Contacts of the helix formed by residues 240 - 247 (chain C) in PDB entry 3GUT
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 SER 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LYS* 4.7 13.4 + - - -
239C PHE* 1.3 81.0 - - - +
241C GLN* 1.3 55.8 + - - +
242C ALA* 2.8 11.2 - - - -
243C ASP* 2.6 46.4 + - - +
244C VAL 3.9 0.3 + - - -
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Residues in contact with GLN 241 (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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221C LYS* 3.4 50.7 - - + +
222C GLU* 3.5 42.0 + - - +
239C PHE* 4.1 1.7 + - - -
240C SER* 1.3 72.3 - - - +
242C ALA* 1.3 58.9 + - - +
243C ASP 3.2 1.2 + - - -
244C VAL* 3.6 17.5 - - - +
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Residues in contact with ALA 242 (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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221C LYS* 5.5 0.9 - - - +
240C SER* 2.7 8.4 + - - -
241C GLN* 1.3 76.3 - - - +
243C ASP* 1.3 63.5 + - - +
244C VAL 3.2 8.3 - - - -
245C HIS* 5.1 0.9 + - - -
552D ARG* 5.2 1.2 + - - -
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Residues in contact with ASP 243 (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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239C PHE* 3.9 6.7 - - + +
240C SER* 2.6 38.5 + - - +
242C ALA* 1.3 82.3 - - - +
244C VAL* 1.3 59.8 + - - +
245C HIS* 3.1 9.7 + - - +
249C ALA 3.4 1.4 - - - +
250C ILE* 4.5 1.1 - - - -
251C VAL* 3.1 45.8 + - - +
552D ARG* 2.9 31.7 + - - +
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Residues in contact with VAL 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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219C VAL* 4.5 9.9 - - + -
221C LYS* 3.5 47.3 - - + +
224C ILE* 4.4 2.2 - - + -
239C PHE* 3.8 29.2 - - + -
241C GLN* 3.6 10.6 - - - +
242C ALA 3.2 3.4 - - - -
243C ASP* 1.3 74.6 - - - +
245C HIS* 1.3 56.3 + - - +
246C ARG* 3.2 7.1 + - - -
247C GLN* 4.0 21.4 + - + +
249C ALA 3.4 6.3 - - - +
250C ILE* 4.0 13.2 - - + +
19X A 4.7 5.0 + - - +
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Residues in contact with HIS 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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242C ALA 5.6 1.3 - - - -
243C ASP 3.1 5.0 + - - +
244C VAL* 1.3 66.7 - - - +
246C ARG* 1.3 89.5 + - + +
247C GLN 3.1 2.1 + - - -
248C VAL* 3.1 14.9 + - - +
249C ALA* 2.6 27.7 + - + +
551D VAL* 4.1 25.3 - - + +
569D LEU* 3.5 37.2 - - + -
570D CYS 2.8 33.1 + - - -
607D PHE* 3.6 19.3 + - + +
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Residues in contact with ARG 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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244C VAL 3.2 5.5 + - - -
245C HIS* 1.3 94.9 + - - +
247C GLN* 1.3 70.3 + - - +
248C VAL* 3.0 15.1 + - - +
570D CYS 4.7 0.4 + - - -
571D ASP* 3.9 25.9 + - - +
572D LYS* 4.8 7.3 - - - +
607D PHE* 3.3 56.1 - - + -
18X G 3.4 48.3 + - - +
19X A 3.1 28.2 + - - +
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Residues in contact with GLN 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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217C ASP 3.2 3.5 - - - +
218C LYS* 3.1 41.4 + - + +
219C VAL* 3.1 56.4 + - - +
220C GLN* 3.9 7.3 - - - +
221C LYS 5.7 1.7 + - - +
244C VAL* 4.0 13.2 + - + +
245C HIS 3.1 2.0 + - - -
246C ARG* 1.3 78.6 + - - +
248C VAL* 1.3 58.1 + - + +
249C ALA 3.8 0.9 - - - -
19X A 3.5 45.4 + - - +
20X C 3.2 20.3 + - - -
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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