Contacts of the helix formed by residues 235 - 246 (chain A) in PDB entry 3EQ6
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.4 27.8 - - + +
45A ASN* 3.7 16.4 - - - -
46A PHE* 5.2 1.7 + - - +
127A ILE* 3.9 19.2 + - + -
130A GLY* 3.1 33.8 + - - -
131A LEU 3.9 5.5 + - - -
210A THR* 3.3 33.8 - - + +
211A GLY 3.5 16.4 - - - +
212A SER 4.8 0.2 - - - -
214A GLU* 3.1 31.7 + - + -
215A ALA 3.2 22.5 + - - -
216A SER* 3.5 22.4 - - - -
234A SER* 1.3 74.3 - - - +
236A SER* 1.3 57.2 + - - +
238A LEU* 5.6 0.4 - - - -
239A GLY* 3.0 25.6 + - - -
274A MET* 5.6 0.5 - - - +
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Residues in contact with SER 236 (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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38A GLN* 4.5 7.4 + - - -
40A VAL* 4.6 6.1 - - - -
44A PHE* 4.3 4.2 - - - -
212A SER* 2.8 36.6 + - - -
213A GLN* 3.8 9.4 + - - -
234A SER* 3.0 6.9 + - - -
235A TYR* 1.3 76.5 - - - +
237A SER* 1.3 60.2 + - - +
238A LEU 3.1 2.0 - - - -
240A LEU* 3.0 29.6 + - - +
241A LYS* 3.0 28.8 + - - +
420A ILE* 3.9 5.4 - - - +
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Residues in contact with SER 237 (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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38A GLN* 6.1 0.7 - - - -
233A HIS* 2.8 26.5 + - - +
234A SER* 2.7 43.2 + - - -
236A SER* 1.3 73.9 + - - +
238A LEU* 1.3 58.0 + - - +
241A LYS* 3.1 19.8 - - - +
270A LEU* 5.4 1.2 - - - +
418A ARG* 5.6 0.9 - - - -
421A GLY* 3.3 22.9 - - - +
422A ILE 3.3 25.3 + - - -
423A PHE* 4.3 0.4 - - - -
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Residues in contact with LEU 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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133A PHE* 4.2 13.9 - - + -
216A SER* 4.7 6.5 - - - +
217A ALA* 3.7 30.3 - - + +
219A TYR* 5.1 0.9 - - + -
233A HIS* 3.7 34.5 - - + +
234A SER 3.3 10.0 + - - +
235A TYR* 4.7 0.4 - - - +
236A SER 3.1 0.9 - - - -
237A SER* 1.3 77.7 - - - +
239A GLY* 1.3 59.8 + - - +
241A LYS* 3.6 1.4 + - - +
242A ALA* 2.9 32.2 + - - +
266A ILE* 4.2 7.4 - - + -
269A ILE* 4.1 15.9 - - + -
270A LEU* 4.0 23.8 - - + +
274A MET* 3.6 19.4 - - + +
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Residues in contact with GLY 239 (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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44A PHE* 3.3 16.4 - - - -
46A PHE* 3.8 14.7 - - - -
235A TYR 3.0 14.7 + - - -
238A LEU* 1.3 77.9 - - - +
240A LEU* 1.3 60.8 + - - +
242A ALA* 4.0 0.7 - - - -
243A LYS* 3.1 26.2 + - - +
274A MET* 3.8 17.2 - - - +
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Residues in contact with LEU 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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40A VAL* 4.2 7.9 - - + -
41A PRO* 3.9 32.1 - - + -
44A PHE* 3.2 29.5 - - + -
235A TYR 3.8 0.6 + - - -
236A SER* 3.0 22.2 + - - +
239A GLY* 1.3 72.1 - - - +
241A LYS* 1.3 65.8 + - - +
243A LYS* 3.1 22.1 + - + +
244A MET* 3.0 45.8 + - + +
420A ILE* 4.1 20.6 - - + -
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Residues in contact with LYS 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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236A SER 3.0 6.4 + - - +
237A SER 3.1 26.5 - - - +
238A LEU* 3.8 1.8 - - - +
239A GLY 3.3 0.2 - - - -
240A LEU* 1.3 76.4 - - - +
242A ALA* 1.3 59.6 + - - +
244A MET* 3.1 5.7 + - - -
245A ASP* 2.6 56.2 + - - +
270A LEU* 5.8 5.2 - - + -
366A THR 4.4 1.1 + - - +
367A GLY* 5.1 1.1 - - - -
368A LEU* 2.6 38.3 + - - +
387A ALA* 4.1 6.9 - - - +
389A CYS* 4.2 11.4 - - - -
390A TYR* 3.8 25.5 + - - -
420A ILE* 3.7 20.8 - - + +
421A GLY* 3.7 11.7 - - - +
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Residues in contact with ALA 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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46A PHE* 5.0 0.4 - - + -
238A LEU 2.9 20.6 + - - +
239A GLY 4.0 2.0 - - - +
241A LYS* 1.3 72.6 - - - +
243A LYS* 1.3 67.9 + - - +
245A ASP* 3.7 6.1 - - - +
246A ALA* 2.8 27.4 + - - +
270A LEU* 4.6 13.5 - - + +
274A MET* 3.5 36.1 - - + -
275A GLU* 4.6 2.5 - - + +
278A ALA* 4.7 2.5 - - - -
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Residues in contact with LYS 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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44A PHE* 4.7 5.8 - - + -
46A PHE* 5.2 0.6 - - + -
49A ASP 5.4 4.0 - - - -
50A VAL* 4.2 23.6 - - + -
239A GLY 3.1 14.8 + - - +
240A LEU* 3.1 27.3 + - + +
242A ALA* 1.3 79.5 - - - +
244A MET* 1.3 63.8 + - + +
246A ALA* 3.4 13.9 - - - +
278A ALA* 4.1 20.3 - - + +
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Residues in contact with MET 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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240A LEU* 3.0 48.2 + - + +
241A LYS 3.1 7.4 + - - +
243A LYS* 1.3 81.3 - - + +
245A ASP* 1.3 63.1 + - - +
246A ALA 3.3 2.2 - - - +
388A SER* 4.1 15.2 + - - +
389A CYS* 4.1 27.6 - - - -
420A ILE* 4.3 16.6 - - + -
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Residues in contact with ASP 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 LYS* 2.6 55.8 + - - +
242A ALA* 4.1 5.6 - - - +
244A MET* 1.3 78.3 - - - +
246A ALA* 1.3 68.2 + - - +
248A TRP* 3.0 38.3 + - + +
275A GLU* 4.1 2.0 - - - +
368A LEU* 3.8 13.2 - - + +
371A MET* 3.8 15.3 - - + +
387A ALA* 4.0 8.5 - - - +
388A SER* 4.4 8.8 + - - -
389A CYS* 5.3 0.5 + - - -
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Residues in contact with ALA 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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242A ALA 2.8 17.8 + - - +
243A LYS 3.4 12.8 - - - +
244A MET 3.3 3.3 - - - +
245A ASP* 1.3 79.1 - - - +
247A GLY* 1.3 57.8 + - - +
275A GLU* 3.2 15.9 + - - +
278A ALA* 3.7 22.7 - - + -
279A LEU* 3.9 22.2 - - + +
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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