Contacts of the helix formed by residues 240 - 247 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93E LYS* 4.8 11.7 + - - -
239G PHE* 1.3 81.1 - - - +
241G GLN* 1.3 61.1 + - - +
242G ALA* 4.0 9.4 - - - -
243G ASP* 2.7 40.6 + - - +
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Residues in contact with GLN 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G LYS* 3.4 47.6 - - + +
222G GLU* 3.8 34.3 + - - +
239G PHE* 4.1 2.0 + - + -
240G SER* 1.3 72.7 - - - +
242G ALA* 1.3 60.9 + - - +
243G ASP 3.1 1.1 + - - -
244G VAL* 3.4 26.3 + - - +
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Residues in contact with ALA 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G LYS* 5.5 1.3 - - - +
240G SER* 2.9 7.5 + - - -
241G GLN* 1.3 77.4 - - - +
243G ASP* 1.3 63.1 + - - +
244G VAL 3.2 6.2 + - - +
245G HIS* 5.0 0.7 + - - -
552H ARG* 5.1 1.2 + - - -
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Residues in contact with ASP 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239G PHE* 3.8 6.6 - - + -
240G SER* 2.7 42.0 + - - +
242G ALA* 1.3 82.1 - - - +
244G VAL* 1.3 60.8 + - - +
245G HIS* 3.2 9.8 + - - +
249G ALA 3.3 1.7 - - - +
250G ILE* 4.6 0.7 - - - -
251G VAL* 3.2 44.4 + - - +
552H ARG* 3.0 29.8 + - - +
569H LEU* 5.8 0.3 - - - +
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Residues in contact with VAL 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G VAL* 4.6 4.0 - - + -
221G LYS* 3.4 40.9 - - + +
224G ILE* 4.6 1.1 - - + -
239G PHE* 3.9 27.4 - - + -
241G GLN* 3.4 20.1 - - - +
242G ALA* 3.2 4.0 - - - +
243G ASP* 1.3 73.7 - - - +
245G HIS* 1.3 57.0 + - - +
246G ARG 3.1 8.1 + - - -
247G GLN* 4.0 23.6 + - + +
249G ALA 3.5 5.2 - - - +
250G ILE* 4.0 17.7 - - + -
19I A 5.3 2.4 + - - +
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Residues in contact with HIS 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242G ALA 5.5 1.3 - - - -
243G ASP 3.2 4.6 + - - +
244G VAL* 1.3 67.2 - - - +
246G ARG* 1.3 89.5 + - + +
247G GLN 3.1 0.7 - - - -
248G VAL* 2.9 19.8 + - - +
249G ALA* 2.7 27.0 + - + +
551H VAL* 4.1 26.8 - - + +
569H LEU* 3.5 33.8 - - + +
570H CYS 2.8 33.6 + - - -
607H PHE* 3.6 20.9 + - + +
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Residues in contact with ARG 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244G VAL 3.1 5.6 + - - -
245G HIS* 1.3 90.0 + - + +
247G GLN* 1.3 73.8 + - - +
248G VAL* 3.0 12.5 + - - +
570H CYS 4.5 0.6 + - - -
571H ASP* 4.0 31.1 + - - +
572H LYS* 4.9 6.1 - - - +
607H PHE* 3.4 55.6 - - + -
18I G 3.4 50.2 + - - +
19I A 3.6 24.0 + - - +
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Residues in contact with GLN 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G ASP 3.4 3.1 - - - +
218G LYS* 3.2 44.9 + - + +
219G VAL* 3.0 39.6 + - - +
220G GLN* 3.8 6.9 - - - +
221G LYS 5.8 0.9 - - - +
244G VAL* 4.0 19.4 + - + +
245G HIS 3.0 2.0 + - - -
246G ARG* 1.3 79.6 + - - +
248G VAL* 1.3 64.3 + - + +
249G ALA 4.0 0.2 - - - -
19I A 3.4 50.5 + - - +
20I C 3.1 17.3 + - - -
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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