Contacts of the helix formed by residues 241 - 252 (chain A) in PDB entry 3QLE
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ASN* 1.3 88.3 + - - +
242A MET* 1.3 67.0 + - - +
243A MET* 3.2 14.4 - - + +
244A TYR* 2.9 37.4 + + + +
245A SER* 3.3 8.3 + - - -
265A LYS* 3.6 46.3 + - + +
266A GLU* 3.5 33.0 - - + +
275A HIS* 4.6 8.5 + + - -
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Residues in contact with MET 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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240A ASN 3.6 0.6 + - - -
241A TYR* 1.3 72.4 - - - +
243A MET* 1.3 62.6 + - - +
246A ASP* 2.9 48.6 + - + +
264A PHE* 3.5 41.0 - - + +
266A GLU* 3.0 35.1 + - - +
267A HIS* 4.9 10.5 - - - +
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Residues in contact with MET 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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241A TYR* 4.4 14.4 - - + -
242A MET* 1.3 78.7 - - - +
244A TYR* 1.3 104.4 + - + +
246A ASP* 4.9 1.1 - - - -
247A LYS* 4.8 11.6 + - - +
266A GLU* 4.6 2.3 + - - +
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Residues in contact with TYR 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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213A TRP* 6.4 0.4 - - - -
240A ASN* 3.4 36.3 + - - +
241A TYR* 2.9 20.2 + + + +
243A MET* 1.3 120.6 - - + +
245A SER* 1.3 58.3 + - - +
246A ASP 3.8 0.7 - - - -
247A LYS* 4.7 12.7 - - - +
248A ILE* 4.2 12.6 - - - +
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Residues in contact with SER 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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198A LEU* 4.1 8.2 - - - +
199A GLU* 3.6 11.4 - - - -
238A SER* 2.8 27.7 + - - -
240A ASN* 3.6 8.5 - - - +
241A TYR 3.3 12.2 + - - -
244A TYR* 1.3 78.1 - - - +
246A ASP* 1.3 67.1 + - - +
247A LYS 3.3 2.9 - - - -
248A ILE* 3.2 12.4 + - - +
249A ALA* 3.0 24.3 + - - +
264A PHE* 3.4 10.0 - - - -
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Residues in contact with ASP 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 MET* 2.9 37.1 + - - +
243A MET* 5.3 1.3 - - - -
244A TYR 3.8 0.6 - - - -
245A SER* 1.3 78.0 + - - +
247A LYS* 1.3 57.7 + - + +
249A ALA* 3.5 3.1 + - - +
250A GLU* 3.1 29.1 + - - +
264A PHE* 3.8 23.2 - - + -
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Residues in contact with LYS 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 MET 4.8 10.8 + - - -
244A TYR* 4.7 12.3 - - - +
246A ASP* 1.3 77.4 - - + +
248A ILE* 1.3 74.5 + - + +
250A GLU* 3.3 13.8 + - - +
251A LYS* 3.0 23.9 + - - +
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Residues in contact with ILE 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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198A LEU* 4.1 9.4 - - + -
203A VAL* 4.1 27.4 - - + -
205A SER* 4.2 7.4 - - - +
215A THR* 3.6 28.0 - - + +
244A TYR 4.2 17.9 - - - +
245A SER* 3.2 12.7 + - - +
247A LYS* 1.3 82.7 - - + +
249A ALA* 1.3 61.0 + - - +
251A LYS* 2.8 46.8 - - + +
252A LEU* 3.5 4.3 + - - +
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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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198A LEU* 4.2 12.5 - - + +
236A LEU* 3.9 19.7 - - + +
238A SER* 5.9 0.4 - - - -
245A SER 3.0 17.1 + - - +
246A ASP* 3.6 5.4 - - - +
248A ILE* 1.3 77.1 - - - +
250A GLU* 1.3 62.0 + - - +
252A LEU* 3.2 18.9 + - - +
253A ASP* 3.8 4.7 + - - +
259A VAL* 5.9 0.3 - - - +
262A ASN* 3.7 23.7 - - - +
264A PHE* 4.4 12.6 - - + -
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Residues in contact with GLU 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 ASP* 3.1 20.4 + - - +
247A LYS* 3.6 14.2 - - - +
248A ILE 3.3 0.2 - - - -
249A ALA* 1.3 78.0 - - - +
251A LYS* 1.3 61.2 + - - +
253A ASP 3.0 6.7 + - - +
254A PRO* 3.0 33.5 - - + +
256A HIS* 4.2 24.9 + - + -
262A ASN* 6.2 1.3 - - - +
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Residues in contact with LYS 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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203A VAL* 4.1 11.6 - - - +
215A THR* 4.0 29.9 + - - +
217A LYS* 4.2 23.8 + - + +
222A ASP* 5.3 1.4 - - - +
247A LYS 3.0 13.1 + - - +
248A ILE* 2.8 38.1 + - + +
250A GLU* 1.3 77.2 - - - +
252A LEU* 1.3 72.6 + - + +
254A PRO* 3.2 16.9 - - - +
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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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198A LEU* 3.4 32.8 - - + -
202A LEU* 3.7 24.9 - - + -
203A VAL* 4.1 11.9 - - + -
217A LYS* 3.8 32.5 - - + -
221A ALA* 4.7 8.7 - - + -
222A ASP* 4.1 15.9 - - - +
225A LEU* 3.9 21.7 - - + +
236A LEU* 4.2 9.0 - - + -
248A ILE 3.9 9.4 - - - +
249A ALA 3.2 8.2 + - - +
250A GLU 3.1 1.2 - - - -
251A LYS* 1.3 89.3 - - + +
253A ASP* 1.3 61.5 + - + +
254A PRO* 3.6 2.4 - - - +
258A PHE* 5.2 4.0 - - - -
259A VAL* 5.9 0.2 - - + -
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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