Contacts of the helix formed by residues 203 - 216 (chain C) in PDB entry 4U8T
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 THR 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C SER* 1.3 87.3 + - - +
204C PHE* 1.3 62.5 + - - +
206C GLY* 3.0 19.4 + - - -
207C ASN* 2.8 33.4 + - - +
259C ARG* 3.1 37.0 - - - +
297C ASP* 4.3 3.1 + - - +
-1Q G 3.5 42.9 + - - +
0Q 6MZ 4.2 11.4 - - + +
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Residues in contact with PHE 204 (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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203C THR* 1.3 78.3 - - - +
205C TYR* 1.3 83.3 + + + +
207C ASN* 3.7 5.8 - - - +
208C LYS* 3.2 28.8 + - + +
288E ASP* 3.4 44.4 - - + -
-2P G 3.4 75.6 - + - +
-2Q G 5.7 0.2 - - - +
-1Q G 6.0 1.1 - - - +
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Residues in contact with TYR 205 (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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203C THR* 3.3 1.8 + - - -
204C PHE* 1.3 92.3 - + + +
206C GLY* 1.3 65.5 + - - +
208C LYS* 3.2 21.2 + - - +
209C ARG* 3.0 26.9 + - - +
-2P G 3.4 45.6 + + - -
-2Q G 3.3 24.5 + - + +
-1Q G 3.3 71.1 + + + +
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Residues in contact with GLY 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C SER* 3.4 23.8 - - - -
203C THR* 3.0 13.3 + - - -
205C TYR* 1.3 78.1 - - - +
207C ASN* 1.3 55.0 + - - +
209C ARG* 3.4 5.8 + - - +
210C LEU* 3.0 33.1 + - - +
298C THR* 3.8 17.6 - - - +
-1Q G 4.0 1.9 - - - -
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Residues in contact with ASN 207 (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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201C SER* 3.5 16.2 + - - -
202C SER* 2.9 27.7 + - - -
203C THR 2.8 24.1 + - - +
204C PHE* 3.7 6.1 + - - +
206C GLY* 1.3 70.4 - - - +
208C LYS* 1.3 58.8 + - - +
210C LEU* 4.0 4.3 - - - +
211C SER* 2.9 34.1 + - - -
245C LEU* 3.7 37.8 - - + +
262C HIS* 4.5 11.1 + - - +
264C PHE* 3.7 13.3 - - - -
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Residues in contact with LYS 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C PHE* 3.2 21.6 + - + +
205C TYR* 3.2 30.3 + - + +
207C ASN* 1.3 78.7 - - - +
209C ARG* 1.3 61.9 + - - +
211C SER* 3.7 4.8 - - - -
212C GLU* 3.1 52.3 + - - +
245C LEU* 5.9 0.2 - - - -
285E PRO 5.6 0.9 - - - -
286E ALA* 3.7 28.1 + - - +
287E ASN* 5.8 0.2 - - - -
288E ASP 6.1 0.7 - - - +
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Residues in contact with ARG 209 (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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181C PHE* 4.3 16.2 - - + -
205C TYR* 3.0 14.7 + - - +
206C GLY* 3.6 4.0 - - - +
208C LYS* 1.3 75.4 - - - +
210C LEU* 1.3 63.1 + - - +
212C GLU* 3.5 9.6 + - - +
213C ALA* 3.2 22.2 + - - +
298C THR* 3.1 40.0 + - - +
-1Q G 2.7 50.5 + - - -
-3R A 3.5 21.4 + - - -
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Residues in contact with LEU 210 (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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181C PHE* 3.7 45.3 - - + -
183C ILE* 3.9 21.5 - - + -
202C SER* 4.5 5.6 - - - -
206C GLY 3.0 21.0 + - - +
207C ASN* 4.0 3.4 - - - +
209C ARG* 1.3 73.4 - - - +
211C SER* 1.3 65.4 + - - +
213C ALA* 3.4 3.9 + - - +
214C TYR* 3.0 24.8 + - - +
223C ILE* 4.9 0.9 - - + -
225C LEU* 4.5 0.4 - - + -
241C MSE 3.8 30.7 - - + +
264C PHE* 3.7 30.7 - - + -
298C THR* 3.9 11.4 - - + -
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Residues in contact with SER 211 (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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207C ASN 2.9 20.2 + - - -
208C LYS 3.7 4.7 - - - -
210C LEU* 1.3 78.2 - - - +
212C GLU* 1.3 63.0 + - - +
214C TYR* 3.3 4.1 + - - +
215C GLU* 3.1 24.3 + - - +
241C MSE 5.8 0.2 - - - -
244C ASN* 2.8 29.1 + - - -
245C LEU* 4.8 6.7 - - - +
264C PHE* 6.3 0.2 - - - -
285E PRO* 3.5 18.8 - - - +
286E ALA* 3.5 16.6 + - - +
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Residues in contact with GLU 212 (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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208C LYS* 3.1 46.3 + - - +
209C ARG* 3.9 7.6 - - - +
210C LEU 3.3 0.2 - - - -
211C SER* 1.3 79.3 - - - +
213C ALA* 1.3 62.5 + - - +
215C GLU* 3.4 5.4 + - - +
216C SER* 3.0 28.1 + - - +
286E ALA* 3.9 19.0 - - + +
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Residues in contact with ALA 213 (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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179C ARG* 3.4 34.8 + - - +
181C PHE* 4.1 14.6 - - + -
209C ARG 3.2 14.8 + - - +
210C LEU 3.9 1.8 - - - +
212C GLU* 1.3 78.9 - - - +
214C TYR* 1.3 64.9 + - - +
216C SER* 3.4 9.7 + - - -
217C LEU* 3.4 18.0 + - - +
223C ILE* 3.4 17.9 - - + +
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Residues in contact with TYR 214 (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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210C LEU 3.0 18.4 + - - +
211C SER* 3.6 5.6 - - - +
212C GLU 3.2 0.2 - - - -
213C ALA* 1.3 78.7 - - - +
215C GLU* 1.3 67.3 + - - +
217C LEU* 3.3 26.0 + - + +
222C LYS* 6.4 0.4 - - - -
223C ILE* 3.3 12.7 - - + +
241C MSE 3.6 40.8 - - + -
242C SER* 3.6 6.6 + - - -
243C SER* 3.4 29.2 + - - -
244C ASN* 3.3 36.1 - - + -
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Residues in contact with GLU 215 (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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211C SER 3.1 13.2 + - - +
212C GLU* 3.8 6.3 - - - +
213C ALA 3.3 0.2 - - - -
214C TYR* 1.3 86.5 - - - +
216C SER* 1.3 59.9 + - - +
217C LEU 3.2 6.4 + - - +
244C ASN* 4.2 14.3 + - - +
302E PRO* 3.5 28.6 - - + +
303E ALA* 3.3 28.9 + - - +
304E THR* 4.8 3.9 + - - +
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Residues in contact with SER 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ARG* 4.7 9.4 - - - -
212C GLU* 3.0 20.0 + - - +
213C ALA* 3.9 7.4 - - - -
214C TYR 3.3 0.6 - - - -
215C GLU* 1.3 76.4 - - - +
217C LEU* 1.3 65.2 + - - +
218C PRO* 3.3 8.1 - - - +
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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