Contacts of the helix formed by residues 249 - 255 (chain A) in PDB entry 1W1J
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 TYR 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A TRP* 5.4 1.3 + + - -
195A MET* 5.7 8.2 - - + -
197A HIS* 3.3 21.5 + - - -
213A GLY* 5.7 0.4 - - - -
243A PRO* 3.4 34.6 - - + +
244A TYR* 4.0 32.8 - + - +
247A GLY 3.5 0.6 + - - -
248A PRO* 1.3 69.5 - - - +
250A ILE* 1.3 61.0 + - - +
251A ASP* 3.0 41.4 + - + -
252A GLY 4.4 4.9 + - - -
183B ARG* 4.0 17.0 - - - +
194B TRP* 4.4 18.2 - + - -
195B MET* 5.8 4.1 - - + +
249B TYR* 5.6 2.5 - + - +
252B GLY* 2.7 40.0 + - - +
253B LEU* 3.8 0.5 + - - +
255B SER* 3.8 3.6 + - - +
524B PHE* 5.6 0.4 - - - -
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Residues in contact with ILE 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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210A LEU* 4.3 9.6 - - + -
212A THR* 4.5 1.6 - - + -
248A PRO 3.3 11.1 + - - +
249A TYR* 1.3 71.7 - - - +
251A ASP* 1.3 62.9 + - - +
252A GLY 3.1 3.1 - - - -
253A LEU* 2.7 45.1 + - + +
254A PHE* 4.0 17.3 - - + -
253B LEU* 4.1 18.6 - - + -
524B PHE* 3.6 28.9 - - + -
527B PHE* 3.4 37.9 - - + -
528B ASN* 3.7 26.5 - - - +
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Residues in contact with ASP 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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194A TRP* 3.4 15.5 - - + -
197A HIS* 3.1 34.3 - - + +
199A GLY 4.6 3.1 + - - -
200A MET* 4.0 2.9 - - - +
212A THR* 3.3 33.3 + - - -
213A GLY 4.1 5.2 + - - -
243A PRO 4.0 6.4 - - - +
249A TYR* 3.0 37.3 - - + -
250A ILE* 1.3 77.8 + - - +
252A GLY* 1.3 61.6 + - - +
254A PHE* 3.1 25.0 + - - +
524B PHE* 5.5 0.5 - - - -
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Residues in contact with GLY 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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194A TRP* 3.8 15.2 - - - -
249A TYR* 4.4 6.3 + - - -
250A ILE 2.8 1.6 + - - -
251A ASP* 1.3 74.0 - - - +
253A LEU* 1.3 56.9 + - - +
254A PHE 2.9 10.5 + - - -
255A SER* 3.1 14.7 + - - -
249B TYR* 3.0 46.3 + - - -
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Residues in contact with LEU 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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250A ILE* 2.7 22.9 + - + +
252A GLY* 1.3 68.9 - - - -
254A PHE* 1.3 57.4 + - + -
255A SER 3.5 0.4 - - - -
257A SER* 2.6 28.2 + - - -
259A MET* 3.5 38.9 - - + +
528A ASN* 5.2 0.4 - - - +
531A LEU* 3.8 19.1 - - + -
248B PRO* 4.9 5.2 - - + -
249B TYR 3.7 7.1 + - - +
250B ILE* 4.3 9.9 - - + -
253B LEU* 3.7 25.8 - - + -
527B PHE* 3.8 16.6 - - + -
531B LEU* 3.5 32.5 - - + -
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Residues in contact with PHE 254 (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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181A VAL* 3.8 19.1 - - - +
194A TRP* 4.9 2.0 - - - -
200A MET* 4.1 21.8 - - + -
202A VAL* 3.8 35.7 - - + -
204A LEU* 4.0 17.3 - - + -
210A LEU* 5.0 2.7 - - + -
212A THR* 4.2 7.4 - - + -
250A ILE* 4.0 28.7 - - + -
251A ASP* 3.1 16.9 + - - +
252A GLY 2.9 1.0 - - - -
253A LEU* 1.3 84.0 - - + +
255A SER* 1.3 60.3 + - - +
256A GLN 4.0 1.0 + - - -
257A SER* 3.6 9.2 + - - +
259A MET* 3.1 36.8 - - + -
260A GLY* 4.4 2.7 - - - +
262A VAL* 4.6 7.0 - - + +
1561A FAD 5.6 2.1 + - - -
527B PHE* 4.1 20.2 - + - -
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Residues in contact with SER 255 (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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181A VAL* 3.3 13.0 - - - +
183A ARG* 2.5 52.0 + - - -
194A TRP* 4.0 22.9 - - - -
251A ASP 4.1 0.4 + - - -
252A GLY* 3.1 15.0 + - - -
254A PHE* 1.3 78.4 - - - +
256A GLN* 1.3 67.5 + - - +
257A SER 3.1 2.6 + - - -
248B PRO* 3.3 12.8 - - - +
249B TYR* 3.7 4.2 - - - +
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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