Contacts of the helix formed by residues 239 - 251 (chain A) in PDB entry 1IN7
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 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A GLU* 3.4 27.6 + - - +
204A ALA* 3.6 8.5 - - - -
237A ARG* 3.4 8.2 + - - +
238A ILE* 1.3 73.3 - - - +
240A THR* 1.3 65.1 + - - +
241A ASP* 3.1 13.8 + - - +
242A ILE* 2.8 43.8 + - - +
243A VAL* 3.2 22.2 + - - +
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Residues in contact with THR 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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201A GLU* 4.6 2.0 + - - +
203A ALA* 4.0 36.1 - - + +
204A ALA* 4.0 1.3 - - - +
207A MET* 3.6 31.4 - - + -
239A ASN* 1.3 72.8 - - - +
241A ASP* 1.3 67.1 + - - +
243A VAL* 3.3 3.4 + - - +
244A LEU* 3.0 33.7 + - - +
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Residues in contact with ASP 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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239A ASN* 3.1 14.0 + - - +
240A THR* 1.3 80.7 + - - +
242A ILE* 1.3 71.0 + - - +
244A LEU* 3.3 10.9 + - - +
245A LYS* 3.0 42.8 + - - +
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Residues in contact with ILE 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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226A VAL* 3.8 20.2 - - + +
229A MET* 3.8 22.3 - - + +
230A LEU* 3.9 9.0 - - + +
233A VAL* 3.4 37.7 - - + -
235A ALA* 4.4 7.2 - - + -
237A ARG 4.5 7.9 - - - +
238A ILE* 4.7 2.5 - - + -
239A ASN* 2.8 38.7 + - - +
241A ASP* 1.3 86.3 - - - +
243A VAL* 1.3 60.1 + - - +
245A LYS* 3.4 8.5 + - + +
246A THR* 2.9 28.4 + - - -
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Residues in contact with VAL 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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204A ALA* 3.8 15.3 - - + +
207A MET* 3.9 21.8 - - + -
208A ILE* 3.7 25.1 - - + -
226A VAL* 4.1 9.2 - - + -
238A ILE* 3.7 20.4 - - + -
239A ASN 3.2 14.6 + - - +
240A THR 3.7 5.8 - - - +
241A ASP 3.3 0.2 - - - -
242A ILE* 1.3 76.0 - - - +
244A LEU* 1.3 58.6 + - - +
246A THR* 3.2 3.3 + - - -
247A MET* 2.9 52.8 + - + +
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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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207A MET* 3.6 29.6 - - + -
211A ARG* 4.2 16.6 - - - +
240A THR* 3.0 30.9 + - - +
241A ASP* 3.6 9.0 - - - +
243A VAL* 1.3 73.4 - - + +
245A LYS* 1.3 66.9 + - + +
247A MET* 3.3 6.8 + - + +
248A GLU* 3.1 36.4 + - + +
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Residues in contact with LYS 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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229A MET* 4.0 21.1 - - + -
233A VAL* 3.2 28.5 - - - +
241A ASP* 3.0 42.1 + - - +
242A ILE* 3.7 10.8 - - + +
244A LEU* 1.3 76.9 - - + +
246A THR* 1.3 63.1 + - - +
248A GLU* 3.4 14.4 + - - +
249A VAL* 3.2 26.9 + - - +
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Residues in contact with THR 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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225A ARG* 3.7 19.5 - - + +
226A VAL* 3.5 26.9 - - + -
229A MET* 3.1 29.2 - - + +
242A ILE 2.9 15.5 + - - -
243A VAL 3.5 7.4 - - - -
244A LEU 3.2 0.2 - - - -
245A LYS* 1.3 74.9 - - - +
247A MET* 1.3 60.1 + - - +
249A VAL* 3.1 5.0 + - + +
250A LEU* 2.9 55.6 + - + +
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Residues in contact with MET 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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208A ILE* 4.4 13.0 - - + -
211A ARG* 3.3 44.9 - - + +
222A LEU* 4.2 23.3 - - + -
226A VAL* 5.0 4.9 - - + -
243A VAL* 2.9 43.6 + - + +
244A LEU* 3.3 8.7 + - + +
246A THR* 1.3 78.0 - - - +
248A GLU* 1.3 58.6 + - + +
250A LEU* 3.3 4.6 + - - +
251A ASN* 2.8 24.8 + - - -
252A ILE* 3.0 47.0 + - + +
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Residues in contact with GLU 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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244A LEU* 3.1 25.8 + - - +
245A LYS* 3.6 14.9 - - - +
247A MET* 1.3 77.4 - - + +
249A VAL* 1.3 62.8 + - + +
251A ASN* 3.3 18.3 + - - +
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Residues in contact with VAL 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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229A MET* 3.9 18.2 - - + -
245A LYS 3.2 14.5 + - - +
246A THR* 3.1 10.2 + - + +
248A GLU* 1.3 79.6 - - + +
250A LEU* 1.3 70.2 + - + +
251A ASN* 3.5 5.0 + - - +
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Residues in contact with LEU 250 (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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222A LEU* 3.6 29.6 - - + -
225A ARG* 3.8 34.5 - - + -
246A THR* 2.9 38.2 + - + +
247A MET* 3.9 3.4 - - - +
249A VAL* 1.3 83.7 - - + +
251A ASN* 1.3 71.2 + - - +
252A ILE* 3.8 19.5 - - + +
258A ASP* 5.5 1.2 - - - +
259A GLU* 4.8 4.9 - - - +
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Residues in contact with ASN 251 (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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247A MET 2.8 8.6 + - - -
248A GLU* 3.3 14.0 + - - +
249A VAL 3.3 8.5 - - - +
250A LEU* 1.3 82.0 - - - +
252A ILE* 1.3 55.8 + - - +
257A LEU 3.7 1.9 - - - +
258A ASP* 3.8 6.1 - - - -
259A GLU* 3.9 26.3 + - + +
262A ARG* 2.8 39.0 + - - +
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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