Contacts of the helix formed by residues 223 - 235 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221E ASP* 2.8 14.5 + - - +
222E GLY* 1.3 77.7 - - - +
224E CYS* 1.3 63.6 + - - +
225E LEU 3.3 2.5 - - - -
226E PHE* 2.9 9.7 + - + -
227E ARG* 2.9 20.0 + - - +
240E HIS* 3.4 33.7 - - + +
244E ARG* 3.6 11.0 - - - +
276E ASN 3.4 17.6 + - - +
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Residues in contact with CYS 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E MET* 4.4 0.6 - - - +
219E LYS 3.6 20.9 - - - +
221E ASP* 3.1 4.4 + - - -
222E GLY 3.5 0.8 - - - -
223E ALA* 1.3 76.4 - - - +
225E LEU* 1.3 71.9 + - - +
227E ARG* 3.5 6.2 - - - +
228E ALA* 2.9 24.9 + - - +
334E HIS* 3.6 10.8 - - + +
335E TYR* 3.5 21.8 - - - +
75F GLY 3.5 3.1 - - - -
76F GLZ 1.7 76.3 - - - +
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Residues in contact with LEU 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E GLY 5.2 0.2 + - - -
223E ALA 3.1 0.8 + - - -
224E CYS* 1.3 81.8 - - - +
226E PHE* 1.3 66.3 + - + +
228E ALA* 3.5 1.6 + - - +
229E VAL* 2.9 36.4 + - + +
280E GLY* 3.7 32.1 - - - +
281E ASN 3.8 5.8 - - - +
284E GLU* 4.4 3.1 - - + -
285E MET* 3.7 39.5 - - + -
288E MET* 3.8 20.0 - - + -
296E VAL* 6.3 0.4 - - + -
327E VAL* 4.8 6.3 - - + -
335E TYR* 3.8 37.9 - - + -
75F GLY 4.7 0.8 + - - +
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Residues in contact with PHE 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E ALA* 2.9 11.7 + - + +
225E LEU* 1.3 78.8 - - + +
227E ARG* 1.3 58.3 + - - +
229E VAL* 3.8 1.7 - - - +
230E ALA* 2.9 29.6 + - - +
240E HIS* 3.6 25.0 - - + +
243E VAL* 3.9 23.9 - - + +
244E ARG* 3.4 53.2 - - + +
247E CYS* 4.3 2.2 - - - -
248E MET* 3.8 29.2 - - + -
273E LYS* 5.9 0.4 - - + -
280E GLY* 3.8 26.5 - - - -
284E GLU* 3.9 14.4 - - + -
288E MET* 3.9 24.9 - - + -
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Residues in contact with ARG 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E MET* 3.7 7.4 - - + -
219E LYS* 3.5 35.9 - - - +
221E ASP* 2.9 42.5 + - - -
223E ALA* 2.9 15.6 + - - +
224E CYS* 3.5 7.4 - - - +
226E PHE* 1.3 73.9 - - - +
228E ALA* 1.3 55.8 + - - +
230E ALA 3.1 1.0 + - - -
231E ASP* 2.8 33.1 + - - +
237E GLN* 2.9 58.8 + - + +
238E ASP* 3.8 13.9 + - - -
240E HIS* 3.6 33.4 + - + -
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Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E MET* 3.6 13.5 - - + -
224E CYS 2.9 17.6 + - - +
225E LEU 3.6 5.2 - - - +
227E ARG* 1.3 75.2 - - - +
229E VAL* 1.3 62.5 + - - +
231E ASP* 3.3 2.6 + - - +
232E GLN* 3.0 29.9 + - - +
327E VAL* 3.8 14.8 - - + -
335E TYR* 4.6 4.9 - - + -
336E ASN 3.8 29.6 - - - +
337E SER* 4.0 3.2 + - - +
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Residues in contact with VAL 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E LEU* 2.9 29.7 + - + +
226E PHE 4.0 4.5 - - - +
228E ALA* 1.3 74.4 - - - +
230E ALA* 1.3 57.7 + - - +
232E GLN* 3.2 6.6 + - - +
233E VAL* 2.8 32.9 + - + +
243E VAL* 3.8 14.4 - - + -
285E MET* 6.4 0.2 - - + -
288E MET* 3.9 25.1 - - + -
292E TYR* 3.8 31.6 - - + -
296E VAL* 5.5 4.9 - - + -
325E ILE* 4.2 19.5 - - + -
327E VAL* 4.6 4.9 - - + -
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E PHE 2.9 20.1 + - - +
227E ARG 3.6 4.3 - - - +
229E VAL* 1.3 74.0 - - - +
231E ASP* 1.3 59.4 + - - +
234E TYR* 2.8 34.4 + - - +
235E GLY 3.2 4.5 + - - -
236E ASP 3.4 17.6 + - - +
237E GLN 4.0 0.9 - - - +
239E MET* 3.7 26.0 - - + -
240E HIS* 3.7 2.5 - - - +
243E VAL* 3.7 15.2 - - + +
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Residues in contact with ASP 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E LYS* 2.6 47.2 + - - +
218E MET* 4.0 12.9 - - - +
227E ARG 2.8 16.5 + - - +
228E ALA 3.6 5.2 - - - +
230E ALA* 1.3 77.2 - - - +
232E GLN* 1.3 58.0 + - - +
235E GLY* 2.9 33.8 + - - -
236E ASP* 3.5 8.7 + - - +
237E GLN* 4.2 6.3 + - - +
337E SER* 2.8 22.7 + - - +
339E VAL* 3.9 6.9 - - - +
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Residues in contact with GLN 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E ALA 3.0 17.0 + - - +
229E VAL 3.2 8.0 + - - +
231E ASP* 1.3 77.9 + - - +
233E VAL* 1.3 59.6 + - - +
294E ARG* 3.8 18.2 + - - +
324E PRO 3.8 5.7 - - - +
325E ILE* 3.6 31.0 - - + -
326E ARG* 3.0 35.4 + - - +
327E VAL* 4.9 0.2 - - + -
337E SER* 2.7 24.1 + - - +
338E VAL 3.0 22.9 + - - +
339E VAL* 4.2 7.5 - - - +
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Residues in contact with VAL 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E VAL* 2.8 29.4 + - + +
230E ALA* 4.7 0.2 - - - -
232E GLN* 1.3 77.0 - - - +
234E TYR* 1.3 96.1 + - + +
235E GLY 3.6 0.4 - - - -
292E TYR* 3.9 24.2 - - + -
294E ARG* 4.2 14.8 + - - +
325E ILE* 3.9 28.7 - - + -
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Residues in contact with TYR 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E ALA 2.8 14.8 + - - +
233E VAL* 1.3 95.6 - - + +
235E GLY* 1.3 63.2 + - - +
236E ASP* 3.5 3.6 + - - +
239E MET* 3.9 35.7 - - + -
242E VAL* 4.0 25.2 - - + +
243E VAL* 3.9 24.2 - - + -
246E HIS* 4.1 13.3 + - - -
292E TYR* 4.1 10.9 + - - -
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Residues in contact with GLY 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E LYS* 4.5 6.3 + - - -
231E ASP* 2.9 30.1 + - - +
232E GLN 4.6 0.2 - - - -
233E VAL 3.6 1.2 - - - -
234E TYR* 1.3 77.6 - - - +
236E ASP* 1.3 60.7 + - - +
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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