Contacts of the helix formed by residues 242 - 253 (chain A) in PDB entry 1P9W
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 THR 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A GLY 3.5 2.7 + - - +
241A MSE 1.3 74.9 - - - +
243A ALA* 1.3 66.2 + - - +
244A HIS* 3.2 7.5 + - - +
245A ASN* 3.3 25.5 + - - +
246A HIS* 2.9 22.1 + - - +
481A ASP* 3.0 32.1 + - - +
484A ASP* 5.4 8.1 - - + +
485A LYS* 5.3 7.0 - - + +
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Residues in contact with ALA 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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242A THR* 1.3 73.3 - - - +
244A HIS* 1.3 60.9 + - - +
246A HIS* 3.6 7.9 - - - +
247A ASP* 3.1 24.9 + - - +
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Residues in contact with HIS 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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242A THR* 3.2 8.5 + - - +
243A ALA* 1.3 76.2 - - - +
245A ASN* 1.3 70.4 + - - +
247A ASP* 3.2 9.6 + - - +
248A ASN* 3.0 53.6 + - - -
474A THR 5.0 11.3 + - - -
476A PRO* 5.7 8.5 - - + -
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Residues in contact with ASN 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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241A MSE 3.4 21.6 - - + +
242A THR* 3.3 23.8 + - - +
244A HIS* 1.3 83.7 - - - +
246A HIS* 1.3 58.0 + - - +
248A ASN* 4.8 1.1 + - - +
249A PHE* 2.9 34.5 + - - +
445A HIS* 3.9 25.3 + - + +
447A LEU* 3.7 30.0 + - + +
476A PRO* 5.7 4.5 - - - +
481A ASP* 3.9 16.4 + - - -
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Residues in contact with HIS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.8 25.2 + - + +
237A HIS* 3.6 33.9 - - + +
241A MSE 4.0 21.2 + - + +
242A THR 2.9 18.8 + - - +
243A ALA* 3.6 7.6 - - - +
245A ASN* 1.3 76.5 - - - +
247A ASP* 1.3 57.8 + - - +
249A PHE* 3.9 0.9 - - + +
250A ARG* 3.0 72.0 + - + +
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Residues in contact with ASP 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 ALA 3.1 14.8 + - - +
244A HIS* 3.5 9.4 + - - +
246A HIS* 1.3 83.0 - - - +
248A ASN* 1.3 61.9 + - - +
250A ARG* 3.4 8.1 + - - +
251A ARG* 2.9 51.0 + - - +
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Residues in contact with ASN 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 HIS* 3.0 48.1 + - - +
245A ASN* 5.1 1.4 + - - +
247A ASP* 1.3 83.1 - - - +
249A PHE* 1.3 61.1 + - - +
250A ARG 3.4 0.2 - - - -
251A ARG* 3.5 15.4 + - - +
252A LEU* 3.0 27.4 + - - +
447A LEU* 3.6 20.1 - - + +
449A LEU* 4.0 26.8 - - + +
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Residues in contact with PHE 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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236A LEU* 3.7 36.8 - - + -
241A MSE 3.3 18.4 - - + -
245A ASN 2.9 18.9 + - - +
246A HIS* 4.1 2.5 - + - +
248A ASN* 1.3 74.1 - - - +
250A ARG* 1.3 66.0 + - - +
252A LEU* 3.2 7.7 + - + +
253A ILE* 3.1 47.7 + - + +
260A ILE* 4.2 21.3 - - + -
262A VAL* 4.7 3.8 - - + -
273A THR* 4.6 10.1 - - - -
277A GLY* 4.8 5.6 - - - -
355A MSE 4.2 12.6 - - + -
388A LEU* 3.6 31.4 - - + -
447A LEU* 3.6 17.2 - - + +
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Residues in contact with ARG 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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236A LEU* 4.1 20.0 - - + -
246A HIS* 3.0 53.7 + - + +
247A ASP* 3.7 8.1 - - - +
248A ASN 3.4 0.2 - - - -
249A PHE* 1.3 78.4 - - - +
251A ARG* 1.3 60.5 + - + +
253A ILE* 3.6 12.9 - - - +
254A LYS* 3.4 33.4 + - - +
280A GLU* 3.2 28.9 + - - +
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Residues in contact with ARG 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 ASP* 2.9 40.9 + - - +
248A ASN* 3.8 15.9 + - - +
249A PHE 3.2 0.2 - - - -
250A ARG* 1.3 78.3 - - + +
252A LEU* 1.3 63.6 + - - +
254A LYS* 3.7 13.6 + - - +
255A ARG* 3.7 14.9 + - - +
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Residues in contact with LEU 252 (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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248A ASN 3.0 17.1 + - - +
249A PHE* 3.2 11.2 + - + +
251A ARG* 1.3 74.0 - - - +
253A ILE* 1.3 58.3 + - - +
254A LYS 3.1 4.5 - - - -
255A ARG* 3.1 36.9 + - + +
260A ILE* 3.7 38.5 - - + +
353A LEU* 4.3 0.3 - - - +
385A LEU* 4.2 24.6 - - + +
386A GLY* 3.9 22.7 - - - +
447A LEU* 4.6 10.5 - - + -
449A LEU* 3.8 26.2 - - + -
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Residues in contact with ILE 253 (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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236A LEU* 3.9 16.4 - - + -
249A PHE* 3.1 32.0 + - + +
250A ARG* 3.6 9.2 - - - +
252A LEU* 1.3 74.2 - - + +
254A LYS* 1.3 60.4 + - + +
255A ARG 3.3 1.8 - - - +
260A ILE* 3.9 15.7 - - + -
277A GLY* 3.8 17.5 - - - +
280A GLU* 3.8 29.2 - - + -
281A LEU* 3.3 26.5 - - + +
286A ARG* 5.5 0.2 + - - -
329A VAL* 5.6 0.2 - - - +
353A LEU* 3.5 18.3 - - - +
355A MSE 3.8 32.1 - - + -
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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