Contacts of the helix formed by residues 240 - 252 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A HIS* 5.7 0.2 + - - -
156A ASN 4.4 6.1 - - - +
157A ILE* 3.8 36.9 - - + +
158A GLN 5.6 1.0 - - - +
58B ARG* 2.7 33.1 + - - +
102B HIS* 5.0 2.1 - - - -
105B GLU* 3.1 13.4 - - - +
238B ASP* 2.7 11.3 + - - +
239B PHE* 1.3 111.2 - - - +
241B HIS* 1.3 55.7 + - - +
243B SER* 3.8 2.9 - - - -
244B ASN* 2.9 26.9 + - - +
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Residues in contact with HIS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLU* 3.3 32.0 + - + +
106B THR* 3.6 25.4 - - + +
187B PRO 4.3 3.7 + - - -
188B ALA 2.9 31.8 + - - -
189B SER* 5.0 0.7 - - - -
226B LEU* 4.2 11.3 - - + +
234B VAL* 3.6 24.2 - - + -
238B ASP* 3.2 24.9 + - + +
239B PHE 3.6 1.6 + - - -
240B ASN* 1.3 77.1 - - - +
242B ALA* 1.3 67.8 + - + +
244B ASN* 3.4 1.9 - - - +
245B ASP* 2.8 33.1 + - + +
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLU* 3.0 19.3 + - + +
187B PRO 6.0 0.2 - - - +
189B SER* 4.1 23.3 - - - -
190B TYR* 3.6 28.0 - - + +
241B HIS* 1.3 87.4 + - + +
243B SER* 1.3 59.7 + - - +
245B ASP* 3.5 1.0 + - - +
246B THR* 2.8 37.1 + - - -
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR 5.2 9.9 - - - -
156A ASN* 5.6 4.5 + - - -
157A ILE* 5.0 2.5 - - - -
58B ARG* 4.4 6.7 + - - -
59B GLY 4.0 6.9 + - - -
60B PHE* 3.5 31.9 - - - +
105B GLU* 2.7 30.8 + - - -
190B TYR* 3.8 2.0 - - - -
240B ASN* 3.8 9.2 - - - -
242B ALA* 1.3 73.6 - - - +
244B ASN* 1.3 59.1 + - - +
247B PHE* 3.0 33.5 + - - +
306B TYR* 5.9 0.5 - - - -
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Residues in contact with ASN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 3.7 24.7 - - + +
238B ASP* 2.9 22.8 + - - +
240B ASN 2.9 19.1 + - - +
241B HIS 3.4 5.2 - - - +
243B SER* 1.3 77.0 - - - +
245B ASP* 1.3 56.7 + - - +
247B PHE* 3.8 3.4 - - - +
248B GLN* 3.0 43.0 + - - +
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Residues in contact with ASP 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B SER* 2.9 31.2 + - - -
191B ARG* 3.1 35.9 + - - -
192B LYS* 4.6 4.2 + - - -
241B HIS* 2.8 22.3 + - + +
242B ALA 3.9 3.4 - - - +
243B SER 3.4 0.2 - - - -
244B ASN* 1.3 74.4 - - - +
246B THR* 1.3 58.3 + - - +
248B GLN* 3.9 4.1 - - - +
249B ALA* 3.0 27.2 + - - +
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Residues in contact with THR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE* 3.4 32.5 - - + -
94B PHE* 5.1 6.7 - - + -
190B TYR* 3.6 22.3 + - + +
191B ARG* 4.1 18.3 + - + +
242B ALA 2.8 18.6 + - - -
243B SER 4.2 0.2 - - - -
245B ASP* 1.3 75.0 + - - +
247B PHE* 1.3 66.4 + - - +
249B ALA* 3.5 1.7 + - - +
250B ILE* 3.2 26.5 + - + +
256B PRO* 4.2 21.5 - - + -
299B LEU* 5.8 0.4 - - + -
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Residues in contact with PHE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.7 48.0 - - + -
155A THR* 3.6 39.3 - - + +
60B PHE* 3.7 14.2 - + + -
243B SER 3.0 19.3 + - - +
244B ASN* 3.8 4.3 - - - +
246B THR* 1.3 79.2 - - - +
248B GLN* 1.3 73.2 + - - +
251B GLU* 3.0 39.1 + - + +
302B ASN* 3.1 52.6 + - + -
303B VAL* 4.9 2.7 - - + -
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Residues in contact with GLN 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR* 5.7 1.4 - - - +
244B ASN* 3.0 33.6 + - - +
245B ASP* 4.0 4.7 - - - +
247B PHE* 1.3 93.1 - - - +
249B ALA* 1.3 59.6 + - - +
251B GLU* 3.6 7.9 - - - +
252B ASN* 2.8 60.6 + - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ARG* 3.4 38.4 - - - +
245B ASP 3.0 16.3 + - - +
246B THR 3.8 5.2 - - - +
247B PHE 3.4 0.4 - - - -
248B GLN* 1.3 75.1 - - - +
250B ILE* 1.3 59.2 + - - +
252B ASN* 3.4 4.3 + - - +
253B GLY 3.2 3.5 + - - -
254B ASP* 2.7 49.1 + - + +
256B PRO* 4.6 2.9 - - + -
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Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE* 4.4 4.7 - - + -
62B ALA* 3.7 28.9 - - + -
246B THR* 3.2 18.3 + - + +
249B ALA* 1.3 77.6 - - - +
251B GLU* 1.3 63.2 + - - +
253B GLY* 3.1 10.4 + - - -
254B ASP 4.6 0.2 - - - -
255B PHE* 3.3 16.9 - - + -
256B PRO* 3.5 19.3 - - + -
299B LEU* 3.4 26.7 - - + +
300B ASN 3.8 5.8 - - - +
301B LYS* 3.8 11.7 - - - +
302B ASN* 3.4 42.0 - - - +
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Residues in contact with GLU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 2.8 31.9 + - - -
247B PHE* 3.0 28.1 + - + +
248B GLN* 3.1 15.0 + - - +
250B ILE* 1.3 79.2 - - - +
252B ASN* 1.3 64.0 + - - +
253B GLY 3.5 0.3 + - - -
302B ASN* 2.8 30.0 + - - +
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Residues in contact with ASN 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B GLN* 2.8 43.2 + - - +
249B ALA* 3.9 5.9 - - - +
251B GLU* 1.3 79.7 - - - +
253B GLY* 1.3 58.4 + - - +
254B ASP* 3.4 5.5 + - + +
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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