Contacts of the helix formed by residues 203 - 216 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B SER* 1.3 84.0 + - - +
204B PHE* 1.3 60.4 + - - +
205B TYR 3.7 0.3 + - - -
206B GLY* 3.1 18.9 + - - -
207B ASN* 2.8 29.2 + - - +
260B TYR* 5.1 7.4 - - + +
297B ASP* 4.3 3.5 + - - +
-1P G 3.4 46.2 + - - +
0P 6MZ 4.3 26.7 - - + +
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Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B THR* 1.3 77.0 - - - +
205B TYR* 1.3 80.6 + + + +
207B ASN* 3.9 4.2 - - - +
208B LYS* 3.3 28.4 + - + +
288F ASP* 3.7 37.9 - - + -
-2P G 4.9 1.3 - - - +
-1P G 5.9 1.6 - - - +
-2Q G 3.3 88.4 - + - +
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Residues in contact with TYR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B THR* 3.3 1.6 + - - -
204B PHE* 1.3 91.9 - + + +
206B GLY* 1.3 66.5 + - - +
207B ASN 3.2 0.2 - - - -
208B LYS* 3.1 20.1 + - + +
209B ARG* 3.0 27.0 + - - +
-2P G 3.7 31.2 + - + +
-1P G 3.3 70.7 - + + +
-2Q G 2.5 54.5 + + - +
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B SER* 3.4 22.2 - - - -
203B THR* 3.1 12.4 + - - -
205B TYR* 1.3 78.4 - - - +
207B ASN* 1.3 62.6 + - - +
209B ARG* 3.3 4.8 + - - +
210B LEU* 3.0 28.6 + - - +
297B ASP* 4.9 0.4 - - - -
298B THR* 3.7 18.6 - - - -
-1P G 4.0 2.7 - - - -
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Residues in contact with ASN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B SER* 3.3 21.4 + - - -
202B SER* 2.8 31.5 + - - -
203B THR 2.8 18.7 + - - +
204B PHE* 3.9 5.1 - - - +
206B GLY* 1.3 76.0 - - - +
208B LYS* 1.3 55.9 + - - +
210B LEU* 4.0 3.8 - - - +
211B SER* 3.0 31.2 + - - -
245B LEU* 4.0 28.0 - - + +
261B ARG 6.1 0.2 - - - +
262B HIS* 3.6 16.5 + - + +
264B PHE* 3.6 14.1 - - - -
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Residues in contact with LYS 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.3 20.2 + - + +
205B TYR* 3.1 26.0 + - + +
207B ASN* 1.3 77.9 - - - +
209B ARG* 1.3 58.2 + - - +
211B SER* 3.9 4.9 - - - -
212B GLU* 2.8 60.1 + - - +
245B LEU* 5.4 0.4 - - - +
285F PRO 5.8 0.7 - - - -
286F ALA* 3.7 26.0 + - - +
-2Q G 4.8 13.9 - - - +
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Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PHE* 4.5 15.2 - - + -
205B TYR* 3.0 17.3 + - - +
206B GLY* 3.6 3.8 - - - +
208B LYS* 1.3 75.8 - - - +
210B LEU* 1.3 64.9 + - - +
212B GLU* 3.5 7.1 + - - +
213B ALA* 3.2 23.4 + - + +
298B THR* 2.9 41.8 + - - +
300B GLU* 6.3 0.2 - - - -
-1P G 2.8 45.7 + - - -
-3S A 3.5 22.3 + - - -
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B PHE* 3.8 41.3 - - + -
183B ILE* 4.1 13.5 - - + -
202B SER* 4.3 7.6 - - - -
206B GLY 3.0 21.1 + - - +
207B ASN* 4.0 3.6 - - - +
209B ARG* 1.3 73.2 - - - +
211B SER* 1.3 60.5 + - - +
213B ALA* 3.4 4.3 + - - +
214B TYR* 2.9 29.7 + - - +
223B ILE* 5.5 0.2 - - - -
225B LEU* 4.3 1.6 - - + -
241B MSE 3.3 36.0 - - + +
264B PHE* 3.8 23.8 - - + -
298B THR* 4.0 18.4 - - + -
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Residues in contact with SER 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASN 3.0 20.2 + - - -
208B LYS 3.9 4.0 - - - -
210B LEU* 1.3 76.7 - - - +
212B GLU* 1.3 63.9 + - - +
214B TYR* 3.1 5.0 + - - +
215B GLU* 3.0 23.6 + - - +
241B MSE 5.8 0.2 - - - -
244B ASN* 2.8 29.4 + - - -
245B LEU* 4.6 6.5 - - - +
264B PHE* 6.3 0.6 - - - -
285F PRO* 3.6 19.3 - - - +
286F ALA* 3.7 17.5 + - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LYS* 2.8 49.1 + - - +
209B ARG* 4.0 5.6 - - - +
210B LEU 3.4 0.2 - - - -
211B SER* 1.3 77.8 - - - +
213B ALA* 1.3 61.0 + - - +
215B GLU* 3.6 5.7 + - - +
216B SER* 2.9 30.5 + - - +
286F ALA* 3.9 20.2 - - + +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ARG* 3.5 36.7 + - - +
181B PHE* 4.0 12.3 - - + -
209B ARG 3.2 18.4 + - - +
210B LEU 3.8 1.6 - - - +
212B GLU* 1.3 76.5 - - - +
214B TYR* 1.3 62.7 + - - +
216B SER* 3.5 7.4 + - - -
217B LEU* 3.4 20.3 + - - +
223B ILE* 3.5 16.8 - - + +
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B LEU 2.9 18.6 + - - +
211B SER* 3.1 7.6 + - - +
213B ALA* 1.3 78.7 - - - +
215B GLU* 1.3 64.7 + - - +
216B SER 3.5 0.2 + - - -
217B LEU* 3.5 25.6 + - + +
222B LYS* 6.5 0.2 - - - -
223B ILE* 3.4 11.2 - - + +
241B MSE 3.7 39.7 - - + -
242B SER* 3.7 6.1 + - - -
243B SER* 3.5 31.0 + - - -
244B ASN* 3.5 32.8 - - + -
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B SER 3.0 14.7 + - - +
212B GLU* 3.8 6.5 - - - +
214B TYR* 1.3 81.3 - - - +
216B SER* 1.3 62.4 + - - +
217B LEU 3.2 5.1 + - - +
244B ASN* 4.2 13.4 + - - +
302F PRO* 3.4 30.2 - - + +
303F ALA* 3.0 30.3 + - - +
304F THR* 4.7 1.8 + - - -
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Residues in contact with SER 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 4.7 9.4 - - - -
212B GLU* 2.9 19.1 + - - +
213B ALA* 3.9 7.9 - - - -
214B TYR 3.2 0.6 - - - -
215B GLU* 1.3 78.0 - - - +
217B LEU* 1.3 65.0 + - - +
218B PRO* 3.3 7.3 - - - +
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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