Contacts of the helix formed by residues 246 - 257 (chain A) in PDB entry 3UYT
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A CYS* 6.3 0.7 - - - -
244A TYR 3.2 5.0 + - - -
245A PRO* 1.3 69.8 - - - +
247A GLU* 1.3 75.2 + - - +
248A PHE 3.2 0.4 - - - -
249A ALA* 3.0 21.2 + - - +
250A THR* 3.2 17.2 + - - -
259D ARG* 4.5 21.1 - - - -
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Residues in contact with GLU 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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245A PRO* 2.9 22.4 + - - +
246A SER* 1.3 84.3 + - - +
248A PHE* 1.3 61.4 + - - +
250A THR* 3.3 10.2 + - - -
251A TYR* 3.1 23.6 + - - +
272A LEU* 3.5 39.8 - - + +
273A PHE* 4.0 20.8 - - + -
275A ASN* 5.8 1.2 - - - +
276A LEU* 3.8 31.5 + - + +
279A ARG* 5.2 4.2 + - - -
296C SO4 4.5 11.6 + - - -
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Residues in contact with PHE 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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102A LEU* 4.1 17.7 - - + -
105A VAL* 3.8 16.8 - - + -
106A LEU* 3.5 25.1 - - + -
109A ALA* 5.5 0.2 - - + -
200A GLY 5.8 0.4 - - - -
203A LEU* 4.1 18.2 - - + -
204A MET* 3.6 23.3 - - + +
207A ASN* 3.2 32.8 - - - -
241A CYS* 3.8 6.3 - - + -
244A TYR* 4.6 2.2 - - + -
245A PRO* 3.3 26.8 + - + +
246A SER 3.2 1.4 + - - -
247A GLU* 1.3 76.8 - - + +
249A ALA* 1.3 59.9 + - - +
251A TYR* 3.5 4.5 + - + +
252A LEU* 3.4 26.7 + - - +
273A PHE* 3.5 26.7 - + - -
276A LEU* 4.4 5.8 - - + -
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Residues in contact with ALA 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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237A ILE* 3.3 27.7 - - + +
238A GLU* 4.9 5.6 - - - -
241A CYS* 3.7 17.0 - - + +
246A SER* 3.0 14.1 + - - +
248A PHE* 1.3 76.3 - - - +
250A THR* 1.3 64.7 + - - +
252A LEU 3.5 0.2 + - - -
253A ASN* 3.1 33.4 + - - +
259D ARG* 5.7 9.4 - - + -
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Residues in contact with THR 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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246A SER* 3.2 15.8 + - - -
247A GLU* 3.5 10.8 - - - -
249A ALA* 1.3 80.7 - - - +
251A TYR* 1.3 61.9 + - - +
253A ASN* 3.6 6.6 + - - +
254A PHE* 3.2 21.7 + - - +
268A TYR* 3.3 26.2 - - - +
272A LEU* 3.6 15.9 - - + +
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Residues in contact with TYR 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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113A ILE* 3.8 13.5 - - + -
196A LEU* 3.1 27.6 + - - +
199A LEU* 3.4 20.7 - - + +
200A GLY* 3.3 33.2 - - - -
203A LEU* 5.2 2.2 - - + -
247A GLU 3.1 15.6 + - - +
248A PHE 3.7 4.7 - - - +
249A ALA 3.3 0.4 - - - -
250A THR* 1.3 76.9 - - - +
252A LEU* 1.3 67.7 + - + +
254A PHE* 3.2 15.1 + - - +
255A CYS* 3.3 30.5 + - - -
269A LEU* 3.7 36.7 - - + +
272A LEU* 3.8 8.9 - - + +
273A PHE* 3.7 30.3 - + + -
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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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197A GLU* 4.0 13.6 - - + +
200A GLY* 3.3 45.1 - - - +
201A TYR* 3.8 20.2 - - + +
204A MET* 4.4 3.1 - - + -
237A ILE* 3.8 20.2 - - + -
240A LEU* 3.9 28.3 - - + -
241A CYS* 4.3 11.2 - - - -
248A PHE 3.4 16.3 + - - +
249A ALA 3.5 2.0 + - - +
251A TYR* 1.3 81.3 - - + +
253A ASN* 1.3 63.5 + - - +
255A CYS* 3.2 5.7 + - - +
256A ARG* 3.2 25.2 + - + +
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Residues in contact with ASN 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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237A ILE* 3.3 30.5 - - - +
238A GLU* 5.7 0.6 - - - +
249A ALA* 3.1 26.4 + - - +
250A THR* 3.9 6.6 - - - +
251A TYR 3.3 0.2 - - - -
252A LEU* 1.3 77.3 - - - +
254A PHE* 1.3 61.4 + - - +
256A ARG* 3.6 4.9 + - - +
257A SER* 3.2 26.0 + - - -
256D ARG 4.2 4.9 - - - +
257D SER* 3.6 47.7 + - - +
259D ARG* 6.1 1.8 - - - +
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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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250A THR 3.2 11.3 + - - +
251A TYR 3.2 10.0 + - - +
252A LEU 3.1 0.4 - - - -
253A ASN* 1.3 79.6 - - - +
255A CYS* 1.3 65.8 + - - +
257A SER* 3.3 14.4 + - - -
258A LEU* 3.6 32.0 + - + +
264A PRO* 4.9 0.4 - - + -
265A ASP* 3.6 42.6 - - + -
268A TYR* 3.7 24.5 - + + +
269A LEU* 3.6 31.2 - - + -
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Residues in contact with CYS 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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193A ARG* 4.5 7.1 - - - +
196A LEU* 3.6 36.8 - - - -
197A GLU* 3.9 25.9 - - + +
251A TYR* 3.3 33.6 + - - -
252A LEU* 3.2 10.1 + - - +
254A PHE* 1.3 80.7 - - - +
256A ARG* 1.3 61.7 + - - +
257A SER 3.2 1.4 + - - -
258A LEU* 3.2 29.8 + - + +
269A LEU* 4.9 4.7 - - - -
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Residues in contact with ARG 256 (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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182A ILE* 3.4 53.2 - - + +
183A ASN* 3.8 27.4 + - - +
186A LEU* 6.3 0.2 - - - +
197A GLU* 3.3 26.6 + - + +
201A TYR* 4.8 3.4 - - - +
237A ILE* 4.9 10.3 - - + -
252A LEU* 3.2 15.3 + - + +
253A ASN* 4.1 7.6 - - - +
254A PHE 3.4 0.4 - - - -
255A CYS* 1.3 77.3 - - - +
257A SER* 1.3 60.0 + - - +
258A LEU 3.4 4.0 + - - +
233D MET 5.8 1.8 + - - -
253D ASN* 4.4 3.2 - - - +
256D ARG* 4.9 13.5 - - - +
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Residues in contact with SER 257 (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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253A ASN 3.2 13.0 + - - -
254A PHE* 3.3 10.9 + - - -
255A CYS 3.2 1.4 - - - -
256A ARG* 1.3 77.3 - - - +
258A LEU* 1.3 64.3 + - - +
259A ARG* 3.7 6.6 + - - +
262A ASP* 5.0 0.2 - - - +
253D ASN* 3.4 45.7 + - - +
257D SER* 4.1 9.9 + - - -
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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