Contacts of the helix formed by residues 237 - 246 (chain A) in PDB entry 5W5T
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 ASP 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ASP* 3.5 7.4 - - - +
229A THR* 4.4 2.8 - - - +
230A SER* 2.9 29.1 + - - +
231A SER* 2.6 34.8 + - - -
232A ARG 3.0 4.9 + - - -
233A ASP* 2.8 31.7 + - - +
236A LYS* 1.3 85.1 - - - +
238A ILE* 1.3 70.3 + - - +
239A ILE 3.5 0.2 - - - -
240A PRO* 3.6 0.2 - - - +
241A TYR* 3.3 23.2 + - - +
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Residues in contact with ILE 238 (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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112A ALA* 3.7 19.1 - - + -
212A PHE* 4.4 15.0 - - + -
217A LEU* 5.1 0.7 - - + -
220A ALA* 3.6 31.0 - - + +
221A LEU* 4.0 9.9 - - + -
224A ASP* 3.8 21.3 - - + +
233A ASP 3.0 16.5 + - - +
234A PHE* 3.7 29.8 - - + +
237A ASP* 1.3 75.0 - - - +
239A ILE* 1.3 66.3 + - + +
241A TYR* 3.3 4.5 - - - +
242A ILE* 3.1 37.1 + - + +
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.5 34.3 - - + -
159A ILE* 3.7 21.3 - - + -
175A MET* 3.9 13.7 - - + -
186A PHE* 5.1 1.8 - - + -
210A TYR* 3.9 31.9 - - + +
212A PHE* 4.3 11.4 - - + -
234A PHE* 2.8 28.1 + - + +
235A GLY 4.3 4.3 - - - +
238A ILE* 1.3 76.5 - - + +
240A PRO* 1.3 64.6 - - + +
242A ILE* 2.9 7.6 + - + +
243A VAL* 2.7 42.1 + - + +
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Residues in contact with PRO 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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186A PHE* 4.0 20.0 - - + +
235A GLY 3.3 24.9 - - - +
236A LYS* 3.0 31.4 - - - +
237A ASP 3.6 2.9 - - - +
239A ILE* 1.3 89.7 - - + +
241A TYR* 1.3 51.2 + - - +
243A VAL* 3.0 11.8 + - + +
244A GLU* 2.8 37.9 + - - +
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Residues in contact with TYR 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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223A ARG* 3.3 47.4 + - - -
237A ASP 3.3 18.8 + - - +
238A ILE* 3.3 5.8 + - - +
240A PRO* 1.3 78.4 - - - +
242A ILE* 1.3 57.9 + - + +
244A GLU* 3.1 1.9 + - - -
245A HIS* 2.7 84.7 + + + +
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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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156A ASP* 3.9 21.5 - - + +
157A VAL* 3.4 34.1 - - + -
212A PHE* 5.1 4.5 - - + -
220A ALA* 4.9 9.2 - - + -
223A ARG* 4.7 9.6 - - - +
238A ILE* 3.1 29.7 + - + +
239A ILE* 2.9 11.2 + - + +
241A TYR* 1.3 87.3 - - + +
243A VAL* 1.3 59.3 + - - +
246A GLY* 2.6 40.0 + - - +
247A LYS 4.1 8.5 - - - +
248A ALA* 4.5 0.2 - - + -
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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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175A MET* 5.0 0.2 - - - -
183A ILE* 3.4 34.8 - - + +
184A ILE* 3.7 6.9 - - - +
185A ASP* 3.7 28.5 - - - +
186A PHE* 4.6 6.5 - - + +
239A ILE* 2.7 41.3 + - + +
240A PRO* 3.0 10.1 + - + +
242A ILE* 1.3 74.4 - - - +
244A GLU* 1.3 61.4 + - + +
246A GLY 3.8 8.4 - - - +
248A ALA* 4.0 20.2 - - + -
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Residues in contact with GLU 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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184A ILE 5.1 6.1 - - - +
185A ASP* 5.6 1.6 - - - +
240A PRO 2.8 15.8 + - - +
241A TYR* 3.8 2.9 - - - +
243A VAL* 1.3 79.7 - - + +
245A HIS* 1.3 82.6 + - + +
246A GLY 3.7 0.2 - - - -
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Residues in contact with HIS 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 TYR* 2.7 75.6 + + + +
242A ILE* 4.9 0.2 - - - -
244A GLU* 1.3 97.3 - - + +
246A GLY* 1.3 56.5 + - - +
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Residues in contact with GLY 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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156A ASP* 3.7 9.4 - - - -
183A ILE 5.8 0.2 - - - +
242A ILE* 2.6 30.1 + - - +
243A VAL 3.8 9.0 - - - +
244A GLU 3.7 0.2 - - - -
245A HIS* 1.3 74.9 - - - +
247A LYS* 1.3 58.4 + - - -
248A ALA 3.8 1.6 + - - -
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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