Contacts of the helix formed by residues 272 - 284 (chain E) in PDB entry 5JLH
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 272 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E LEU* 5.1 0.2 - - - -
260E LEU 3.3 13.7 - - - -
261E PHE* 4.2 6.7 + - - -
263E PRO* 3.7 16.9 - - - +
271E CYS* 1.3 79.3 - - - +
273E ILE* 1.3 66.3 + - - -
274E HIS 3.3 0.2 - - - -
275E GLU* 3.0 21.1 + - - -
276E THR* 3.0 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E MET* 3.6 32.2 - - + +
159E THR* 4.7 3.4 - - + +
177E LEU* 3.7 17.7 - - + -
179E LEU* 4.3 4.5 - - + -
260E LEU* 3.1 39.7 + - + +
261E PHE* 3.7 25.1 - - + -
272E GLY* 1.3 71.2 - - - -
274E HIS* 1.3 61.0 + - - +
276E THR* 2.3 28.0 + - - -
277E THR* 2.9 17.5 + - - -
298E LEU* 6.5 0.2 - - + -
303E THR* 6.4 1.6 - - + -
308E ILE* 5.1 4.9 - - + -
312E MET* 3.4 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 274 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E PHE* 3.5 29.0 - + + -
262E GLN* 5.5 2.7 + - - -
273E ILE* 1.3 80.1 + - - +
275E GLU* 1.3 102.9 + - - +
277E THR* 3.1 6.1 + - - -
278E PHE* 3.1 25.8 + - - +
311E ARG* 5.5 0.2 - - - -
312E MET* 3.9 19.1 - - - -
315E GLU* 3.0 52.3 + - + +
316E ILE* 4.1 16.4 - - + +
319E LEU* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E PHE 4.8 1.7 - - - +
262E GLN* 5.9 0.5 + - - -
271E CYS* 3.7 22.2 - - + +
272E GLY* 3.0 20.2 - - - +
274E HIS* 1.3 116.8 + - + +
276E THR* 1.3 57.8 - - - +
278E PHE* 3.5 9.4 + - + +
279E ASN* 2.9 24.4 + - - +
319E LEU* 4.3 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 276 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E MET* 4.9 2.6 - - - +
159E THR* 5.7 0.3 - - - +
161E THR* 4.5 10.8 + - - -
175E LEU* 3.5 25.2 - - + +
177E LEU* 3.8 26.1 - - + +
271E CYS* 3.6 20.4 - - + +
272E GLY 3.0 12.7 + - - +
273E ILE* 2.3 31.0 + - - +
275E GLU* 1.3 74.3 - - - +
277E THR* 1.3 59.8 + - - +
279E ASN* 3.2 5.2 + - - +
280E SER* 2.9 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E ILE* 4.0 18.6 - - + -
152E MET* 4.3 13.7 - - + +
161E THR* 4.7 5.0 - - - +
273E ILE 2.9 14.0 + - - -
274E HIS 3.1 8.9 + - - -
276E THR* 1.3 76.5 + - - +
278E PHE* 1.3 56.8 + - + +
280E SER* 2.9 9.3 + - - -
281E ILE* 2.9 47.0 + - + +
296E THR* 4.9 6.5 - - + +
312E MET* 3.9 12.5 - - - +
316E ILE* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E HIS 3.1 13.0 + - - +
275E GLU* 3.5 12.1 - - + +
277E THR* 1.3 72.5 - - + +
279E ASN* 1.3 65.9 + - - +
281E ILE* 4.4 6.1 - - + +
282E MET* 2.8 53.3 + - + +
293E TYR* 3.9 20.0 - + - -
316E ILE* 3.9 21.8 - - + -
319E LEU* 3.3 39.9 - - + -
320E ALA* 3.3 39.7 - - + -
321E PRO* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E LEU* 3.5 26.8 - - + +
275E GLU 2.9 16.2 + - - +
276E THR* 3.2 11.3 + - - +
278E PHE* 1.3 75.2 - - - +
280E SER* 1.3 61.6 + - - +
282E MET* 4.1 4.6 - - - +
283E LYS* 3.3 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 280 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E ILE* 3.5 20.4 - - - -
161E THR* 3.3 16.2 - - - +
163E PRO* 4.6 3.6 - - - -
173E ALA* 3.4 24.8 + - - +
175E LEU* 3.4 12.0 - - - +
276E THR 2.9 14.9 + - - -
277E THR 2.9 8.0 + - - -
279E ASN* 1.3 75.8 - - - +
281E ILE* 1.3 66.5 + - - +
283E LYS* 3.1 16.5 + - - +
284E CYS* 3.1 14.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E ILE* 3.7 20.6 - - + -
277E THR* 2.9 37.5 + - + +
278E PHE* 4.1 5.8 - - + +
280E SER* 1.3 74.6 - - - +
282E MET* 1.3 59.0 + - + +
284E CYS* 3.0 23.6 + - - +
289E ARG* 2.9 44.4 + - + -
292E LEU* 4.1 26.5 - - + +
293E TYR* 3.7 41.3 - - + +
296E THR* 5.0 0.9 - - - +
316E ILE* 5.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 282 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E PHE* 2.8 38.9 + - + +
279E ASN* 4.1 4.9 - - - +
281E ILE* 1.3 79.8 - - + +
283E LYS* 1.3 58.2 + - + +
289E ARG* 2.7 50.6 + - - +
293E TYR* 3.2 26.9 - - - +
321E PRO* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 283 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ASP* 5.0 14.6 + - - +
172E HIS* 3.3 47.5 + - + +
173E ALA* 3.9 16.4 - - - +
174E ILE 5.7 0.9 - - - +
175E LEU* 5.5 8.5 - - + -
279E ASN* 3.3 38.7 + - - +
280E SER 3.1 10.8 + - - +
282E MET* 1.3 77.4 - - + +
284E CYS* 1.3 59.2 + - - +
285E ASP* 4.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 284 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E PRO* 4.0 6.3 - - - -
170E LEU* 3.7 29.8 - - + -
172E HIS* 4.7 1.6 - - - -
173E ALA* 3.9 7.6 - - - -
280E SER 3.1 18.8 - - - -
281E ILE* 3.0 17.7 + - - +
283E LYS* 1.3 81.6 - - - +
285E ASP* 1.3 69.0 + - - +
288E ILE* 4.1 7.9 - - + -
289E ARG* 2.8 29.6 + - + -
292E LEU* 3.8 17.0 - - + -
----------------------------------------------------------
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