Contacts of the helix formed by residues 240 - 249 (chain A) in PDB entry 6QNW
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 GLY 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A PRO 3.2 5.9 + - - -
239A ASN* 1.3 80.9 - - - +
241A TYR* 1.3 67.3 + - - +
242A ILE* 3.2 2.8 + - - -
243A GLU* 3.4 18.1 + - - +
244A GLY* 3.5 8.5 + - - -
90B GLU* 3.4 10.4 + - - -
94B PHE* 5.8 1.6 - - - -
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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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232A TYR* 5.3 2.0 - + - -
236A PHE* 3.9 18.8 - + - -
237A GLU* 3.1 38.0 + - - +
239A ASN* 3.7 21.5 - - + +
240A GLY* 1.3 79.3 - - - +
242A ILE* 1.3 59.8 + - - +
244A GLY* 3.3 2.9 + - - +
245A LYS* 2.9 37.8 + - + +
86B ASP* 3.5 42.8 - - + +
87B CYS* 5.0 2.0 - - - -
90B GLU* 2.9 17.9 + - - +
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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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240A GLY* 3.2 1.0 - - - -
241A TYR* 1.3 76.8 - - - +
243A GLU* 1.3 57.8 + - - +
245A LYS* 3.3 5.5 + - - +
246A LEU* 2.9 41.9 + - + +
87B CYS* 3.8 39.3 - - + +
90B GLU* 3.8 24.9 - - + +
91B ALA* 5.9 0.2 - - + -
94B PHE* 5.4 2.2 - - + -
423B ILE* 6.2 1.1 - - + -
426B LEU* 4.8 21.1 - - + -
465B ARG* 4.8 11.9 - - - +
469B THR* 4.0 26.7 - - + +
472B LEU* 4.3 8.5 - - + +
473B VAL* 5.8 3.1 - - + -
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Residues in contact with GLU 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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240A GLY* 3.4 12.4 + - - +
241A TYR 3.3 0.2 - - - -
242A ILE* 1.3 79.7 - - - +
244A GLY* 1.3 57.6 - - - +
246A LEU* 3.3 15.0 + - - +
247A SER* 2.9 29.9 + - - -
465B ARG* 3.8 30.3 + - - -
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Residues in contact with GLY 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 GLY 3.5 6.9 + - - -
241A TYR* 3.3 6.1 + - - -
242A ILE 3.3 0.4 - - - -
243A GLU* 1.3 79.6 - - - +
245A LYS* 1.3 59.5 + - - +
247A SER* 3.2 8.0 + - - -
248A GLN* 2.9 34.7 + - - +
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Residues in contact with LYS 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* 2.9 24.7 + - + +
242A ILE 3.8 0.2 - - - +
244A GLY* 1.3 77.8 - - - +
246A LEU* 1.3 57.9 + - - +
248A GLN* 3.4 19.7 + - - +
249A MET* 3.0 29.6 + - - +
73B LEU* 4.0 8.8 - - + +
84B GLN* 3.4 28.0 + - + +
86B ASP* 2.9 37.9 + - - +
87B CYS* 3.9 11.6 - - - -
472B LEU* 3.8 29.6 - - + -
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Residues in contact with LEU 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 ILE* 2.9 34.7 + - + +
243A GLU* 3.6 24.0 - - - +
244A GLY 3.2 0.2 - - - -
245A LYS* 1.3 75.0 - - - +
247A SER* 1.3 63.9 + - - +
249A MET* 3.3 8.1 + - + +
251A LYS* 5.0 0.9 - - - -
465B ARG* 4.2 20.6 - - + +
468B ARG* 2.5 66.7 + - + +
469B THR* 4.2 11.7 - - + -
472B LEU* 4.1 18.6 - - + -
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Residues in contact with SER 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 GLU* 2.9 18.7 + - - -
244A GLY* 3.6 7.2 - - - -
246A LEU* 1.3 76.3 - - - +
248A GLN* 1.3 60.8 + - - +
249A MET 3.8 3.1 + - - +
251A LYS* 5.1 8.8 - - - +
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Residues in contact with GLN 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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244A GLY 2.9 19.5 + - - +
245A LYS* 3.8 22.8 - - - +
246A LEU 3.1 0.4 - - - -
247A SER* 1.3 78.4 - - - +
249A MET* 1.3 63.6 + - - +
250A SER* 3.7 1.2 + - - -
73B LEU* 3.9 18.2 - - + +
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Residues in contact with MET 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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245A LYS 3.0 13.7 + - - +
246A LEU* 3.3 9.8 + - + +
247A SER 4.2 2.8 - - - +
248A GLN* 1.3 79.8 - - - +
250A SER* 1.3 72.3 + - - +
251A LYS* 3.7 8.3 + - - +
253A VAL* 3.9 30.7 - - + -
73B LEU* 3.8 11.4 - - + -
74B PRO* 4.0 32.8 - - + +
468B ARG* 3.5 40.7 + - + +
471B LYS* 4.6 3.1 - - + -
472B LEU* 3.7 38.8 - - + +
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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