Contacts of the strand formed by residues 246 - 254 (chain P) in PDB entry 1ZD2
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 VAL 246 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241P THR* 3.4 2.7 - - - +
242P VAL* 2.8 49.4 + - + +
243P LYS* 2.9 23.2 + - + +
244P PRO 3.4 0.4 - - - -
245P ARG* 1.3 87.3 - - + +
247P ARG* 1.3 62.5 + - - +
248P LEU* 4.2 15.3 - - + -
292P LYS* 4.2 14.8 - - + -
298P SER* 3.6 10.3 - - - -
300P PRO* 4.7 4.7 - - + -
305P GLU* 3.8 22.2 - - - +
314P GLU* 3.8 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239P TYR* 3.3 48.7 - - + +
240P VAL 3.3 21.3 - - - +
241P THR* 3.5 20.4 - - + +
245P ARG 4.2 0.2 - - - -
246P VAL* 1.3 74.7 - - - +
248P LEU* 1.3 61.5 + - - +
296P GLU* 3.8 15.5 + - - +
297P SER* 3.3 4.0 - - - -
298P SER* 2.7 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238P GLY 3.7 0.7 - - - +
239P TYR* 3.4 4.6 - - - -
240P VAL* 2.8 32.0 + - - +
242P VAL* 3.7 31.2 - - + -
246P VAL* 4.2 9.0 - - + -
247P ARG* 1.3 79.4 - - - +
249P HIS* 1.3 61.0 + - - +
250P PHE* 4.2 2.8 + - - -
289P MET* 3.8 30.7 - - + -
290P ASP 4.4 1.8 - - - +
291P MET* 5.4 0.2 - - - -
292P LYS* 4.0 37.7 - - + +
297P SER* 3.5 4.9 - - - +
314P GLU* 4.0 15.0 - - + +
315P MET* 4.1 10.3 - - - -
318P PHE* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 249 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237P HIS* 2.6 34.9 + + - +
238P GLY 3.3 8.1 - - - -
239P TYR* 3.2 34.8 - + + -
248P LEU* 1.3 76.0 - - - +
250P PHE* 1.3 74.4 + - - +
251P VAL* 4.1 5.6 - - + -
269P TRP* 3.9 19.5 - + - -
289P MET* 3.9 1.7 - - - +
290P ASP* 2.8 51.7 + - - +
296P GLU* 3.5 40.5 + - + +
297P SER* 2.7 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237P HIS* 3.6 3.1 - - - -
238P GLY* 2.7 71.4 + - - -
239P TYR 3.8 2.5 - - - -
240P VAL* 3.9 8.1 - - + -
248P LEU 4.4 1.6 - - - -
249P HIS* 1.3 81.6 + - - +
251P VAL* 1.3 66.1 + - - +
252P GLU* 3.9 19.1 - - + -
269P TRP* 5.6 0.2 - - - -
287P LEU* 3.7 40.4 - - + -
288P ALA 3.2 14.6 - - - +
289P MET* 3.7 16.4 - - - -
318P PHE* 3.6 28.3 - + - -
322P LEU* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235P MET* 3.3 44.2 - - + -
236P SER 3.4 3.8 - - - +
237P HIS* 3.8 23.3 - - + +
249P HIS* 4.1 0.9 - - + -
250P PHE* 1.3 77.0 - - - +
252P GLU* 1.3 62.7 + - - +
269P TRP* 3.4 47.8 - - + +
276P ILE* 4.7 5.2 - - + +
286P VAL* 3.4 3.5 - - - +
287P LEU* 3.5 1.2 - - - -
288P ALA* 2.9 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 252 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236P SER* 3.1 38.9 + - - +
237P HIS 6.2 0.4 - - - -
238P GLY 5.9 0.9 - - - +
250P PHE* 3.9 18.9 - - + -
251P VAL* 1.3 75.0 - - - +
253P LEU* 1.3 67.9 + - - +
254P GLY 5.2 1.6 - - - +
285P ARG* 2.7 48.6 + - + +
286P VAL 3.2 3.6 - - - +
287P LEU* 2.9 24.3 - - + +
322P LEU* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145P MET* 6.3 2.9 - - + -
230P CYS* 5.6 0.2 - - + -
235P MET* 4.1 22.2 - - + -
252P GLU* 1.3 79.4 - - - +
254P GLY* 1.3 69.8 + - - +
276P ILE* 4.1 31.6 - - + +
277P PRO* 4.2 13.9 - - + -
280P ALA* 3.4 18.9 - - + +
286P VAL* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 254 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252P GLU* 5.2 2.1 - - - +
253P LEU* 1.3 83.1 - - - +
255P SER* 1.3 61.4 + - - -
280P ALA* 4.0 10.5 - - - -
284P TYR 3.2 10.5 - - - -
285P ARG* 3.5 16.8 - - - +
----------------------------------------------------------
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