Contacts of the helix formed by residues 231 - 241 (chain A) in PDB entry 5M7R
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 SER 231 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLU* 2.5 29.5 + - - -
224A CYS* 4.3 2.7 - - - -
225A TYR 3.3 11.0 + - - -
227A ASN 3.3 16.4 + - - -
228A VAL 3.5 10.2 + - - -
229A SER 3.7 0.6 - - - -
230A GLN* 1.3 74.2 - - - +
232A PRO* 1.4 62.9 - - - +
233A TYR* 3.4 4.7 + - - +
234A LEU* 3.1 22.4 + - - -
235A ARG* 2.9 29.6 + - - +
270A ILE* 3.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR* 3.6 16.8 - - + +
226A PRO* 4.2 4.9 - - + -
230A GLN 3.2 9.6 - - - +
231A SER* 1.4 79.1 - - - +
233A TYR* 1.3 67.1 + - - +
235A ARG* 3.9 18.4 - - + +
236A THR* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A HIS* 4.3 15.0 - + + +
190A SER* 5.7 0.9 - - - -
191A PHE* 4.2 9.0 - + + -
192A ALA* 3.6 32.4 - - + +
195A GLN* 2.3 42.6 + - - -
214A PHE* 4.0 1.7 - - - -
216A PRO* 3.4 24.0 - - + +
217A THR* 2.9 26.1 + - - -
218A GLU* 3.6 33.4 - - + +
231A SER* 3.6 8.1 - - - +
232A PRO* 1.3 81.2 - - - +
234A LEU* 1.3 66.9 + - + +
237A VAL* 3.2 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PRO* 4.7 8.1 - - + -
218A GLU* 4.0 21.3 - - - +
224A CYS* 3.7 25.8 - - - -
228A VAL* 4.0 20.4 - - + +
231A SER* 3.1 20.6 + - - +
233A TYR* 1.3 87.1 - - + +
235A ARG* 1.3 59.0 + - - +
237A VAL* 3.7 5.9 - - + +
238A GLY 2.8 26.5 + - - -
247A VAL* 5.9 0.2 - - + -
249A TRP* 4.3 4.5 - - + -
267A VAL* 4.3 9.6 - - + -
270A ILE* 3.4 28.6 - - + +
271A ILE* 3.8 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER 4.6 1.2 + - - -
230A GLN* 4.1 18.4 + - - +
231A SER 2.9 19.2 + - - +
232A PRO* 3.3 22.1 + - + +
234A LEU* 1.3 74.8 - - - +
236A THR* 1.3 58.7 + - - +
238A GLY* 3.3 1.2 + - - -
239A GLU* 3.0 54.1 + - + +
270A ILE* 3.7 24.3 - - + +
272A LYS* 5.4 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A SER* 4.2 3.8 + - - -
192A ALA* 3.7 20.4 - - + +
193A HIS* 3.5 51.0 + - + +
196A VAL* 4.6 1.7 - - + +
232A PRO* 3.0 17.7 + - - +
235A ARG* 1.3 73.3 - - - +
237A VAL* 1.3 58.5 + - - +
239A GLU* 3.2 10.5 + - - +
240A LYS* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA* 4.6 3.1 - - + -
196A VAL* 4.1 17.9 - - + -
214A PHE* 4.0 18.6 - - + -
216A PRO* 5.2 0.7 - - + -
233A TYR* 3.2 38.8 + - + +
234A LEU* 3.2 13.2 + - + +
236A THR* 1.3 75.2 - - - +
238A GLY* 1.3 65.7 + - - +
241A LEU* 3.1 50.4 + - + +
247A VAL* 4.2 16.2 - - + -
271A ILE* 4.5 11.0 - - + -
273A ARG* 4.2 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU 2.8 15.2 + - - -
235A ARG 3.7 0.2 - - - -
237A VAL* 1.3 77.4 - - - +
239A GLU* 1.3 60.6 + - - +
241A LEU 4.6 1.6 - - - +
270A ILE 3.4 21.5 - - - -
271A ILE* 3.4 18.3 - - - +
272A LYS* 3.7 16.8 - - - +
273A ARG* 3.6 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 3.0 44.7 + - + +
236A THR* 3.8 10.3 + - - +
238A GLY* 1.3 79.1 - - - +
240A LYS* 1.3 69.1 + - + +
241A LEU 4.6 2.3 - - - +
272A LYS* 4.7 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A HIS* 3.9 37.3 + - + +
196A VAL* 3.5 14.8 - - + -
200A ASN* 2.8 22.4 + - - +
236A THR* 2.9 19.0 + - + +
239A GLU* 1.3 85.3 - - + +
241A LEU* 1.3 63.2 + - - +
242A LEU* 3.4 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A VAL* 3.6 18.7 - - + +
199A THR* 3.8 33.9 - - + -
200A ASN* 3.8 10.1 - - - +
214A PHE* 3.9 17.9 - - + -
237A VAL* 3.1 25.2 + - + +
238A GLY 4.6 2.4 - - - +
239A GLU 4.6 1.6 - - - +
240A LYS* 1.3 75.7 - - - +
242A LEU* 1.3 61.6 + - - +
243A PRO* 3.4 1.9 - - - +
245A ILE* 3.9 19.7 - - + -
247A VAL* 3.5 31.6 - - + -
273A ARG* 2.7 33.0 + - - +
----------------------------------------------------------
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