Contacts of the helix formed by residues 301 - 313 (chain A) in PDB entry 4FRA
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 HIS 301 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A MET* 4.9 1.8 - - - -
297A GLU* 2.9 39.0 - - + +
298A ALA* 2.9 22.4 + - - -
299A VAL 3.8 15.4 + - - -
300A TRP* 1.3 91.0 - + - +
302A ASP* 1.3 72.1 + - - +
304A SER* 3.1 12.3 + - - -
305A HIS* 3.2 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG* 3.5 32.3 + - - +
189A MET* 4.2 26.9 - - + +
267A GLY* 4.6 7.3 - - - +
270A PHE* 5.8 0.7 - - - -
288A MET* 4.0 26.6 - - - -
300A TRP 4.3 0.5 - - - +
301A HIS* 1.3 82.5 - - - +
303A GLU* 1.3 59.2 + - - +
305A HIS* 3.1 4.5 + - - +
306A LEU* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A HIS* 3.9 1.2 - - - -
264A TYR* 2.6 35.2 + - - +
265A TYR 3.7 4.3 - - - +
266A MET* 3.6 8.7 - - - +
267A GLY* 2.8 33.5 + - - +
300A TRP* 3.0 15.6 + - + +
302A ASP* 1.3 81.9 - - - +
304A SER* 1.3 61.5 + - - +
306A LEU* 3.7 6.5 - - - +
307A ASN* 3.0 40.1 + - - +
402A GAL 2.7 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A THR 4.8 1.2 + - - -
246A TYR* 5.9 1.6 - - - +
247A GLU* 4.3 11.5 + - - +
254A ALA* 3.8 16.8 - - - +
256A ILE* 5.1 0.9 - - - +
264A TYR* 5.2 2.2 - - - -
298A ALA* 3.5 18.8 - - - +
299A VAL* 3.7 8.7 - - - +
300A TRP* 2.9 32.9 + - - +
301A HIS 3.1 10.1 + - - -
303A GLU* 1.3 76.5 - - - +
305A HIS* 1.3 58.2 + - - +
307A ASN* 3.3 7.7 + - - +
308A LYS* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLN* 4.4 0.6 - - - +
254A ALA* 3.7 19.8 + - + +
284A CYS* 3.7 22.6 - - + -
287A ALA* 3.5 33.0 + - + +
288A MET* 3.4 27.2 - - + +
291A ASP* 3.4 26.5 + - + -
297A GLU* 6.1 0.9 - - - -
298A ALA* 3.6 21.1 - - + -
301A HIS* 3.2 19.1 + - - -
302A ASP* 3.1 8.4 + - - +
304A SER* 1.3 72.5 - - - +
306A LEU* 1.3 61.9 + - - +
308A LYS* 3.2 5.2 + - + +
309A TYR* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A MET* 4.3 7.9 - - + -
230A GLY* 6.0 0.7 - - - -
265A TYR* 4.5 13.7 - - + +
266A MET 3.6 26.2 - - - +
267A GLY* 3.7 15.3 - - - +
270A PHE* 4.1 24.2 - - + -
280A LEU* 3.6 35.9 - - + -
284A CYS* 3.7 8.2 - - - -
302A ASP 2.8 19.2 + - - +
303A GLU* 3.7 5.2 - - - +
304A SER 3.4 0.2 - - - -
305A HIS* 1.3 73.1 - - - +
307A ASN* 1.3 57.2 + - - +
309A TYR* 3.2 2.0 + - - +
310A LEU* 2.9 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 3.5 26.7 - - + -
256A ILE* 4.0 4.1 - - + +
263A PHE 3.5 8.8 - - - +
264A TYR* 3.6 11.0 - - + -
265A TYR* 2.8 62.2 + - - +
303A GLU* 3.0 34.3 + - - +
304A SER* 3.6 6.3 - - - +
305A HIS 3.2 0.4 - - - -
306A LEU* 1.3 73.8 - - - +
308A LYS* 1.3 66.8 + - - +
310A LEU* 3.4 1.2 + - - +
311A LEU* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A SER 4.9 0.2 + - - -
253A GLN 2.9 30.1 + - - +
254A ALA* 3.9 13.2 - - - +
255A TYR* 2.9 33.0 + - - +
256A ILE* 3.8 16.2 - - + +
304A SER 3.0 13.9 + - - +
305A HIS* 3.2 9.2 + - + +
307A ASN* 1.3 76.4 - - - +
309A TYR* 1.4 62.8 + - - +
311A LEU* 3.3 5.1 + - + +
312A ARG* 3.2 59.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.2 10.1 - - + -
276A GLU* 4.6 7.9 + - - -
279A ARG* 3.7 24.2 - - - +
280A LEU* 3.7 42.3 + - + -
283A ALA* 3.6 33.0 - - + -
284A CYS* 4.2 9.0 - - - -
305A HIS 2.9 16.1 + - - +
306A LEU* 3.6 5.2 - - - +
308A LYS* 1.4 76.8 - - - +
310A LEU* 1.3 57.9 + - + +
312A ARG* 3.2 1.4 + - - -
313A HIS* 2.8 91.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.7 36.3 - - + -
229A PHE 4.9 1.8 - - - +
230A GLY* 4.0 18.6 - - - -
262A ASP* 4.7 0.7 - - - +
265A TYR* 3.6 47.7 + - + -
280A LEU* 4.1 12.1 - - + -
306A LEU* 2.9 39.2 + - + +
307A ASN 4.2 0.4 - - - +
309A TYR* 1.3 74.7 - - + +
311A LEU* 1.3 65.4 + - - +
313A HIS 3.2 17.3 - - - +
314A LYS* 3.7 4.7 - - - +
315A PRO* 3.7 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 5.8 1.3 - - - +
256A ILE* 3.7 41.1 - - + -
260A GLU* 3.8 19.5 - - + +
261A GLY* 3.9 25.6 - - - +
262A ASP* 4.0 9.2 - - - +
265A TYR* 5.0 1.5 - - - -
307A ASN 3.0 18.1 + - - +
308A LYS* 3.5 6.7 - - + +
309A TYR 3.2 0.2 - - - -
310A LEU* 1.3 78.6 - - - +
312A ARG* 1.3 73.1 + - - +
314A LYS* 2.8 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TYR 5.5 0.2 + - - -
257A PRO* 6.1 1.8 - - - +
260A GLU* 4.4 14.8 + - - -
308A LYS* 3.2 46.6 + - + +
309A TYR* 3.2 2.0 + - - -
311A LEU* 1.3 94.7 - - - +
313A HIS* 1.3 78.1 + - + +
314A LYS* 4.1 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.8 6.3 - - + +
309A TYR* 2.8 74.0 + + + +
310A LEU* 3.2 22.1 - - - +
312A ARG* 1.3 89.1 + - + +
314A LYS* 1.3 67.4 + - - +
315A PRO* 3.4 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