Contacts of the strand formed by residues 291 - 298 (chain E) in PDB entry 5AQP
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 ILE 291 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASN* 4.9 4.9 - - - +
245E PHE* 3.9 16.3 - - + -
249E HIS* 3.5 39.9 - - + +
251E LYS* 3.7 34.8 - - + -
286E SER* 3.9 0.2 - - - -
287E LEU* 2.8 30.8 + - - +
288E TYR 3.0 19.2 + - - +
289E GLU 3.9 9.0 - - - +
290E GLY* 1.4 76.6 - - - +
292E ASP* 1.3 71.3 + - - +
293E PHE 3.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E HIS* 4.5 5.9 + - - -
284E ILE 3.5 4.9 - - - +
285E ASP* 3.5 17.9 - - - +
286E SER* 2.8 28.3 + - - +
290E GLY 3.6 5.8 + - - +
291E ILE* 1.3 85.1 - - - +
293E PHE* 1.3 58.4 + - - +
294E TYR* 3.8 26.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E PHE* 3.8 47.1 - + + -
244E GLU* 3.8 19.5 - - + -
245E PHE* 3.4 35.7 - + + -
248E LYS* 5.0 6.3 - - + -
249E HIS* 4.8 7.6 - - - -
263E LEU* 4.1 13.5 - - + -
282E ILE* 3.6 7.5 - - + +
284E ILE* 2.7 41.0 + - + +
287E LEU* 3.7 30.1 - - + -
291E ILE 3.8 0.4 + - - -
292E ASP* 1.3 70.7 - - - +
294E TYR* 1.4 62.5 - - - +
295E THR* 3.6 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E ILE 3.3 5.6 - - - +
283E GLU* 3.8 41.5 + - + +
284E ILE 4.1 5.2 - - - -
285E ASP* 2.6 32.7 + - - -
292E ASP* 3.8 24.0 + - + -
293E PHE* 1.4 81.9 - - - +
295E THR* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 295 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E PHE* 3.4 26.6 - - + -
244E GLU* 2.7 32.0 + - - -
281E SER* 3.7 3.1 - - - -
282E ILE* 2.9 41.8 + - + +
293E PHE* 3.6 25.8 - - + -
294E TYR* 1.3 74.6 - - - +
296E SER* 1.3 72.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 296 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E HIS* 5.1 1.9 + - - -
241E PHE* 4.3 7.8 - - - -
244E GLU* 4.8 2.4 - - - +
279E GLN* 4.5 12.1 - - - +
280E ALA 3.2 15.0 - - - -
281E SER* 4.0 12.1 - - - -
282E ILE* 4.7 1.1 - - - +
295E THR* 1.3 85.5 + - - +
297E ILE* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E MET* 3.9 27.8 - - + -
240E HIS* 4.0 14.4 - - + +
241E PHE* 4.0 15.5 - - + -
270E ALA* 4.5 3.8 - - + -
274E LEU* 3.6 16.8 - - + +
279E GLN* 3.5 2.9 - - - -
280E ALA* 2.9 44.3 + - + +
282E ILE* 5.1 0.9 - - + -
296E SER* 1.3 74.5 - - - +
298E THR* 1.3 73.9 + - - +
301E ARG* 4.1 10.8 - - + -
302E PHE* 4.1 13.7 - - + +
305E LEU* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 298 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E LEU* 4.0 2.2 - - - +
278E THR 3.4 9.9 - - - +
279E GLN* 4.1 15.5 - - + +
296E SER 6.2 0.2 - - - -
297E ILE* 1.3 82.7 - - - +
299E ARG* 1.4 63.7 + - - +
300E ALA* 3.8 9.2 + - - +
301E ARG* 3.1 24.9 + - - +
302E PHE* 3.1 19.9 + - - +
----------------------------------------------------------
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