Contacts of the helix formed by residues 243 - 250 (chain C) in PDB entry 1T9G
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 ALA 243 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C ILE* 3.6 35.2 - - + +
240C GLY 3.3 16.4 + - - +
241C ASP 2.9 5.4 + - - +
242C GLY* 1.3 78.6 - - - +
244C GLY* 1.3 64.3 + - - +
245C PHE 3.1 3.4 + - - -
246C LYS* 3.2 16.5 + - + +
247C VAL* 3.4 13.6 + - + +
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Residues in contact with GLY 244 (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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177C PHE* 4.9 0.5 - - - -
179C LEU* 3.5 20.5 - - - +
194C PHE 2.8 21.4 + - - -
195C THR* 3.7 3.8 - - - +
196C GLY* 3.4 25.0 - - - +
240C GLY 4.4 0.2 + - - -
243C ALA* 1.3 72.2 - - - +
245C PHE* 1.3 60.9 + - - -
247C VAL* 3.4 6.3 + - - +
248C ALA* 3.1 18.7 + - - +
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Residues in contact with PHE 245 (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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144C VAL* 3.9 21.3 - - + -
145C ALA* 3.9 30.5 - - + -
179C LEU* 4.7 5.2 - - + -
190C ALA* 3.3 44.1 + - + +
191C ASN* 4.8 6.1 - - + -
194C PHE* 4.0 21.6 + + + +
242C GLY 4.7 0.4 + - - +
243C ALA 3.1 3.4 + - - -
244C GLY* 1.3 72.5 - - - +
246C LYS* 1.4 59.7 + - - +
248C ALA* 3.5 2.5 + - + +
249C MET* 3.0 67.0 + - + +
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Residues in contact with LYS 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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110C ILE* 5.2 0.3 - - - +
191C ASN* 6.0 1.4 - - - +
243C ALA* 3.2 10.1 + - + +
245C PHE* 1.4 76.6 - - - +
247C VAL* 1.3 63.2 + - + +
249C MET* 3.4 7.0 + - - +
250C GLY* 2.9 28.4 + - - -
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Residues in contact with VAL 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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107C PRO* 4.1 11.4 - - + +
110C ILE* 3.6 18.2 - - - +
111C ALA* 3.7 29.6 - - + -
177C PHE* 4.0 26.0 - - + -
196C GLY* 5.4 0.2 - - - -
238C LEU* 4.3 13.2 - - + -
239C ILE* 3.9 19.1 - - + -
243C ALA* 3.4 15.9 + - + +
244C GLY* 3.6 10.5 - - - +
245C PHE 3.2 0.4 - - - -
246C LYS* 1.3 82.5 - - + +
248C ALA* 1.3 60.9 + - - +
250C GLY 3.4 5.5 + - - -
251C ALA* 3.7 4.0 + - - +
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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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107C PRO* 5.5 0.7 - - - -
133C TYR* 3.5 26.0 + - - +
135C VAL* 5.2 0.9 - - + -
144C VAL* 5.6 4.7 - - + -
177C PHE* 4.3 10.8 - - + -
179C LEU* 4.3 21.3 - - + -
244C GLY 3.1 15.6 + - - +
245C PHE* 4.0 3.1 - - + +
247C VAL* 1.3 73.7 - - - +
249C MET* 1.3 66.7 + - - +
250C GLY 3.1 3.1 + - - -
251C ALA* 3.2 19.1 + - - +
252C PHE* 3.9 9.4 - - + -
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Residues in contact with MET 249 (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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144C VAL* 5.6 9.6 - - + -
245C PHE* 3.0 56.6 + - + +
246C LYS* 3.5 9.6 - - - +
248C ALA* 1.3 80.4 - - - +
250C GLY* 1.3 57.5 + - - +
251C ALA 3.4 0.4 + - - -
252C PHE* 4.1 31.1 + - + +
253C ASP* 4.9 3.8 + - - +
388C ARG* 5.8 6.5 - - - +
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Residues in contact with GLY 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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110C ILE* 3.4 25.3 - - - +
246C LYS 2.9 16.0 + - - -
247C VAL 3.4 0.6 + - - -
248C ALA 3.1 0.8 - - - -
249C MET* 1.3 75.0 - - - +
251C ALA* 1.3 62.9 - - - +
252C PHE 3.3 1.3 + - - -
253C ASP* 4.0 17.5 - - - +
254C LYS* 4.6 2.6 + - - +
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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