Contacts of the helix formed by residues 223 - 235 (chain G) in PDB entry 3TMP
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 ALA 223 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221G ASP* 2.9 12.7 + - - +
222G GLY* 1.3 77.7 - - - +
224G CYS* 1.3 66.1 + - - +
225G LEU 2.9 4.1 + - - -
226G PHE* 2.9 7.5 + - + -
227G ARG* 2.9 21.7 + - - +
240G HIS* 3.5 33.4 - - + +
244G ARG* 3.5 13.0 - - - +
276G ASN 3.6 14.5 + - - +
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Residues in contact with CYS 224 (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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218G MET* 4.4 0.4 - - + +
219G LYS 3.4 22.2 - - - +
221G ASP* 3.3 1.8 + - - -
222G GLY 3.4 1.2 + - - -
223G ALA* 1.3 77.2 - - - +
225G LEU* 1.3 64.7 + - - +
227G ARG* 3.3 7.0 + - - +
228G ALA* 2.9 24.3 + - - +
334G HIS* 3.6 11.2 - - + +
335G TYR* 3.4 23.9 - - - +
75H GLY 3.4 2.9 - - - -
76H GLZ 2.0 59.9 - - - +
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Residues in contact with LEU 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G GLY 5.1 0.2 + - - -
223G ALA 2.9 1.2 + - - -
224G CYS* 1.3 79.9 - - - +
226G PHE* 1.3 66.8 + - + +
228G ALA* 3.3 4.5 + - - +
229G VAL* 2.9 34.4 + - + +
280G GLY* 3.7 33.7 - - - +
281G ASN 4.0 1.1 - - - +
284G GLU* 4.2 5.4 - - + -
285G MET* 3.9 39.5 - - + -
288G MET* 3.8 27.8 - - + -
296G VAL* 6.1 0.4 - - + -
327G VAL* 4.8 6.7 - - + -
335G TYR* 4.0 33.7 - - + -
75H GLY 4.7 1.5 + - - +
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Residues in contact with PHE 226 (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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223G ALA* 2.9 9.8 + - + +
225G LEU* 1.3 77.1 - - + +
227G ARG* 1.3 55.2 + - - +
229G VAL* 3.8 1.9 - - - +
230G ALA* 2.8 34.2 + - - +
240G HIS* 3.7 24.9 - - + +
243G VAL* 4.0 8.0 - - + +
244G ARG* 3.3 61.2 - - + +
247G CYS* 4.2 4.5 - - - -
248G MET* 3.7 29.8 - - + -
273G LYS* 5.9 0.2 - - + -
280G GLY* 3.8 25.1 - - - -
284G GLU* 3.9 13.9 - - + -
288G MET* 4.0 32.3 - - + -
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Residues in contact with ARG 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G MET* 3.5 14.3 - - + +
219G LYS* 3.4 45.9 - - - +
221G ASP* 2.9 36.7 + - - -
223G ALA* 2.9 15.0 + - - +
224G CYS* 3.5 7.2 - - - +
226G PHE* 1.3 74.3 - - - +
228G ALA* 1.3 60.0 + - - +
230G ALA 3.2 0.7 + - - -
231G ASP* 2.8 25.8 + - - +
237G GLN* 3.0 57.9 + - + +
238G ASP* 4.0 8.1 + - - -
240G HIS* 3.6 32.1 + - + +
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Residues in contact with ALA 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G MET* 3.6 13.1 - - + -
224G CYS 2.9 13.5 + - - +
225G LEU 3.5 8.7 - - - +
227G ARG* 1.3 75.1 - - - +
229G VAL* 1.3 63.2 + - - +
231G ASP* 3.3 3.6 + - - +
232G GLN* 3.0 29.2 + - - +
327G VAL* 3.7 14.6 - - + -
335G TYR* 4.6 3.8 - - + -
336G ASN* 3.5 32.3 - - - +
337G SER* 3.9 3.6 + - - +
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Residues in contact with VAL 229 (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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225G LEU* 2.9 26.7 + - + +
226G PHE 4.0 0.4 - - - +
228G ALA* 1.3 75.5 - - - +
230G ALA* 1.3 57.7 + - - +
232G GLN* 3.1 6.1 + - - +
233G VAL* 2.9 35.5 + - + +
243G VAL* 3.6 27.4 - - + -
288G MET* 3.8 25.4 - - + -
292G TYR* 3.7 23.1 - - + -
296G VAL* 5.7 4.5 - - + -
325G ILE* 4.0 20.9 - - + -
327G VAL* 4.6 4.5 - - + -
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Residues in contact with ALA 230 (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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226G PHE 2.8 20.9 + - - +
227G ARG 3.2 4.7 + - - +
229G VAL* 1.3 74.7 - - - +
231G ASP* 1.3 56.1 + - - +
234G TYR* 2.8 34.7 + - - +
235G GLY 3.3 4.5 + - - -
236G ASP 3.5 18.7 + - - +
237G GLN* 4.0 2.5 - - - -
239G MET* 3.6 7.9 - - + -
240G HIS* 3.6 22.0 - - - +
243G VAL* 3.8 12.8 - - + -
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Residues in contact with ASP 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216G LYS* 2.8 40.2 + - - +
218G MET* 3.8 18.2 - - + +
227G ARG 2.8 16.3 + - - +
228G ALA 3.5 4.9 - - - +
230G ALA* 1.3 77.6 - - - +
232G GLN* 1.3 58.8 + - - +
235G GLY* 3.1 32.4 + - - +
236G ASP* 3.7 8.7 + - - +
237G GLN 4.3 5.9 + - - +
337G SER* 2.8 22.0 + - - +
339G VAL* 4.0 6.6 - - - +
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Residues in contact with GLN 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 ALA 3.0 19.7 + - - +
229G VAL 3.1 6.5 + - - +
231G ASP* 1.3 77.1 + - - +
233G VAL* 1.3 61.7 + - - +
235G GLY 4.6 0.2 - - - -
294G ARG* 3.7 17.8 + - - +
323G GLU* 5.7 0.3 - - - +
324G PRO 3.7 5.9 - - - +
325G ILE* 3.5 30.7 - - + -
326G ARG* 2.9 36.2 + - - +
337G SER* 2.9 20.7 + - - +
338G VAL 2.9 26.3 + - - +
339G VAL* 4.1 4.9 - - - +
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Residues in contact with VAL 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G VAL* 2.9 34.3 + - + +
232G GLN* 1.3 80.1 - - - +
234G TYR* 1.3 97.1 + - + +
235G GLY 3.7 0.6 + - - -
292G TYR* 3.9 22.2 - - + -
294G ARG* 3.9 18.1 + - - +
325G ILE* 3.9 20.6 - - + -
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Residues in contact with TYR 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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230G ALA 2.8 12.8 + - - +
233G VAL* 1.3 95.0 - - + +
235G GLY* 1.3 62.5 + - - +
236G ASP* 3.3 4.4 + - - +
239G MET* 4.0 34.2 - - + +
242G VAL* 4.2 15.4 - - + +
243G VAL* 3.7 26.7 - - + -
246G HIS* 4.0 23.0 + - - -
292G TYR* 4.1 12.0 + - - -
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Residues in contact with GLY 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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216G LYS* 4.4 7.1 + - - -
231G ASP* 3.1 29.8 + - - +
232G GLN 4.6 0.4 + - - -
233G VAL 3.7 1.4 - - - -
234G TYR* 1.3 75.2 - - - +
236G ASP* 1.3 61.1 + - - +
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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