Contacts of the helix formed by residues 227 - 239 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C GLY* 5.9 5.2 - - - +
152D ARG* 4.7 13.0 - - + -
225D PRO* 3.7 13.9 - - + +
226D ARG* 1.3 94.4 - - + +
228D LYS* 1.3 71.3 + - + +
229D SER* 3.6 1.8 - - - +
230D VAL* 3.3 13.7 + - - +
231D SER* 3.0 26.1 + - - -
54F GLU* 4.8 4.5 - - - +
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Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C GLU* 4.8 3.6 + - - +
235C SER* 5.1 0.6 - - - -
236C ILE* 4.7 26.8 - - + +
151D GLU* 3.7 40.6 + - + -
152D ARG* 5.4 0.4 - - + +
226D ARG 3.6 3.0 + - - -
227D LEU* 1.3 86.1 - - + +
229D SER* 1.3 58.9 + - - +
230D VAL 3.1 0.8 + - - -
231D SER* 3.1 14.8 + - - +
232D GLU* 2.7 84.1 + - - +
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Residues in contact with SER 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D GLU* 3.6 9.3 + - - -
152D ARG* 5.7 0.2 - - - -
222D LEU* 3.4 40.2 - - - +
226D ARG 4.8 1.1 - - - -
227D LEU 4.8 4.0 - - - -
228D LYS* 1.3 74.0 - - - +
230D VAL* 1.3 57.0 + - - +
232D GLU* 4.5 5.0 - - - +
233D ARG* 3.1 30.6 + - - +
47F GLU* 2.6 31.2 + - - -
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Residues in contact with VAL 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ARG* 3.9 12.6 - - + -
227D LEU* 3.3 24.7 + - - +
228D LYS 3.1 0.6 - - - -
229D SER* 1.3 77.3 - - - +
231D SER* 1.3 58.7 + - - +
233D ARG* 3.4 8.3 + - - +
234D LEU* 3.0 27.8 + - - +
47F GLU* 4.3 13.5 - - + +
50F ASP* 3.7 19.7 - - + -
51F MET* 3.3 40.4 - - + +
54F GLU* 3.4 22.4 - - - +
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Residues in contact with SER 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C SER* 2.7 42.8 + - - -
236C ILE* 4.6 0.9 - - - -
238C LYS* 4.6 5.4 - - - +
239C GLY* 3.9 20.5 - - - -
227D LEU* 3.0 14.3 + - - +
228D LYS* 3.1 20.1 + - - +
230D VAL* 1.3 72.6 - - - +
232D GLU* 1.3 55.9 + - - +
233D ARG 2.9 10.3 + - - -
234D LEU* 3.5 7.8 + - - +
235D SER 3.4 13.2 + - - -
54F GLU* 5.1 5.6 + - - -
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Residues in contact with GLU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LYS* 5.4 3.1 - - - +
231C SER* 5.3 0.2 + - - -
232C GLU* 3.6 33.6 - - + +
235C SER* 3.3 16.0 + - - +
151D GLU* 5.1 4.9 - - - +
228D LYS* 2.7 59.5 + - - +
229D SER* 4.6 5.0 - - - +
231D SER* 1.3 71.1 + - - +
233D ARG* 1.3 56.4 + - - +
235D SER 4.5 0.7 - - - -
236D ILE* 3.2 27.8 - - + +
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Residues in contact with ARG 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D SER 5.3 5.3 + - - -
229D SER* 3.1 27.7 + - - +
230D VAL* 3.4 3.6 - - - +
232D GLU* 1.3 77.0 - - + +
234D LEU* 1.3 59.0 + - - +
235D SER 3.3 0.7 - - - -
236D ILE* 3.1 15.5 + - + +
237D LEU* 3.0 23.2 + - - +
36F MET* 5.7 0.5 - - - +
43F PRO* 4.0 9.4 - - - +
44F THR* 2.7 49.9 + - - +
47F GLU* 2.8 50.5 + - - +
48F LEU* 3.4 15.8 - - - +
51F MET* 3.4 15.8 - - + +
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C LEU* 6.2 2.7 - - + -
238C LYS* 3.8 44.2 - - + +
230D VAL 3.0 15.6 + - - +
231D SER* 3.5 8.5 + - - +
233D ARG* 1.3 73.6 - - - +
235D SER* 1.3 56.8 + - - +
237D LEU* 3.2 27.2 + - + +
238D LYS* 2.9 31.0 + - + +
51F MET* 3.4 32.2 - - + +
54F GLU* 5.4 0.7 - - - +
71F MET* 4.9 11.2 - - + -
145F MET* 6.2 3.8 - - - -
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Residues in contact with SER 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C SER* 2.7 39.6 + - - -
234C LEU* 3.6 17.1 - - - +
235C SER* 3.1 34.3 - - - -
238C LYS* 6.2 0.6 - - - +
231D SER 3.4 3.8 + - - -
232D GLU 4.8 0.7 - - - -
233D ARG 3.3 0.4 - - - -
234D LEU* 1.3 82.6 - - - +
236D ILE* 1.3 54.3 + - - +
238D LYS* 3.7 7.5 - - - +
239D GLY* 2.9 26.0 + - - -
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Residues in contact with ILE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C SER* 4.2 10.1 - - - +
232D GLU* 3.2 26.5 - - + +
233D ARG* 3.1 16.1 + - + +
235D SER* 1.3 74.3 - - - +
237D LEU* 1.3 58.2 + - - +
239D GLY* 3.9 2.1 + - - -
240D SER* 2.7 32.0 + - - +
36F MET* 3.9 10.4 - - + +
41F GLN* 4.0 24.7 - - - +
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Residues in contact with LEU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ARG 3.0 11.9 + - - +
234D LEU* 3.4 26.5 - - + +
236D ILE* 1.3 74.0 - - - +
238D LYS* 1.3 53.7 + - - +
240D SER* 2.8 27.3 + - - +
241D ARG* 3.1 33.7 + - + +
19F PHE* 4.4 15.3 - - + -
32F LEU* 4.0 44.0 - - + -
35F VAL* 6.1 1.3 - - + -
36F MET* 4.1 15.1 - - + +
51F MET* 4.5 7.6 - - + -
52F ILE* 6.2 1.1 - - + -
71F MET* 6.0 4.3 - - + -
72F MET* 6.0 5.4 - - + -
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Residues in contact with LYS 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU* 4.0 23.7 - - + +
234D LEU* 2.9 26.2 + - + +
235D SER* 3.3 10.5 + - - +
237D LEU* 1.3 71.7 - - - +
239D GLY* 1.3 57.2 + - - +
240D SER 3.3 3.8 + - - -
241D ARG* 3.9 19.0 + - - +
127F GLU* 2.7 44.1 + - - -
144F MET* 2.8 30.7 + - - +
145F MET* 4.2 31.6 - - + +
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Residues in contact with GLY 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C SER* 5.7 2.5 - - - -
235D SER 2.9 15.6 + - - -
236D ILE* 3.9 2.0 + - - -
237D LEU 3.2 0.4 + - - -
238D LYS* 1.3 75.6 - - - +
240D SER* 1.3 62.5 + - - +
127F GLU* 5.9 1.3 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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