Contacts of the strand formed by residues 224 - 231 (chain A) in PDB entry 1NPR
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 LYS 224 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A HIS* 3.1 34.1 + - + -
222A LYS* 3.2 29.6 - - + +
223A ARG* 1.3 75.6 - - - +
225A LEU* 1.3 60.8 + - - +
239A GLU* 4.6 19.5 + - + +
240A LEU 3.1 10.6 - - - +
241A ASP* 2.5 42.7 + - - +
242A PHE* 3.1 15.2 - - - -
244A GLN* 5.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PHE* 3.6 35.7 - - + -
201A VAL* 5.3 0.4 - - + -
215A VAL* 3.9 20.2 - - + -
217A GLU 3.8 1.8 - - - -
218A VAL* 3.6 33.9 - - + -
219A HIS* 3.9 1.1 - - - -
224A LYS* 1.3 74.3 - - - +
226A THR* 1.3 60.9 + - - +
227A VAL* 3.7 15.2 + - + -
238A VAL 3.3 1.4 - - - +
239A GLU* 3.2 10.6 - - - +
240A LEU* 2.6 38.5 + - + +
241A ASP 5.7 0.2 - - - -
242A PHE* 3.4 28.5 - - + -
245A VAL* 4.3 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A VAL* 3.6 1.2 - - - -
216A GLU* 2.6 50.2 + - + +
217A GLU* 3.0 24.7 + - + +
219A HIS* 3.0 18.2 + - - -
225A LEU* 1.3 70.2 - - - +
227A VAL* 1.3 55.1 + - - +
237A PRO* 4.9 14.8 - - + -
238A VAL 3.5 3.4 - - - +
239A GLU* 2.5 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A VAL* 3.9 21.3 - - + -
203A VAL* 5.8 0.7 - - + -
213A GLY* 3.9 5.8 - - - -
214A THR 3.5 24.5 - - - +
215A VAL* 4.4 7.6 - - + -
216A GLU* 4.4 0.7 - - - -
225A LEU* 4.0 24.7 - - + -
226A THR* 1.3 76.5 - - - +
228A MET* 1.3 60.2 + - - +
229A ILE* 3.3 25.3 + - + +
236A THR 3.5 0.2 - - - +
237A PRO* 3.3 2.2 - - - +
238A VAL* 2.6 43.5 + - - +
240A LEU* 4.4 17.5 - - + -
245A VAL* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLY* 3.1 3.6 - - - -
214A THR* 2.9 34.4 + - - +
216A GLU* 3.6 37.1 - - + +
227A VAL* 1.3 71.2 - - - +
229A ILE* 1.3 58.9 + - - +
230A SER 3.8 0.3 + - - -
235A MET* 3.8 31.3 - - + +
236A THR 3.5 10.3 - - - -
237A PRO* 3.2 44.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 3.8 26.7 - - + -
208A PHE* 4.0 16.2 - - + -
211A PHE* 3.5 23.1 - - + -
212A THR 3.4 13.7 - - - +
213A GLY* 4.0 0.4 - - - -
227A VAL* 3.8 20.4 - - + +
228A MET* 1.3 72.7 - - - +
230A SER* 1.3 67.7 + - - +
231A ILE* 3.3 15.5 + - + -
234A ARG 3.4 0.3 - - - +
235A MET* 3.3 3.9 - - - -
236A THR* 2.6 46.4 + - - +
238A VAL* 3.8 26.2 - - + -
240A LEU* 4.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 3.6 13.7 - - - +
212A THR* 2.8 28.7 + - - +
213A GLY* 5.2 1.3 - - - -
228A MET 3.8 2.0 + - - -
229A ILE* 1.3 70.5 - - - +
231A ILE* 1.3 58.8 + - - +
232A PHE* 3.1 6.4 + - - -
233A GLY* 3.2 21.0 + - - -
235A MET* 3.6 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A PHE* 4.1 20.9 - - + -
211A PHE* 3.9 30.1 - - + -
229A ILE* 3.8 18.2 - - + +
230A SER* 1.3 70.2 - - - +
232A PHE* 1.3 72.2 + - + +
233A GLY 3.2 0.4 - - - -
234A ARG* 3.1 34.9 + - + +
236A THR* 3.2 33.2 - - + +
----------------------------------------------------------
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