Contacts of the strand formed by residues 246 - 251 (chain A) in PDB entry 4NDH
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 PHE 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TYR* 3.7 26.2 - + + -
202A TRP* 3.7 26.9 - + - -
235A ILE* 3.6 48.0 - - + -
239A ALA* 4.0 13.2 - - + -
242A SER* 4.9 0.9 - - - -
244A LEU* 3.7 26.0 + - + -
245A ARG* 1.3 85.4 + - - +
247A ARG* 1.3 67.3 + - - +
248A LEU* 4.6 4.3 - - + +
263A VAL* 4.1 1.1 - - + -
264A ILE 3.4 26.0 - - - -
265A SER* 3.5 16.6 - - - -
266A GLN* 4.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ARG* 4.1 15.3 - - - +
246A PHE* 1.3 79.4 - - - +
248A LEU* 1.3 65.1 + - - +
262A HIS 3.7 1.2 - - - +
263A VAL* 3.7 1.9 - - - -
264A ILE* 3.0 33.2 + - + +
266A GLN* 3.3 36.4 + - + +
282A PHE 3.3 24.2 + - - -
283A ASN* 4.8 7.9 + - - +
284A THR 5.3 2.2 + - - -
287A PHE* 3.5 40.6 + - + +
289A GLU* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A HIS* 3.7 43.7 - - + +
231A GLY* 4.1 10.1 - - - -
232A GLU* 4.1 20.9 - - + +
235A ILE* 4.0 20.9 - - + -
246A PHE* 4.6 4.0 - - + +
247A ARG* 1.3 84.7 - - - +
249A GLY* 1.3 57.5 + - - +
261A LEU* 4.3 7.2 - - + -
262A HIS 3.2 6.3 - - - +
263A VAL* 4.3 13.9 - - + -
287A PHE* 3.9 3.0 - - - -
289A GLU* 3.5 13.9 + - - +
290A SER* 2.9 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 1.3 75.6 - - - +
250A TYR* 1.3 65.3 - - - -
261A LEU* 3.4 10.4 - - - +
262A HIS* 2.8 38.4 + - - +
287A PHE* 3.4 16.2 - - - -
288A LEU 3.1 12.1 - - - -
290A SER 3.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 3.7 29.8 - - + -
224A LEU* 3.5 27.6 + - + +
227A MET* 3.5 15.1 - - - +
249A GLY* 1.3 76.5 - - - -
251A HIS* 1.3 67.0 + - - +
259A VAL* 4.2 13.7 - - + -
260A HIS 3.2 31.0 - - - -
261A LEU* 3.6 31.7 - - + +
262A HIS* 4.7 2.7 - - - -
287A PHE* 3.6 2.4 - - - -
288A LEU* 2.7 43.5 + - + +
290A SER* 4.1 15.3 + - - -
293A VAL* 3.7 29.4 - - + -
294A ILE* 6.1 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 5.1 3.8 - - - +
250A TYR* 1.3 78.3 - - - +
252A ALA* 1.3 64.9 + - - +
253A ILE 3.2 8.3 + - - +
254A PRO* 4.0 12.1 - - + +
262A HIS* 3.8 14.9 - + - -
281A SER* 3.0 51.6 + - - -
282A PHE* 3.5 30.6 - + - -
286A TYR* 3.6 15.6 - + + -
287A PHE* 4.0 10.1 - + - -
288A LEU* 4.8 1.4 - - - +
401A AMP 2.8 41.6 + - - +
1D G 5.1 4.2 + - - -
----------------------------------------------------------
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