Contacts of the helix formed by residues 231 - 245 (chain G) in PDB entry 8GCH
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 VAL 231 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103F ILE* 5.4 4.5 - - + -
123F LEU* 3.9 15.7 - - + -
124F PRO* 3.5 17.7 - - + -
209G LEU* 3.4 44.6 - - + +
210G VAL* 3.0 23.4 + - - +
211G GLY* 3.8 8.5 - - - +
212G ILE* 4.1 14.4 - - + -
229G ALA 3.1 3.5 + - - +
230G ARG* 1.3 71.0 - - - +
232G THR* 1.3 58.5 + - - +
234G LEU* 2.9 8.8 + - + +
235G VAL* 2.8 34.6 + - + +
238G VAL* 6.0 0.9 - - + -
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Residues in contact with THR 232 (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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124F PRO* 3.8 6.1 - - + -
125F SER 3.4 19.5 - - - +
126F ALA* 3.5 27.4 - - - +
128F ASP 3.5 20.6 + - - +
130F PHE* 3.7 24.7 - - + -
210G VAL* 4.7 1.4 + - - +
230G ARG* 3.3 23.8 + - + +
231G VAL* 1.3 76.2 - - - +
233G ALA* 1.3 60.9 + - - +
234G LEU 3.3 1.2 + - - -
235G VAL* 3.3 22.6 + - - +
236G ASN* 4.7 0.7 + - - -
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Residues in contact with ALA 233 (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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101F ASN* 5.3 1.1 + - - +
178G ASP* 4.7 2.5 - - + +
179G ALA* 4.0 28.7 - - + +
230G ARG* 3.3 21.1 + - + +
231G VAL 3.2 0.2 - - - -
232G THR* 1.3 77.7 + - - +
234G LEU* 1.3 64.6 + - + +
236G ASN* 5.3 3.5 + - - +
237G TRP 5.7 0.2 + - - -
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Residues in contact with LEU 234 (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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91F ASN* 3.9 15.0 - - - +
101F ASN* 3.4 42.4 - - + +
103F ILE* 3.9 33.0 - - + -
179G ALA* 4.5 3.1 - - + +
212G ILE* 5.4 0.2 - - + -
229G ALA* 3.8 28.0 - - + -
230G ARG 3.2 22.4 - - - +
231G VAL* 2.9 7.0 + - - +
233G ALA* 1.3 88.7 - - + +
235G VAL* 1.3 62.5 + - - +
236G ASN 3.2 3.4 - - - -
237G TRP* 3.2 10.4 + - - +
238G VAL* 3.1 23.0 + - - +
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Residues in contact with VAL 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F LEU* 4.1 25.6 - - + -
124F PRO* 3.2 28.9 - - + +
125F SER 4.0 0.7 - - - -
126F ALA* 3.6 20.9 - - + +
231G VAL* 2.8 22.8 + - + +
232G THR* 3.3 20.2 + - - +
234G LEU* 1.3 71.0 - - - +
236G ASN* 1.3 69.0 + - - +
238G VAL* 3.2 6.8 + - - +
239G GLN* 2.9 38.7 + - + +
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Residues in contact with ASN 236 (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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126F ALA* 3.7 28.8 - - - +
232G THR 4.7 1.1 + - - +
233G ALA 5.3 3.3 - - - +
234G LEU 3.2 1.2 - - - -
235G VAL* 1.3 81.8 - - - +
237G TRP* 1.3 62.7 + - - +
239G GLN* 3.9 7.3 - - - +
240G GLN* 3.0 33.2 + - + +
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Residues in contact with TRP 237 (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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89F PHE* 3.2 29.6 - - + -
90F LYS 3.9 2.5 - - - -
91F ASN* 3.4 52.0 + - + +
93F LYS* 6.2 0.4 - - + -
103F ILE* 3.7 22.2 - - + -
105F LEU* 3.6 31.9 - - + -
300F SO4 2.9 43.6 + - - -
234G LEU* 3.2 10.7 + - - +
236G ASN* 1.3 78.8 - - - +
238G VAL* 1.3 81.2 + - + +
240G GLN* 3.2 9.5 + - + +
241G THR* 2.8 43.9 + - - -
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Residues in contact with VAL 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 3.8 19.1 - - + -
53F VAL* 4.7 3.1 - - + -
103F ILE* 3.8 19.7 - - + -
105F LEU* 3.8 19.1 - - + -
123F LEU* 3.8 29.8 - - + -
231G VAL* 6.0 1.3 - - + -
234G LEU 3.1 14.7 + - - +
235G VAL* 3.2 13.0 + - - +
237G TRP* 1.3 92.6 - - + +
239G GLN* 1.3 59.5 + - - +
241G THR* 3.2 3.1 + - - -
242G LEU* 2.9 32.6 + - + +
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Residues in contact with GLN 239 (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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123F LEU* 4.4 15.6 - - - +
124F PRO 5.5 0.5 - - - +
235G VAL* 2.9 36.6 + - + +
236G ASN* 3.9 8.1 - - - +
238G VAL* 1.3 72.0 - - - +
240G GLN* 1.3 60.4 + - - +
242G LEU* 3.4 18.1 + - - +
243G ALA* 2.9 31.1 + - - +
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Residues in contact with GLN 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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236G ASN* 3.0 29.0 + - + +
237G TRP* 3.5 9.4 - - + +
239G GLN* 1.3 76.0 - - - +
241G THR* 1.3 54.9 + - - +
243G ALA* 3.1 8.1 + - - +
244G ALA* 2.8 37.5 + - - +
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Residues in contact with THR 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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51F TRP* 4.2 5.8 - - + -
89F PHE* 3.7 37.9 - - + -
105F LEU* 3.7 20.9 - - + -
300F SO4 4.1 3.8 + - - +
237G TRP* 2.8 39.0 + - + -
238G VAL 3.5 4.5 - - - -
240G GLN* 1.3 77.3 - - - +
242G LEU* 1.3 61.1 + - - +
244G ALA* 4.8 0.9 - - - -
245G ASN* 2.7 36.7 + - - +
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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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47F ILE* 3.8 20.2 - - + -
48F ASN* 3.3 27.8 - - - +
51F TRP* 3.4 49.3 + - + +
105F LEU* 3.9 11.7 - - + -
123F LEU* 5.9 0.4 - - + -
238G VAL* 2.9 20.2 + - + +
239G GLN* 4.0 20.0 - - - +
241G THR* 1.3 73.0 - - - +
243G ALA* 1.3 67.0 + - - +
245G ASN 3.1 21.8 + - - +
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Residues in contact with ALA 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 GLN 2.9 18.9 + - - +
240G GLN* 3.2 8.7 - - - +
242G LEU* 1.3 80.3 - - - +
244G ALA* 1.3 59.5 + - - +
245G ASN 3.4 3.5 + - - +
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Residues in contact with ALA 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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240G GLN 2.8 17.1 + - - +
241G THR* 4.8 0.9 - - - -
243G ALA* 1.3 75.9 - - - +
245G ASN* 1.3 74.9 + - - +
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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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51F TRP* 3.6 19.4 + - + -
87F LYS* 5.1 2.3 - - + +
89F PHE* 3.4 36.4 - - + -
107F LYS* 2.9 37.1 + - - +
241G THR* 2.7 28.8 + - - +
242G LEU 3.1 17.3 + - - +
243G ALA 4.1 3.5 - - - +
244G ALA* 1.3 93.0 - - - +
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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