Contacts of the helix formed by residues 239 - 247 (chain G) in PDB entry 5U0A
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 LEU 239 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2G THR* 2.7 38.0 + - + +
3G PHE 4.7 0.2 - - - +
4G VAL* 3.7 18.6 - - + -
237G VAL* 3.3 9.4 + - + +
238G ASN* 1.3 72.5 - - - +
240G ASP* 1.3 62.4 + - - +
242G LEU* 4.4 4.9 - - + +
243G VAL* 2.9 36.9 + - + +
252G ALA* 6.0 1.3 - - + -
256G VAL* 3.5 32.5 - - + -
367G ALA* 3.7 35.9 - - + +
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Residues in contact with ASP 240 (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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2G THR* 3.6 34.6 + - - +
3G PHE* 5.9 0.7 - - - -
238G ASN* 3.2 10.8 + - - +
239G LEU* 1.3 79.3 - - - +
241G ARG* 1.3 58.8 + - + +
243G VAL* 3.8 4.1 - - - +
244G GLU* 2.9 29.7 + - - +
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Residues in contact with ARG 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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183G ASP* 4.4 26.0 + - - +
184G GLY 3.4 24.0 + - - +
185G ALA* 4.1 9.4 - - + -
187G GLN* 6.0 1.6 - - - +
238G ASN* 3.1 32.5 + - + +
240G ASP* 1.3 76.1 - - + +
242G LEU* 1.3 61.5 + - - +
244G GLU* 3.6 15.6 - - - +
245G ASN* 2.9 38.2 + - - +
273H ASN* 4.5 14.6 + - - +
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Residues in contact with LEU 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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168G ASN* 3.5 33.7 - - + +
169G LEU* 3.6 29.6 - - + -
185G ALA* 3.8 8.4 - - + +
237G VAL* 4.4 3.4 - - + -
238G ASN 3.0 16.0 + - - +
239G LEU* 4.0 5.4 - - - +
241G ARG* 1.3 76.1 - - - +
243G VAL* 1.3 57.4 + - - +
245G ASN* 3.3 1.3 + - - +
246G THR* 2.9 37.2 + - + -
252G ALA* 3.9 17.9 - - + +
255G ALA* 4.0 9.2 - - + -
256G VAL* 3.4 32.5 - - + -
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Residues in contact with VAL 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 LEU* 2.9 28.1 + - + +
240G ASP* 3.9 4.5 - - - +
242G LEU* 1.3 75.0 - - + +
244G GLU* 1.3 60.1 + - - +
246G THR* 4.0 4.7 - - - -
247G GLY* 2.9 38.7 + - - +
248G ASP 5.0 0.2 - - - -
249G ALA* 4.6 20.0 - - + +
252G ALA* 3.7 19.1 - - + -
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Residues in contact with GLU 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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183G ASP* 4.7 12.7 - - - +
240G ASP 2.9 20.2 + - - +
241G ARG* 3.6 16.6 - - - +
242G LEU 3.2 0.2 - - - -
243G VAL* 1.3 80.0 - - - +
245G ASN* 1.3 67.4 + - - +
247G GLY* 3.8 5.9 + - - -
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Residues in contact with ASN 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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163G ARG* 4.2 22.8 + - - +
168G ASN* 2.9 48.4 + - + +
182G VAL* 3.7 18.6 - - - +
183G ASP* 3.2 28.4 + - - +
185G ALA* 4.4 2.2 - - - +
241G ARG* 2.9 25.7 + - - +
242G LEU 3.3 3.3 + - - +
244G GLU* 1.3 83.3 - - - +
246G THR* 1.3 66.6 + - - +
247G GLY* 3.3 0.7 + - - -
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Residues in contact with THR 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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165G VAL* 5.9 2.5 - - + -
168G ASN* 3.5 34.8 - - + +
242G LEU* 2.9 25.3 + - + +
243G VAL 3.9 0.9 + - - -
245G ASN* 1.3 76.0 - - - +
247G GLY* 1.3 58.4 + - - +
248G ASP* 3.2 25.5 + - - +
251G THR* 3.2 23.9 + - - +
252G ALA* 3.7 11.7 - - - +
255G ALA* 5.3 2.9 - - + -
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Residues in contact with GLY 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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243G VAL* 2.9 27.5 + - - +
244G GLU* 4.2 5.8 - - - -
245G ASN 3.2 2.8 - - - -
246G THR* 1.3 76.9 + - - +
248G ASP* 1.3 58.3 + - - -
249G ALA 3.9 0.7 + - - -
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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