Contacts of the strand formed by residues 303 - 311 (chain A) in PDB entry 4ZGA
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 303 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.1 18.4 - - + +
168A ILE* 3.9 23.8 - - + -
260A LEU* 4.2 12.8 - - + -
261A TRP* 5.5 0.7 - - - -
264A ALA* 4.7 10.8 - - + -
269A VAL* 5.4 1.1 - - + -
270A LYS 3.9 2.9 + - - +
271A ALA* 4.0 22.9 - - + -
272A GLY 2.8 30.7 + - - +
274A PHE* 4.0 13.7 - - + -
301A PRO* 3.5 0.6 - - - +
302A SER* 1.3 81.4 - - - +
304A TYR* 1.3 69.2 + - - +
517A LEU* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO* 4.5 1.8 - - + -
166A LEU 2.7 17.7 + - - +
167A ILE* 3.3 17.1 - - + -
168A ILE* 2.7 39.6 + - - +
272A GLY* 4.1 7.0 - - - -
273A THR 5.5 0.9 - - - +
274A PHE* 4.8 2.2 - - - -
289A ILE* 3.9 29.2 - - + -
292A TRP* 3.6 45.3 + + + -
293A LEU* 3.5 31.2 - - + +
300A ARG* 3.8 1.7 - - - +
301A PRO* 2.6 57.8 + - + +
302A SER 4.1 4.9 - - - -
303A VAL* 1.3 79.6 - - - +
305A ALA* 1.3 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 3.2 13.9 - - + +
273A THR 3.5 13.2 + - - +
274A PHE* 3.6 43.5 - - + +
276A TRP* 2.8 29.8 + - - -
289A ILE* 4.1 4.6 - - - +
304A TYR* 1.3 75.5 - - - +
306A PHE* 1.3 54.7 + - - +
910A 4O3 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 5.0 4.3 - - + +
168A ILE 2.7 13.3 + - - +
169A PHE* 2.9 56.8 - + + -
170A SER* 3.0 27.9 + - - -
276A TRP* 3.7 3.6 - - - +
282A HIS* 3.9 19.5 - + + -
285A ARG* 3.7 31.2 - - + -
286A ILE* 3.9 13.2 - - + -
289A ILE* 3.8 16.4 - - + +
304A TYR 4.3 0.4 - - - -
305A ALA* 1.3 76.3 - - - +
307A TYR* 1.3 71.4 + - - +
308A SER* 3.5 31.2 - - - -
335A ILE* 4.1 4.9 - - + -
339A LEU* 6.2 0.2 - - + -
906A SCN 3.8 9.2 - - - -
910A 4O3 5.1 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER* 3.1 25.1 - - - +
171A VAL 4.8 0.2 - - - -
172A ASP* 3.2 36.1 + - + +
210A THR* 4.1 7.1 - - - +
214A LEU* 4.0 14.6 - - + -
274A PHE 4.7 2.0 - - - +
276A TRP* 3.8 9.7 - - + -
285A ARG* 2.6 34.9 + - - -
306A PHE* 1.3 87.4 - - - +
308A SER* 1.3 79.3 + - - +
309A GLU* 3.8 12.0 - - + +
359A ASP* 4.7 1.6 - - - -
910A 4O3 3.1 73.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER 3.0 8.9 + - - -
171A VAL* 3.5 3.5 - - - -
172A ASP 2.8 31.2 + - - -
282A HIS* 2.9 24.1 + - - -
285A ARG* 4.2 0.2 - - - +
306A PHE* 3.5 9.0 - - - -
307A TYR* 1.3 85.3 - - - +
309A GLU* 1.3 58.0 + - - +
310A GLN* 3.1 16.1 + - - +
906A SCN 3.0 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 3.7 15.7 - - + +
278A VAL* 6.0 2.8 - - - +
282A HIS* 2.8 33.6 + - - -
285A ARG* 4.5 8.2 + - - -
307A TYR* 3.8 14.4 - - + +
308A SER* 1.3 70.8 - - - +
310A GLN* 1.3 62.5 + - + +
312A ASP* 3.4 6.1 + - - +
313A PHE* 3.1 40.7 + - + +
910A 4O3 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 3.3 14.5 - - - +
172A ASP 3.1 18.3 + - - -
282A HIS* 4.9 2.5 - - + -
308A SER* 3.1 13.4 - - - +
309A GLU* 1.3 87.1 + - - +
311A PRO* 1.4 78.0 - - + +
313A PHE* 3.8 23.4 - - - +
314A SER* 3.8 17.2 + - - -
328A PRO* 4.0 24.9 - - + +
332A ILE* 5.5 4.0 - - + -
906A SCN 4.2 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 4.2 1.1 - - + -
172A ASP 3.0 12.8 - - - +
173A GLY 4.2 3.4 - - - +
174A PHE* 3.4 51.4 - - + +
178A TYR* 4.0 19.4 + - + +
310A GLN* 1.4 88.0 - - + +
312A ASP* 1.3 63.7 + - - +
313A PHE 3.3 2.4 + - - -
314A SER* 3.4 2.6 + - - -
315A GLY* 3.1 19.9 + - - -
325A MET* 4.8 6.2 - - - +
328A PRO* 5.3 5.2 - - + +
329A LEU* 3.7 19.7 - - + -
362A MET* 5.1 0.3 - - - +
----------------------------------------------------------
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