Contacts of the helix formed by residues 240 - 249 (chain A) in PDB entry 6T2C
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 ALA 3.8 1.4 - - - -
239A ASN* 1.3 79.7 - - - +
241A ASN* 1.3 63.1 + - - +
242A ILE 3.3 3.1 + - - -
243A GLU* 3.7 20.7 + - - +
244A ALA* 3.8 9.9 + - - +
90B GLU* 3.9 15.2 + - - -
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Residues in contact with ASN 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 PHE* 3.9 15.4 - - - -
238A ALA* 3.8 16.2 - - - +
239A ASN* 3.9 9.5 + - - +
240A GLY* 1.3 72.2 - - - +
242A ILE* 1.3 59.4 + - - +
243A GLU 3.3 0.2 - - - -
244A ALA* 3.2 9.0 + - - +
245A LYS* 3.0 33.4 + - - +
86B ASP* 3.9 38.2 + - + +
87B CYS* 4.9 2.9 - - - -
90B GLU* 2.8 24.1 + - - +
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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 3.3 0.4 - - - -
241A ASN* 1.3 78.1 - - - +
243A GLU* 1.3 63.5 + - + +
245A LYS* 3.3 5.1 + - - +
246A LEU* 2.9 54.6 + - + +
87B CYS* 4.3 19.5 - - + +
90B GLU* 3.4 36.6 - - + +
91B LEU* 3.8 30.3 - - + -
426B LEU* 4.3 16.4 - - + -
465B HIS* 5.6 0.9 - - + +
469B THR* 4.4 12.8 - - + +
472B LEU* 4.1 10.5 - - + -
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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* 3.7 16.1 + - - +
241A ASN 3.3 0.6 - - - -
242A ILE* 1.3 86.0 - - + +
244A ALA* 1.3 56.5 + - - +
246A LEU* 4.1 5.3 - - - +
247A GLY* 2.9 26.2 + - - -
432B LEU* 6.0 1.2 - - - +
434B ARG* 3.7 21.8 + - - -
465B HIS* 4.3 16.7 + - - -
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Residues in contact with ALA 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 3.8 5.7 + - - +
241A ASN* 3.2 14.3 + - - +
243A GLU* 1.3 79.2 - - - +
245A LYS* 1.3 64.0 + - + +
247A GLY* 3.5 1.7 + - - -
248A ALA* 3.0 29.1 + - - +
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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 ASN* 3.0 18.4 + - - +
242A ILE 3.3 0.9 + - - +
244A ALA* 1.3 82.8 - - + +
246A LEU* 1.3 54.1 + - - +
248A ALA* 3.5 4.5 - - + +
249A MET* 2.7 37.5 + - - +
70B ASP* 5.8 0.2 + - - -
73B LEU* 4.6 13.9 - - + +
84B GLN* 3.5 33.5 + - + +
86B ASP* 2.7 30.6 + - - -
87B CYS* 3.7 14.1 - - - -
472B LEU* 3.7 26.2 - - + -
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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 30.2 + - + +
243A GLU* 4.1 7.0 - - - +
245A LYS* 1.3 75.5 - - - +
247A GLY* 1.3 58.4 + - - +
249A MET* 4.0 9.2 + - + +
465B HIS* 3.5 37.2 - - + +
468B ARG* 3.1 78.3 + - + +
469B THR* 3.6 15.0 - - - +
472B LEU* 3.8 13.7 - - + -
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Residues in contact with GLY 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 17.7 + - - -
244A ALA* 3.8 2.0 - - - -
246A LEU* 1.3 76.2 - - - +
248A ALA* 1.3 60.2 + - - +
249A MET 4.3 3.8 - - - +
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Residues in contact with ALA 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 ALA 3.0 19.1 + - - +
245A LYS* 3.1 5.8 + - + +
247A GLY* 1.3 76.2 - - - +
249A MET* 1.3 64.7 + - - +
250A SER* 3.7 1.4 + - - -
73B LEU* 4.3 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 2.7 16.3 + - - +
246A LEU* 4.0 17.1 - - + +
247A GLY 3.5 4.2 - - - +
248A ALA* 1.3 75.9 - - - +
250A SER* 1.3 69.1 + - - +
251A GLU* 5.5 0.5 - - - +
253A VAL* 4.0 29.4 - - - -
73B LEU* 4.3 19.5 - - + +
74B PRO* 3.8 23.8 - - + +
468B ARG* 3.4 48.8 + - + +
471B LYS* 4.3 6.3 - - + -
472B LEU* 3.7 26.0 - - + -
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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