Contacts of the helix formed by residues 231 - 241 (chain G) in PDB entry 1FFT
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 PHE 231 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127G ILE* 3.8 23.1 - - + -
142G TYR* 3.9 15.5 - + - -
154G ALA* 3.3 16.4 - - + -
155G PHE* 3.3 30.1 - - + -
156G PRO* 3.1 33.2 - - + -
225G THR* 4.5 7.2 - - - +
227G ASP 3.7 4.3 + - - +
228G ARG* 2.8 34.0 + - + +
230G ALA* 1.3 75.7 - - - +
232G ASP* 1.3 61.3 + - - +
233G GLN 2.9 5.4 - - - -
234G TRP* 3.0 34.7 + + + +
235G VAL* 3.7 15.0 + - + +
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Residues in contact with ASP 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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228G ARG* 2.2 48.7 + - - +
229G ALA* 3.7 12.4 + - - +
231G PHE* 1.3 78.3 - - - +
233G GLN* 1.3 61.8 + - + +
235G VAL* 3.8 10.4 + - - +
236G ALA* 3.4 16.5 + - - +
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Residues in contact with GLN 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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229G ALA 3.6 15.4 - - - +
230G ALA* 3.2 29.6 + - - +
231G PHE 2.9 0.4 - - - -
232G ASP* 1.3 78.2 - - + +
234G TRP* 1.3 59.2 + - - +
235G VAL 3.1 2.5 - - - -
236G ALA* 3.0 11.9 - - + +
237G LYS* 2.9 31.4 + - - +
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Residues in contact with TRP 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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142G TYR* 3.4 39.0 - + - -
147G ILE* 4.8 4.9 - - + -
149G THR* 3.4 24.7 - - + -
152G GLU* 3.0 42.3 + - - -
153G ILE* 3.6 2.7 - - - -
154G ALA* 3.2 37.2 - - + +
223G ILE* 5.1 3.3 - - + +
225G THR* 6.5 0.4 - - + -
230G ALA 3.6 7.3 + - - +
231G PHE* 3.0 25.0 + + + +
233G GLN* 1.3 79.7 - - - +
235G VAL* 1.3 65.2 + - + +
237G LYS* 3.8 8.7 + - + +
238G ALA* 3.6 14.2 + - - +
265G TYR* 2.7 34.4 + + - -
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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
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142G TYR* 5.3 2.9 - - + -
145G GLN* 4.1 28.9 - - + +
147G ILE* 3.2 40.2 - - + -
231G PHE* 3.8 21.5 - - + +
232G ASP* 3.8 9.4 - - - +
233G GLN 3.1 0.2 - - - -
234G TRP* 1.3 81.5 - - + +
236G ALA* 1.3 56.6 + - - +
238G ALA* 3.0 5.4 + - - +
239G LYS* 2.7 49.1 + - + +
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Residues in contact with ALA 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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232G ASP 3.4 5.8 + - - +
233G GLN* 3.0 26.3 + - + +
235G VAL* 1.3 78.4 - - - +
237G LYS* 1.3 64.6 + - - +
239G LYS* 2.9 29.1 + - - +
240G GLN* 3.2 10.4 + - - +
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Residues in contact with LYS 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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233G GLN 2.9 17.1 + - - +
234G TRP* 4.0 9.9 - - + +
236G ALA* 1.3 71.4 - - - +
238G ALA* 1.3 62.3 + - - +
240G GLN* 3.2 31.3 - - - +
241G SER* 3.5 3.3 + - - -
265G TYR* 4.7 23.6 - - + +
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Residues in contact with ALA 238 (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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147G ILE* 3.4 24.7 - - + -
234G TRP 3.6 3.9 + - - +
235G VAL 3.0 8.6 + - - +
237G LYS* 1.3 74.7 - - - +
239G LYS* 1.3 56.1 + - - +
240G GLN 2.8 4.7 - - - -
241G SER* 2.5 40.1 + - - +
265G TYR* 3.7 43.7 - - + -
266G PHE 4.3 1.6 - - - +
267G SER* 3.5 0.3 - - - -
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Residues in contact with LYS 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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145G GLN 3.0 24.2 + - - +
146G GLY* 3.3 18.8 + - - -
147G ILE* 3.0 26.4 - - + +
235G VAL* 2.7 43.1 + - + +
236G ALA* 3.0 16.6 - - - +
238G ALA* 1.3 70.4 - - - +
240G GLN* 1.3 57.1 + - + +
241G SER 3.9 0.2 - - - +
267G SER* 2.9 26.6 + - - +
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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 ALA 3.7 12.6 - - - +
237G LYS* 3.2 19.6 - - - +
238G ALA 2.7 1.2 + - - -
239G LYS* 1.3 76.2 - - + +
241G SER* 1.3 70.2 + - - +
242G PRO* 3.1 6.9 - - - +
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Residues in contact with SER 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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237G LYS 3.5 3.0 + - - -
238G ALA* 2.5 27.0 + - - -
240G GLN* 1.3 74.8 - - - +
242G PRO* 1.3 65.0 - - - +
243G ASN* 3.0 16.8 + - - -
265G TYR* 3.9 19.3 - - - -
266G PHE 2.9 3.3 - - - -
267G SER* 2.4 56.8 + - - -
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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