Contacts of the helix formed by residues 288 - 295 (chain A) in PDB entry 5JNQ
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 PRO 288 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 3.9 26.7 - - + +
264A GLU* 3.3 32.5 - - + +
267A SER* 3.5 7.9 - - - +
268A VAL* 3.9 14.1 - - + -
286A MET 3.2 6.8 - - - +
287A ALA* 1.4 87.1 - - + +
289A ILE* 1.3 65.2 + - - +
290A HIS* 3.1 6.5 + - + -
291A HIS* 3.1 29.9 + - + +
401A TUM 3.4 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE 5.8 0.2 - - - +
263A VAL* 3.6 35.2 - - + +
264A GLU* 3.4 17.0 - - - +
267A SER* 3.2 18.3 + - - +
284A PHE* 4.3 25.4 - - + -
286A MET 4.4 0.7 - - - -
288A PRO* 1.3 71.2 - - - +
290A HIS* 1.4 61.2 + - - +
291A HIS 3.3 0.2 - - - -
292A HIS* 3.1 30.6 + - + +
293A PHE* 3.2 38.8 - - + -
307A PHE* 3.9 15.5 - - + -
403A PLM 5.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE 3.1 12.8 - - - -
174A THR 4.5 0.7 - - - -
176A GLY* 3.8 10.7 - - - -
177A LEU* 3.9 18.8 - - + -
180A LEU* 3.9 15.0 - - + +
264A GLU* 2.7 26.6 + - - +
288A PRO* 3.1 12.8 + - + +
289A ILE* 1.4 79.3 - - - +
291A HIS* 1.4 103.7 + + - +
293A PHE* 3.6 4.2 + - - +
294A GLU* 3.4 25.4 + - - +
303A VAL* 3.7 22.9 - - + +
307A PHE* 4.0 10.5 - - + -
401A TUM 3.1 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLY 4.8 8.7 - - - -
177A LEU* 5.3 1.1 - - + -
286A MET* 3.7 37.5 - - + +
287A ALA 3.8 6.1 - - - -
288A PRO* 3.1 32.0 + - + +
290A HIS* 1.4 97.5 + + - +
292A HIS* 1.3 63.6 + - - +
294A GLU* 3.5 22.2 + - - +
295A LEU* 3.2 28.4 + - - +
401A TUM 2.9 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE 5.5 0.4 - - - -
284A PHE* 3.8 22.2 - + + +
285A LYS* 3.0 38.1 + - + +
286A MET 3.4 24.2 + - - +
289A ILE* 3.1 25.4 + - + +
291A HIS* 1.3 77.2 - - - +
293A PHE* 1.3 81.6 + + - +
295A LEU* 3.3 6.8 + - - +
296A CYS* 3.1 45.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE* 3.2 49.1 + - + -
290A HIS* 3.6 5.4 + - - +
292A HIS* 1.3 84.3 - + - +
294A GLU* 1.3 58.9 + - - +
296A CYS* 2.9 25.7 + - - +
298A TRP* 3.0 68.0 + + + +
303A VAL* 4.0 4.5 - - + -
307A PHE* 3.9 31.0 - + - -
403A PLM 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 3.3 34.0 - - + +
290A HIS 3.4 10.8 + - - +
291A HIS* 3.6 30.0 + - - +
292A HIS 3.4 0.2 - - - -
293A PHE* 1.3 74.2 - - - +
295A LEU* 1.4 61.2 + - + +
297A GLY* 3.1 19.2 + - - -
298A TRP* 3.5 21.2 + - - +
300A GLU* 4.4 16.0 + - - +
303A VAL* 4.2 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 5.4 1.3 - - - +
285A LYS* 3.2 43.2 + - + +
286A MET* 3.7 37.0 - - + -
291A HIS 3.2 11.9 + - - +
292A HIS 3.6 6.3 - - - +
293A PHE 3.2 0.2 - - - -
294A GLU* 1.4 80.2 - - + +
296A CYS* 1.4 56.2 + - - +
297A GLY 3.3 2.1 + - - -
----------------------------------------------------------
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