Contacts of the helix formed by residues 240 - 252 (chain D) in PDB entry 2J2M
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 ASN 240 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C HIS* 5.6 1.2 + - - -
156C ASN 4.4 6.3 - - - +
157C ILE* 4.0 39.3 - - + +
158C GLN 5.7 0.2 - - - +
58D ARG* 2.7 35.4 + - - +
102D HIS* 5.0 2.1 - - - -
105D GLU* 2.9 15.0 - - - +
238D ASP* 2.8 11.6 + - - +
239D PHE* 1.3 111.2 - - - +
241D HIS* 1.3 61.6 + - - +
243D SER* 3.4 3.3 + - - -
244D ASN* 2.9 21.0 + - - +
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Residues in contact with HIS 241 (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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105D GLU* 3.1 39.9 + - + +
106D THR* 3.5 24.7 - - + +
187D PRO 4.2 1.7 + - - -
188D ALA 3.0 31.7 + - - -
189D SER* 4.9 0.7 - - - -
226D LEU* 4.1 11.1 - - + +
234D VAL* 3.5 24.7 - - + -
238D ASP* 3.5 23.9 + - + +
239D PHE 3.5 2.2 - - - -
240D ASN* 1.3 77.5 - - - +
242D ALA* 1.3 73.5 + - + +
244D ASN* 3.4 2.4 + - - +
245D ASP* 2.9 30.2 + - + +
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Residues in contact with ALA 242 (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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105D GLU* 2.8 18.0 + - + +
187D PRO 5.8 0.4 - - - +
189D SER* 3.9 26.7 - - - -
190D TYR* 3.5 29.4 - - + +
241D HIS* 1.3 85.6 + - + +
243D SER* 1.3 56.9 + - - +
245D ASP* 3.7 0.9 - - - +
246D THR* 2.6 37.7 + - - -
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Residues in contact with SER 243 (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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155C THR 5.1 9.7 - - - +
156C ASN* 5.9 4.2 + - - -
157C ILE* 5.0 2.9 - - - -
58D ARG* 4.4 5.9 + - - -
59D GLY 3.9 7.1 + - - -
60D PHE* 3.4 32.0 - - - +
105D GLU* 2.6 33.6 + - - -
190D TYR* 3.7 4.6 - - - -
240D ASN* 3.8 8.7 - - - -
242D ALA* 1.3 72.3 - - - +
244D ASN* 1.3 58.3 + - - +
247D PHE* 3.0 31.9 + - - +
306D TYR* 5.9 0.3 - - - -
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Residues in contact with ASN 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ILE* 3.7 26.6 - - + +
238D ASP* 3.2 19.3 + - - +
240D ASN 2.9 18.7 + - - +
241D HIS 3.4 5.4 - - - +
242D ALA 3.2 0.2 - - - -
243D SER* 1.3 74.4 - - - +
245D ASP* 1.3 65.2 + - - +
247D PHE* 3.8 3.2 - - - +
248D GLN* 3.0 41.6 + - - +
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Residues in contact with ASP 245 (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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189D SER* 3.0 23.3 + - - -
191D ARG* 2.8 45.6 + - - +
192D LYS* 4.9 2.9 + - - -
241D HIS* 2.9 19.9 + - + +
242D ALA 3.7 4.0 - - - +
244D ASN* 1.3 77.4 - - - +
246D THR* 1.3 56.9 + - - +
248D GLN* 3.9 3.9 - - - +
249D ALA* 2.9 30.5 + - - +
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Residues in contact with THR 246 (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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60D PHE* 3.6 29.8 - - + -
94D PHE* 5.3 5.6 - - + -
190D TYR* 3.6 20.0 + - + +
191D ARG* 4.2 22.1 + - + +
242D ALA 2.6 23.6 + - - -
243D SER 4.4 0.2 - - - -
245D ASP* 1.3 75.8 + - - +
247D PHE* 1.3 66.5 + - - +
249D ALA* 3.6 1.2 + - - +
250D ILE* 3.3 28.4 + - + +
256D PRO* 3.9 24.7 - - + -
299D LEU* 5.9 0.9 - - + -
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Residues in contact with PHE 247 (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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154C ARG* 3.6 50.5 - - + -
155C THR* 3.7 39.3 - - + +
157C ILE* 6.3 0.7 - - + -
60D PHE* 3.8 14.6 - + + -
243D SER 3.0 20.7 + - - +
244D ASN* 3.8 4.9 - - - +
246D THR* 1.3 76.5 - - - +
248D GLN* 1.3 75.8 + - - +
250D ILE 3.2 2.9 + - - -
251D GLU* 3.2 24.5 + - + +
302D ASN* 3.1 58.0 + - + -
303D VAL* 5.0 2.9 - - + -
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Residues in contact with GLN 248 (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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155C THR* 5.5 2.8 - - - +
244D ASN* 3.0 34.6 + - - +
245D ASP* 3.9 4.0 - - - +
247D PHE* 1.3 90.4 - - - +
249D ALA* 1.3 60.5 + - - +
251D GLU* 3.1 9.7 + - - +
252D ASN* 2.8 56.6 + - - +
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Residues in contact with ALA 249 (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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191D ARG* 3.6 31.9 - - - +
245D ASP 2.9 18.6 + - - +
246D THR* 3.7 6.5 - - - +
248D GLN* 1.3 75.9 - - - +
250D ILE* 1.3 59.6 + - - +
252D ASN* 3.5 4.9 + - - +
253D GLY 3.3 2.9 + - - -
254D ASP* 2.8 50.8 + - + +
256D PRO* 4.5 2.7 - - + -
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Residues in contact with ILE 250 (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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60D PHE* 4.3 6.1 - - + -
62D ALA* 3.7 25.4 - - + -
246D THR* 3.3 13.7 - - + +
247D PHE 3.2 6.6 + - - +
248D GLN 3.2 0.6 - - - -
249D ALA* 1.3 74.6 - - - +
251D GLU* 1.3 65.3 + - - +
253D GLY 3.2 9.0 + - - -
255D PHE* 3.5 16.1 - - + -
256D PRO* 3.6 21.8 - - + -
299D LEU* 3.8 15.9 - - + +
300D ASN* 3.7 30.1 - - - +
301D LYS* 3.7 2.9 - - - +
302D ASN* 3.5 30.7 - - - +
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Residues in contact with GLU 251 (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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154C ARG* 3.4 25.5 + - - +
247D PHE* 3.2 24.1 + - + +
248D GLN* 3.1 16.7 + - - +
250D ILE* 1.3 76.9 - - - +
252D ASN* 1.3 63.1 + - - +
253D GLY 3.2 1.0 + - - -
302D ASN* 2.7 33.4 + - - +
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Residues in contact with ASN 252 (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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248D GLN* 2.8 44.5 + - - +
249D ALA* 3.8 7.2 - - - +
251D GLU* 1.3 79.1 - - - +
253D GLY* 1.3 59.4 + - - +
254D ASP* 3.6 6.6 + - + +
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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