Contacts of the helix formed by residues 245 - 253 (chain C) in PDB entry 6B5G
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 THR 245 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLU* 5.2 3.4 + - - +
72C ALA 4.4 3.7 + - - -
73C ASP* 3.4 35.8 - - - +
74C LYS* 5.1 0.3 - - - +
242C TYR* 3.4 27.8 + - + +
243C GLY 3.0 1.2 + - - -
244C PRO* 1.3 82.9 - - + +
246C ALA* 1.3 63.8 + - - -
247C GLY 3.4 0.2 - - - -
248C ALA 3.6 0.2 + - - -
249C ALA* 3.0 30.8 + - - +
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Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ALA* 3.6 28.1 + - + +
73C ASP* 4.7 1.8 - - - +
77C ILE* 3.9 19.8 - - + +
210C LYS* 4.1 15.9 - - + -
239C LEU 4.8 0.2 - - - +
241C GLY* 4.4 3.4 - - - -
242C TYR 3.0 13.9 + - - +
245C THR* 1.3 80.0 + - - +
247C GLY* 1.3 64.0 + - - +
249C ALA* 3.3 3.5 + - - +
250C ILE* 3.1 28.5 + - - +
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Residues in contact with GLY 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ILE* 3.6 16.4 - - - +
210C LYS* 4.0 11.1 - - - +
242C TYR 3.2 4.0 + - - -
243C GLY 3.0 12.3 + - - -
246C ALA* 1.3 78.5 - - - +
248C ALA* 1.3 57.0 + - - +
250C ILE* 3.1 7.8 + - - +
251C ALA* 3.0 22.5 + - - +
601C NAD 3.4 19.4 - - - -
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C GLY 2.8 9.4 + - - +
244C PRO* 3.4 26.7 - - + +
245C THR 3.6 0.6 + - - +
246C ALA 3.4 0.4 - - - -
247C GLY* 1.3 72.7 - - - +
249C ALA* 1.3 60.7 + - - +
251C ALA* 3.9 6.0 - - - +
252C SER* 3.0 31.6 + - - +
601C NAD 3.4 15.8 - - + +
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LYS* 3.9 28.9 - - + -
77C ILE* 3.8 21.5 - - + -
245C THR 3.0 20.6 + - - +
246C ALA 3.5 4.7 - - - +
247C GLY 3.2 0.2 - - - -
248C ALA* 1.3 76.0 - - - +
250C ILE* 1.3 64.1 + - - +
252C SER* 4.0 1.7 - - - -
253C HIS* 3.1 29.2 + - + +
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Residues in contact with ILE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ILE* 3.8 25.6 - - + -
181C GLY* 3.7 30.3 - - - -
182C GLN 4.4 4.0 - - - +
183C ILE* 4.3 9.9 - - + -
208C VAL* 4.4 15.0 - - + +
210C LYS* 3.5 30.5 - - + +
239C LEU* 5.8 0.2 - - + -
246C ALA 3.1 15.6 + - - +
247C GLY 3.1 6.4 + - - +
249C ALA* 1.3 78.3 - - - +
251C ALA* 1.3 62.4 + - - +
252C SER 3.3 0.9 + - - -
253C HIS 3.4 8.1 + - - -
256C ILE* 3.5 21.1 - - + +
259C ILE* 3.8 15.7 - - + +
281C LYS* 3.4 6.8 + - - -
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Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C GLY 3.0 11.7 + - - +
248C ALA* 3.9 8.3 - - - +
249C ALA 3.4 0.2 - - - -
250C ILE* 1.3 71.9 - - - +
252C SER* 1.3 53.5 + - - +
259C ILE* 3.8 12.9 - - + +
271C ILE* 3.7 33.2 - - + +
274C ALA* 3.9 26.0 - - + +
275C ALA* 4.2 1.4 - - - +
278C SER* 3.9 3.3 + - - -
281C LYS* 2.0 35.4 + - - +
601C NAD 5.5 0.2 - - - +
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Residues in contact with SER 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ALA* 3.0 19.7 + - - +
249C ALA* 4.0 2.0 - - - -
251C ALA* 1.3 76.4 - - - +
253C HIS* 1.3 65.5 + - - +
254C ILE* 3.4 6.2 + - - +
274C ALA* 3.8 15.8 - - - +
277C ARG* 4.8 8.7 + - - -
278C SER* 3.4 25.5 - - - -
281C LYS* 3.5 2.5 - - - +
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Residues in contact with HIS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LYS* 6.0 0.9 - - - -
77C ILE* 4.2 8.5 - - + -
78C ASP* 3.1 35.5 + - - +
81C VAL* 3.4 43.6 - - + +
249C ALA* 3.1 17.3 + - + +
250C ILE 3.4 1.8 + - - -
252C SER* 1.3 76.0 - - - +
254C ILE* 1.3 68.5 + - + +
255C GLY* 3.0 30.2 + - - -
256C ILE* 3.7 20.5 + - + -
279C ASN* 3.5 1.7 + - - -
281C LYS* 3.1 23.9 + - - -
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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