Contacts of the helix formed by residues 271 - 283 (chain E) in PDB entry 2NYM
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 LEU 271 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E LEU* 4.0 20.6 - - + -
234E LYS* 4.3 26.5 - - + +
237E LEU* 3.9 13.5 - - + -
238E LEU* 4.6 11.4 - - + -
264E PHE* 3.9 30.1 - - + +
265E LEU* 3.7 13.0 - - + -
268E ASP* 3.5 15.9 + - + +
269E SER 3.4 0.8 - - - -
270E THR* 1.3 78.9 - - + +
272E THR* 1.3 65.1 + - - +
274E PRO* 2.8 30.1 - - + +
275E VAL* 3.0 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 272 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LEU* 3.6 26.9 - - + +
269E SER* 2.5 34.9 + - - -
270E THR 2.8 6.7 + - - -
271E LEU* 1.3 72.3 - - - +
273E GLU* 1.3 64.6 + - - +
275E VAL* 3.0 1.6 + - - +
276E VAL* 2.9 34.2 + - + +
301E ILE* 5.0 0.7 - - + -
305E ILE* 3.7 35.2 - - + +
306E GLU 5.6 0.7 + - - -
309E GLU* 3.5 10.0 + - - +
313E ILE* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E THR 3.7 4.1 + - - +
272E THR* 1.3 79.9 - - - +
274E PRO* 1.3 71.7 - - + +
276E VAL* 3.2 1.2 + - - +
277E MSE 2.9 44.0 + - + +
309E GLU* 4.0 3.0 + - - +
312E LYS* 3.5 51.8 + - + +
313E ILE* 4.3 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 274 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E LEU* 4.0 24.1 - - + +
242E LEU* 4.2 3.1 - - - +
270E THR* 3.9 3.8 - - + +
271E LEU* 2.8 46.0 - - + +
273E GLU* 1.3 93.8 - - + +
275E VAL* 1.3 59.3 + - + +
277E MSE 3.6 6.3 + - + +
278E ALA* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E LEU* 3.7 28.7 - - + -
238E LEU* 5.2 0.4 - - + -
242E LEU* 3.8 17.6 - - + +
261E VAL* 3.6 31.0 - - + -
265E LEU* 4.0 16.6 - - + -
271E LEU 3.0 21.1 + - - +
272E THR 3.4 3.8 - - - +
274E PRO* 1.3 74.2 - - + +
276E VAL* 1.3 67.8 + - + +
278E ALA* 3.3 4.5 + - - +
279E LEU* 3.2 24.1 + - + +
301E ILE* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E THR* 2.9 24.1 + - + +
273E GLU 3.9 0.9 - - - +
275E VAL* 1.3 79.7 - - + +
277E MSE 1.3 63.0 + - + +
279E LEU* 3.5 7.3 + - - +
280E LEU* 3.0 34.3 + - + +
298E LEU* 4.2 17.5 - - + -
301E ILE* 4.3 19.1 - - + -
302E LEU* 6.5 1.1 - - + -
305E ILE* 5.7 1.1 - - + -
313E ILE* 3.2 47.8 - - + -
317E LEU* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E GLU* 2.9 34.8 + - + +
274E PRO* 4.0 6.5 - - + +
276E VAL* 1.3 77.5 - - - +
278E ALA* 1.3 56.8 + - - +
280E LEU* 3.4 12.1 - - + +
281E LYS* 2.9 25.8 + - - +
312E LYS 3.9 7.2 - - - +
313E ILE* 3.6 35.0 - - + +
316E PRO* 3.5 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E LEU* 3.3 38.8 - - + -
274E PRO 3.3 8.1 + - - +
275E VAL 3.3 2.4 + - - +
276E VAL 3.1 0.2 - - - -
277E MSE 1.3 74.0 - - - +
279E LEU* 1.3 57.8 + - - +
280E LEU 2.6 15.0 + - - -
281E LYS* 2.6 18.4 + - - +
282E TYR* 2.7 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E LEU* 4.9 5.2 - - + -
245E HIS* 3.3 29.2 - - + +
275E VAL* 3.2 20.3 + - + +
276E VAL* 3.5 4.7 + - - +
278E ALA* 1.3 77.5 - - - +
280E LEU* 1.3 58.7 + - - +
282E TYR* 4.5 2.9 - - + -
283E TRP* 3.0 26.1 + - - +
294E PHE* 3.4 29.9 - - + +
297E GLU* 3.2 27.6 - - + +
298E LEU* 3.8 21.3 - - + +
301E ILE* 3.3 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E VAL* 3.0 39.9 + - + +
277E MSE 3.4 21.3 - - + +
278E ALA 2.6 4.9 + - - -
279E LEU* 1.3 74.6 - - - +
281E LYS* 1.3 69.7 + - - +
282E TYR 3.2 0.3 + - - -
283E TRP* 3.3 25.0 - - + +
298E LEU* 5.0 6.3 - - + -
316E PRO* 4.5 8.7 - - + +
317E LEU* 4.2 21.1 - - + +
320E GLN* 4.0 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 281 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ASP* 3.9 49.5 + - + +
62D GLU* 4.8 2.5 - - - +
63D ASP* 5.2 6.1 + - - -
100D GLU* 5.1 7.9 + - - -
277E MSE 2.9 15.9 + - - +
278E ALA* 2.6 14.3 + - - +
280E LEU* 1.3 74.4 - - - +
282E TYR* 1.3 84.4 + - + +
283E TRP 4.6 1.4 - - - +
285E LYS* 5.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 282 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLU* 3.8 18.0 + - - -
238E LEU 5.6 0.7 + - - -
242E LEU* 3.8 18.1 - - + +
243E PRO* 3.7 36.2 - - + +
245E HIS* 4.5 9.2 - + + -
246E LYS* 4.0 35.2 - - + +
278E ALA* 2.7 30.3 + - + +
279E LEU* 4.7 2.2 - - + -
281E LYS* 1.3 102.3 + - + +
283E TRP* 1.3 71.2 + - - +
284E PRO* 3.3 3.6 - - - +
294E PHE* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 283 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E LEU 3.0 23.3 + - - +
280E LEU* 3.3 22.9 - - + +
281E LYS 4.6 1.2 - - - +
282E TYR* 1.3 78.8 - - - +
284E PRO* 1.3 97.3 - - + +
285E LYS* 4.4 12.6 - - - -
291E GLU* 3.1 24.6 + - + +
294E PHE* 3.8 23.0 - + + -
295E LEU* 3.4 33.0 - - + -
298E LEU* 3.3 31.4 - - + -
320E GLN* 3.0 45.1 - - + +
321E LEU* 4.9 1.3 - - + -
324E CYS* 3.4 24.7 - - - -
----------------------------------------------------------
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