Contacts of the helix formed by residues 238 - 249 (chain A) in PDB entry 2H6D
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A GLU* 3.1 30.7 + - - -
236A TYR 4.1 1.0 + - - -
237A LEU* 1.3 77.9 - - - +
239A ARG* 1.3 66.2 - - - +
240A SER* 3.1 13.2 + - - +
241A VAL* 2.8 39.1 + - - +
242A ALA* 3.2 19.7 + - - +
267A TRP* 4.2 4.5 - - - -
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Residues in contact with ARG 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASN* 1.3 72.0 - - - +
240A SER* 1.3 66.8 + - - +
242A ALA* 3.2 9.7 + - - +
243A THR* 3.0 23.7 + - - -
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Residues in contact with SER 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASN* 3.1 13.7 + - - +
239A ARG* 1.3 77.2 - - - +
241A VAL* 1.3 61.1 + - - +
243A THR* 2.8 31.2 + - - +
244A LEU 3.3 0.3 + - - -
265A HIS* 3.1 22.4 - - - -
266A GLU* 4.7 6.1 - - - +
267A TRP* 3.7 17.4 + - - +
270A GLN* 5.6 2.2 + - - -
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU* 5.2 1.3 - - - +
204A LEU* 4.5 7.6 - - + -
208A LEU* 3.6 20.9 - - + -
237A LEU* 4.0 26.5 - - + -
238A ASN* 2.8 37.8 + - - +
240A SER* 1.3 73.7 - - - +
242A ALA* 1.3 65.5 + - - +
244A LEU* 3.3 5.5 + - + +
245A LEU* 3.0 24.4 + - + +
267A TRP* 3.4 48.0 - - + +
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ILE* 4.1 39.3 - - + +
238A ASN 3.2 14.4 + - - +
239A ARG* 3.2 15.6 + - - +
241A VAL* 1.3 79.1 - - + +
243A THR* 1.3 56.9 + - - +
245A LEU* 3.3 3.9 + - - +
246A MET* 2.9 39.3 + - - +
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ARG 3.0 12.1 + - - +
240A SER* 2.8 28.3 - - - +
242A ALA* 1.3 74.3 - - - +
244A LEU* 1.3 62.7 + - - +
246A MET* 3.3 17.5 + - - +
247A HIS* 3.0 24.4 + - - +
265A HIS* 2.9 25.7 - - + +
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 4.8 2.2 - - + -
204A LEU* 4.0 15.9 - - + -
240A SER 4.1 0.4 - - - +
241A VAL* 3.3 9.7 + - + +
243A THR* 1.3 80.2 - - - +
245A LEU* 1.3 64.8 + - - +
247A HIS* 3.3 9.4 + - + +
248A MET* 3.0 36.8 + - + +
262A ILE* 4.0 35.7 - - + -
265A HIS* 3.6 38.1 - - + +
267A TRP* 3.7 31.4 - - + -
268A PHE* 4.3 12.3 - - + -
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLY* 3.6 27.1 - - - +
204A LEU* 3.7 24.5 - - + -
205A TYR* 3.8 25.1 - - + +
208A LEU* 4.4 9.9 - - + -
231A PHE* 4.0 13.0 - - + -
233A ILE* 4.0 21.5 - - + -
237A LEU* 4.3 16.2 - - + -
241A VAL 3.0 21.3 + - - +
242A ALA 3.6 4.0 - - - +
244A LEU* 1.3 77.4 - - - +
246A MET* 1.3 56.0 + - - +
248A MET* 3.2 4.7 + - - +
249A LEU* 2.9 38.8 + - + +
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Residues in contact with MET 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PHE* 3.9 24.6 - - + -
233A ILE* 5.8 5.2 - - + -
242A ALA* 2.9 26.6 + - - +
243A THR* 3.5 16.6 - - - +
244A LEU 3.3 0.2 - - - -
245A LEU* 1.3 76.6 - - - +
247A HIS* 1.3 60.9 + - - +
249A LEU 3.4 1.7 + - - -
250A GLN* 3.1 35.2 + - - +
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Residues in contact with HIS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A THR 3.0 16.3 + - - +
244A LEU* 3.7 8.7 - - + +
246A MET* 1.3 75.4 - - - +
248A MET* 1.3 62.1 + - - +
250A GLN* 3.4 17.7 + - - +
255A LYS 3.3 23.5 + - - -
256A ARG* 3.5 3.6 - - - -
257A ALA* 3.0 45.5 + - + -
261A ASP* 3.8 25.3 + - + -
265A HIS* 6.1 5.4 - + + -
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Residues in contact with MET 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 3.6 31.6 - - + -
197A ILE* 3.5 17.3 - - + +
198A TRP* 3.7 11.8 + - - -
200A CYS* 3.6 7.6 - - + -
201A GLY* 3.3 37.2 - - - +
204A LEU* 4.4 7.0 - - - -
244A LEU* 3.0 34.7 + - + +
245A LEU* 3.8 4.7 - - - +
247A HIS* 1.3 76.2 - - - +
249A LEU* 1.3 58.6 + - - +
250A GLN 3.3 0.9 - - - -
256A ARG* 3.2 24.4 - - - +
257A ALA* 4.0 7.2 - - + -
262A ILE* 3.7 29.4 - - + -
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Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TRP* 3.5 53.4 + - + +
201A GLY* 3.9 15.9 - - - +
202A VAL* 3.8 16.2 - - + +
205A TYR* 5.0 1.1 - - + -
213A PRO* 4.4 16.8 - - + -
214A PHE* 4.3 7.6 - - + -
229A GLY* 4.9 8.0 - - - +
231A PHE* 3.8 43.7 - - + -
245A LEU* 2.9 21.0 + - + +
246A MET 3.4 3.1 + - - +
248A MET* 1.3 76.8 - - - +
250A GLN* 1.3 65.7 + - - +
251A VAL* 3.2 9.5 + - - +
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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