2.9 25.8 + - + +
375E ALA* 3.6 5.2 - - - +
377E ILE* 1.3 77.4 - - + +
379E ALA* 1.3 57.1 + - - +
381E THR* 3.2 8.0 + - - -
382E LEU* 2.9 27.1 + - + +
393E MET* 3.7 32.5 - - + -
397E VAL* 5.2 3.8 - - + -
429E LEU* 5.8 2.7 - - + -
434E MET* 4.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E GLY* 4.4 2.0 - - - -
147E ILE* 3.5 32.8 - - + +
149E VAL* 4.1 10.3 - - + -
216E ALA* 3.9 17.0 - - + -
219E ALA* 4.8 1.3 - - + -
249E ILE* 3.6 12.5 - - + +
375E ALA 2.9 13.3 + - - +
376E GLY* 3.1 10.5 + - - +
378E ILE* 1.3 74.3 - - - +
380E LEU* 1.3 65.3 + - - +
382E LEU 3.2 0.7 + - - -
383E GLU* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E VAL* 4.3 4.3 - - + -
137E ALA* 3.8 24.5 - - + -
138E TRP* 4.2 5.2 - - - +
142E TYR* 3.5 12.1 - - + +
143E THR* 3.2 42.0 - - - +
144E GLY 3.3 1.3 - - - +
215E VAL* 3.6 34.1 - - + +
216E ALA* 3.8 4.5 - - - -
376E GLY 3.1 11.9 + - - +
377E ILE* 3.2 9.2 + - - +
379E ALA* 1.3 76.0 - - - +
381E THR* 1.3 62.2 + - - +
383E GLU* 3.3 8.8 + - - +
384E ALA* 3.1 20.8 + - - +
431E ALA* 4.5 5.2 - - + -
435E VAL* 3.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 381 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E ILE 2.8 14.4 + - - -
378E ILE* 3.4 11.0 - - - -
380E LEU* 1.3 74.9 - - - +
382E LEU* 1.3 64.1 + - - +
384E ALA* 3.1 6.1 + - - +
385E ASN 3.0 17.0 + - - -
388E LEU* 3.7 16.8 - - + +
393E MET* 3.8 10.5 - - - -
396E LEU* 3.8 12.6 - - + -
434E MET* 3.5 31.5 - - + +
435E VAL* 4.1 8.4 - - - +
438E ALA* 3.7 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ILE* 3.9 13.9 - - + -
248E HIS* 3.9 31.0 - - + -
249E ILE* 4.0 17.5 - - + -
282E ARG* 3.4 35.9 - - - +
288E ILE* 4.6 5.2 - - + -
378E ILE 2.9 12.1 + - - +
379E ALA 3.2 5.6 + - - +
381E THR* 1.3 72.6 - - - +
383E GLU* 1.3 65.7 + - - +
385E ASN 3.7 15.3 - - - +
386E LYS* 2.9 36.3 + - - +
388E LEU* 4.2 4.0 - - + -
393E MET* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E GLY 3.9 10.9 - - - +
142E TYR* 3.5 16.6 - - + +
143E THR* 2.9 14.0 + - - -
144E GLY* 2.6 28.7 + - - -
145E HIS* 3.4 38.1 - - - +
147E ILE* 3.9 12.9 - - + +
379E ALA 3.1 12.4 + - - +
380E LEU 3.5 9.0 - - - +
382E LEU* 1.3 77.9 - - - +
384E ALA* 1.3 61.9 + - - +
385E ASN* 3.2 1.6 + - - -
386E LYS* 4.3 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 384 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E TYR* 3.3 33.6 + - + +
380E LEU 3.1 11.5 + - - +
381E THR 3.1 10.9 + - - +
383E GLU* 1.3 77.6 - - - +
385E ASN* 1.3 59.3 + - - +
435E VAL* 3.8 26.2 - - + +
438E ALA* 4.2 4.9 - - + -
439E GLN* 4.0 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 385 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381E THR 3.0 4.9 + - - -
382E LEU* 2.9 9.9 + - - +
383E GLU 3.1 0.4 - - - -
384E ALA* 1.3 81.5 - - - +
386E LYS* 1.3 60.6 + - - +
387E ASN* 2.9 27.0 + - - +
388E LEU* 3.2 44.4 + - + +
438E ALA* 2.8 29.5 + - + +
439E GLN* 4.5 5.9 + - - -
441E TRP 3.9 14.8 + - - -
----------------------------------------------------------
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