Contacts of the helix formed by residues 223 - 235 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C ASP* 2.9 13.9 + - - +
222C GLY* 1.3 78.2 - - - +
224C CYS* 1.3 63.7 + - - +
225C LEU 3.3 2.5 - - - -
226C PHE* 2.9 17.2 + - + -
227C ARG* 2.9 16.5 + - - +
240C HIS* 3.5 32.1 - - + +
244C ARG* 3.6 11.4 - - - +
276C ASN 3.4 18.0 + - - +
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Residues in contact with CYS 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C MET* 4.4 0.8 - - + +
219C LYS 3.5 21.5 - - - +
221C ASP* 3.2 4.8 + - - -
222C GLY 3.4 0.8 + - - -
223C ALA* 1.3 77.0 - - - +
225C LEU* 1.3 71.8 + - - +
227C ARG* 3.4 6.9 - - - +
228C ALA* 3.0 25.5 + - - +
334C HIS* 3.6 12.8 - - + -
335C TYR* 3.4 24.0 - - - +
75D GLY 3.5 2.7 - - - -
76D GLZ 1.8 57.2 - - - -
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Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C GLY 5.2 0.4 + - - -
223C ALA 3.0 1.2 + - - -
224C CYS* 1.3 81.8 - - - +
226C PHE* 1.3 63.1 + - + +
228C ALA* 3.4 2.4 + - - +
229C VAL* 2.9 38.1 + - + +
280C GLY* 3.7 33.0 - - - +
281C ASN 3.8 7.0 - - - +
284C GLU* 4.4 3.4 - - + -
285C MET* 3.7 38.1 - - + -
288C MET* 3.9 17.0 - - + -
296C VAL* 6.3 0.2 - - + -
327C VAL* 4.8 6.5 - - + -
335C TYR* 3.9 38.4 - - + -
75D GLY 4.5 3.1 + - - +
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Residues in contact with PHE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C ALA* 2.9 10.7 + - + +
225C LEU* 1.3 76.2 - - + +
227C ARG* 1.3 57.5 + - - +
229C VAL* 3.8 2.0 - - - +
230C ALA* 2.8 34.8 + - - +
240C HIS* 3.7 24.6 - - + +
243C VAL* 4.1 7.0 - - + +
244C ARG* 3.3 57.0 - - + +
247C CYS* 4.3 3.4 - - - -
248C MET* 3.8 28.5 - - + -
273C LYS* 5.7 0.4 - - + -
280C GLY* 3.8 34.1 - - - -
284C GLU* 3.9 13.2 - - + -
288C MET* 4.0 28.7 - - + -
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Residues in contact with ARG 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C MET* 3.5 8.6 - - + +
219C LYS* 3.4 41.4 - - - +
221C ASP* 2.9 37.8 + - - -
223C ALA* 2.9 13.6 + - - +
224C CYS* 3.4 10.5 - - - +
226C PHE* 1.3 73.2 - - - +
228C ALA* 1.3 54.5 + - - +
230C ALA 3.2 0.9 + - - -
231C ASP 2.8 29.6 + - - -
237C GLN* 2.8 59.4 + - + +
238C ASP* 4.9 1.6 - - - +
240C HIS* 3.5 43.1 + - + +
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C MET* 3.5 13.3 - - + -
224C CYS 3.0 19.4 + - - +
225C LEU 3.6 4.9 - - - +
227C ARG* 1.3 69.5 - - - +
229C VAL* 1.3 60.5 + - - +
231C ASP* 3.4 2.6 + - - +
232C GLN* 3.0 34.1 + - - +
327C VAL* 3.8 15.0 - - + -
335C TYR* 4.5 3.8 - - + -
336C ASN* 3.6 32.1 - - - +
337C SER* 4.0 3.6 + - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LEU* 2.9 30.9 + - + +
226C PHE 4.0 3.6 - - - +
228C ALA* 1.3 71.5 - - - +
230C ALA* 1.3 57.6 + - - +
232C GLN* 3.2 6.2 + - - +
233C VAL* 2.9 34.9 + - + +
243C VAL* 3.9 13.9 - - + -
288C MET* 3.7 26.9 - - + -
292C TYR* 3.7 31.9 - - + -
296C VAL* 5.6 4.7 - - + -
325C ILE* 4.2 19.1 - - + -
327C VAL* 4.6 4.9 - - + -
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C PHE 2.8 22.6 + - - +
227C ARG 3.2 4.9 + - - +
229C VAL* 1.3 75.3 - - - +
231C ASP* 1.3 55.4 + - - +
234C TYR* 2.7 35.0 + - - +
235C GLY 3.1 4.7 + - - -
236C ASP 3.4 17.7 - - - +
237C GLN 4.1 0.9 - - - +
239C MET* 3.6 27.6 - - + -
240C HIS* 3.7 2.0 - - - +
243C VAL* 3.7 13.2 - - + +
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Residues in contact with ASP 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LYS* 2.8 44.0 + - - +
218C MET* 3.8 13.9 - - + +
227C ARG 2.8 19.2 + - - +
228C ALA 3.6 5.2 - - - +
230C ALA* 1.3 72.6 - - - +
232C GLN* 1.3 60.8 + - - +
235C GLY* 2.9 33.4 + - - +
236C ASP* 3.8 11.8 + - - +
237C GLN 4.3 3.2 + - - +
337C SER* 2.7 23.9 + - - +
339C VAL* 3.8 7.1 - - - +
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Residues in contact with GLN 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ALA 3.0 19.0 + - - +
229C VAL 3.5 7.2 - - - +
231C ASP* 1.3 79.8 + - - +
233C VAL* 1.3 60.0 + - - +
235C GLY 4.8 0.2 + - - -
294C ARG* 3.8 15.3 + - - -
324C PRO 3.8 7.1 - - - +
325C ILE* 3.7 23.9 - - + -
326C ARG* 3.1 41.6 + - - +
327C VAL* 4.8 0.2 - - + -
337C SER* 2.7 22.1 + - - +
338C VAL 2.9 24.7 + - - +
339C VAL* 4.1 7.1 - - - +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL* 2.9 30.0 + - + +
232C GLN* 1.3 76.7 - - - +
234C TYR* 1.3 91.0 + - + +
235C GLY 3.6 0.2 - - - -
292C TYR* 4.0 23.6 - - + +
294C ARG* 4.1 17.7 + - - +
325C ILE* 3.8 30.3 - - + -
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Residues in contact with TYR 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ALA 2.7 15.5 + - - +
233C VAL* 1.3 94.6 - - + +
235C GLY* 1.3 62.9 + - - +
236C ASP* 3.3 2.8 + - - +
239C MET* 3.7 52.9 - - + -
242C VAL* 4.1 3.5 - - + +
243C VAL* 3.8 25.6 - - + -
246C HIS* 3.8 25.6 + - - -
292C TYR* 4.1 9.4 + - - -
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Residues in contact with GLY 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LYS* 4.3 7.1 + - - -
230C ALA 3.1 0.2 + - - -
231C ASP* 2.9 31.7 + - - +
232C GLN 4.5 0.2 - - - -
233C VAL 3.6 1.0 - - - -
234C TYR* 1.3 76.5 - - - +
236C ASP* 1.3 65.1 + - - +
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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