Contacts of the helix formed by residues 227 - 239 (chain C) in PDB entry 3J41
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 LEU 227 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C PRO* 5.3 2.0 - - + -
226C ARG* 1.3 96.3 - - + +
228C LYS* 1.3 66.4 + - + +
229C SER 3.3 0.2 - - - -
230C VAL* 3.6 9.7 - - - +
231C SER* 3.0 28.4 + - - -
9D PHE* 4.8 19.1 - - + +
123F GLU* 2.9 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C PRO* 6.1 1.6 - - + -
226C ARG 2.8 8.1 + - - +
227C LEU* 1.3 85.8 - - + +
229C SER* 1.3 58.8 + - - +
231C SER* 3.7 7.3 + - - -
232C GLU* 2.7 57.0 + - - +
9D PHE* 5.7 4.9 - - + +
62D ILE 6.0 2.5 - - - +
85D ARG* 4.0 30.5 - - - +
232D GLU* 4.8 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C PRO* 4.1 8.7 + - - +
226C ARG 3.6 19.7 + - - -
228C LYS* 1.3 76.7 - - - +
230C VAL* 1.3 63.3 + - - +
232C GLU* 3.1 19.1 + - - +
233C ARG* 2.8 41.0 + - - +
120F GLU* 2.5 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ARG* 4.2 2.0 - - - -
227C LEU* 3.6 14.8 - - - +
229C SER* 1.3 72.8 - - - +
231C SER* 1.3 57.0 + - - +
233C ARG* 2.9 20.4 + - - +
234C LEU* 2.9 13.9 + - + -
120F GLU* 3.8 21.3 - - + +
123F GLU* 3.1 52.0 - - + +
124F MET* 3.5 41.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LEU 3.0 19.4 + - - -
228C LYS* 3.8 8.5 - - - -
230C VAL* 1.3 75.0 - - - +
232C GLU* 1.3 51.6 + - - +
233C ARG 3.1 0.5 + - - -
234C LEU* 4.5 3.1 - - - -
235C SER* 2.6 32.9 + - - -
235D SER* 2.7 44.5 + - - -
236D ILE* 3.9 12.1 + - - +
239D GLY* 5.7 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LYS* 2.7 42.1 + - - +
229C SER* 3.1 12.5 + - - +
231C SER* 1.3 72.1 - - - +
233C ARG* 1.3 82.2 + - + +
235C SER* 3.5 18.0 - - - -
236C ILE* 3.5 22.7 - - + +
228D LYS* 5.0 2.2 - - - +
232D GLU* 3.6 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ARG 5.4 4.6 + - - -
229C SER* 2.8 31.1 + - - -
230C VAL 2.9 6.5 + - - +
232C GLU* 1.3 110.4 + - + +
234C LEU* 1.3 58.3 + - - +
235C SER 3.1 0.4 - - - -
236C ILE* 2.9 24.6 + - + +
237C LEU* 2.9 13.3 + - - +
109F MET* 3.8 14.9 - - + +
114F GLU* 4.9 0.9 - - - +
116F LEU* 3.6 38.1 - - + +
117F THR 6.0 0.2 - - - -
120F GLU* 2.8 62.2 + - - -
121F VAL* 5.8 1.6 - - + -
124F MET* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C VAL* 2.9 9.5 + - + +
231C SER* 4.5 2.0 - - - -
233C ARG* 1.3 72.9 - - - +
235C SER* 1.3 55.2 + - - +
237C LEU* 3.4 17.6 + - + +
238C LYS* 2.9 36.3 + - + +
234D LEU* 6.2 2.5 - - + -
235D SER* 3.6 21.3 - - - +
238D LYS* 4.0 28.3 - - + +
124F MET* 3.5 29.5 - - + +
127F GLU* 4.0 21.3 - - - +
145F MET* 4.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C SER 2.6 28.3 + - - -
232C GLU* 3.5 14.5 - - - -
234C LEU* 1.3 76.6 - - - +
236C ILE* 1.3 58.1 + - - +
238C LYS* 3.9 2.1 - - - +
239C GLY 2.9 14.6 + - - -
228D LYS* 5.1 0.9 - - - -
231D SER* 2.7 41.9 + - - -
232D GLU* 3.3 24.2 + - - -
235D SER* 3.1 14.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C GLU* 3.5 22.7 - - + +
233C ARG* 2.9 10.9 + - + +
235C SER* 1.3 74.2 - - - +
237C LEU* 1.3 62.6 + - - +
239C GLY* 3.2 5.3 + - - +
240C SER* 2.9 31.9 + - - +
228D LYS* 4.7 26.7 - - + +
231D SER* 4.6 0.9 - - - -
109F MET* 5.1 4.7 - - + -
112F LEU* 5.1 11.7 - - + -
114F GLU* 3.5 34.8 - - + +
116F LEU* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ARG 2.9 12.2 + - - +
234C LEU* 3.5 21.3 - - + +
236C ILE* 1.3 74.6 - - - +
238C LYS* 1.3 55.9 + - - +
240C SER* 3.0 21.6 + - - -
241C ARG* 3.3 17.4 + - - +
92F PHE* 3.5 32.5 - - + -
105F LEU* 4.2 22.4 - - + -
108F VAL* 4.9 2.0 - - + -
109F MET* 3.8 31.7 - - + +
121F VAL* 6.2 0.7 - - + -
124F MET* 4.7 17.0 - - + -
141F PHE* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU* 2.9 26.2 + - + +
235C SER* 4.5 3.1 - - - +
237C LEU* 1.3 67.8 - - - +
239C GLY* 1.3 56.5 + - - +
240C SER 2.9 9.0 + - - -
241C ARG* 3.0 36.4 + - + +
231D SER* 4.6 5.8 - - - +
234D LEU* 3.8 37.8 - - + +
235D SER 6.2 0.2 - - - +
51F MET 4.0 7.9 + - - -
54F GLU* 2.6 45.2 + - - +
55F VAL* 4.1 16.0 - - - +
71F MET* 6.0 0.2 - - - +
75F LYS* 4.9 7.0 - - + +
145F MET* 6.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C SER 2.9 18.2 + - - -
236C ILE* 3.2 13.4 + - - -
238C LYS* 1.3 72.5 - - - +
240C SER* 1.3 56.7 + - - +
241C ARG 3.8 0.2 - - - -
227D LEU* 5.9 5.0 - - - +
231D SER* 3.9 14.9 - - - -
----------------------------------------------------------
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