Contacts of the helix formed by residues 203 - 216 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A SER* 1.3 87.4 + - - +
204A PHE* 1.3 61.5 + - - +
205A TYR 3.7 0.2 + - - -
206A GLY* 2.9 20.8 + - - -
207A ASN* 2.8 28.5 + - - +
259A ARG* 3.8 34.3 - - - +
260A TYR* 5.0 3.6 - - + -
297A ASP* 4.4 4.2 + - - +
-1O G 3.6 33.0 + - - +
0O 6MZ 4.3 21.3 - - + +
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A THR* 1.3 79.3 - - - +
205A TYR* 1.3 79.2 + + + +
207A ASN* 3.7 5.0 + - - +
208A LYS* 3.4 27.2 + - + +
259A ARG 5.9 0.8 + - - -
288C ASP* 3.8 38.4 - - + -
-2O G 5.2 0.9 - - - +
-1O G 5.9 0.9 - - - +
-2R G 3.2 84.8 - + + +
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 3.3 1.2 + - - -
204A PHE* 1.3 92.3 - + + +
206A GLY* 1.3 60.0 + - - +
208A LYS* 3.2 18.7 + - - +
209A ARG* 3.0 30.8 + - - +
205F TYR* 5.0 1.6 + - - -
-2O G 3.3 38.5 + - + +
-1O G 3.3 69.3 - + + +
-2R G 3.3 48.8 + + - -
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Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 3.4 15.3 - - - -
203A THR* 2.9 19.2 + - - -
205A TYR* 1.3 75.1 - - - +
207A ASN* 1.3 62.8 + - - +
209A ARG* 3.4 10.8 + - - +
210A LEU* 3.1 28.9 + - - +
297A ASP* 5.2 0.4 - - - -
298A THR* 3.8 12.5 - - - +
-1O G 4.0 2.5 - - - -
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Residues in contact with ASN 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A SER* 3.4 18.8 + - - -
202A SER* 2.8 31.8 + - - -
203A THR 2.8 20.8 + - - +
204A PHE* 3.9 4.9 - - - +
206A GLY* 1.3 69.4 - - - +
208A LYS* 1.3 60.5 + - - +
210A LEU* 3.3 4.9 + - - +
211A SER* 2.8 34.0 + - - -
245A LEU* 3.8 34.9 - - + +
260A TYR* 6.2 0.2 - - - +
262A HIS* 4.1 9.5 + - - +
264A PHE* 3.8 13.0 - - - -
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PHE* 3.4 21.4 + - + +
205A TYR* 3.2 24.9 + - + +
207A ASN* 1.3 78.8 - - - +
209A ARG* 1.3 58.1 + - - +
211A SER* 3.8 5.0 - - - -
212A GLU* 2.8 68.4 + - - +
285C PRO 5.5 0.7 - - - -
286C ALA* 3.6 26.7 + - - +
-3R A 5.7 5.8 - - - -
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 4.4 15.7 - - + -
205A TYR* 3.0 13.3 + - - +
206A GLY* 3.6 7.4 - - - +
208A LYS* 1.3 78.8 - - - +
210A LEU* 1.3 57.0 + - - +
212A GLU* 3.5 7.9 + - - +
213A ALA* 3.1 28.0 + - + +
298A THR* 3.1 40.5 + - - +
-1O G 2.8 47.7 + - - -
-3T A 3.5 20.5 + - - -
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PHE* 3.9 41.7 - - + -
183A ILE* 4.0 18.8 - - + -
202A SER* 4.2 7.9 - - - -
206A GLY 3.1 20.3 + - - +
207A ASN 3.9 2.9 - - - +
209A ARG* 1.3 73.9 - - - +
211A SER* 1.3 65.9 + - - +
213A ALA* 3.8 3.8 - - - +
214A TYR* 3.0 26.2 + - - +
223A ILE* 5.0 0.4 - - + -
225A LEU* 4.2 10.8 - - + -
241A MSE 4.0 18.7 - - + +
264A PHE* 3.5 32.8 - - + -
298A THR* 4.0 12.6 - - + -
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASN 2.8 18.4 + - - -
208A LYS 3.8 3.8 - - - -
210A LEU* 1.3 77.4 - - - +
212A GLU* 1.3 61.7 + - - +
214A TYR* 3.7 3.4 - - - +
215A GLU* 3.0 24.8 + - - +
241A MSE 4.8 3.1 - - - +
244A ASN* 2.8 28.6 + - - -
245A LEU* 4.7 7.4 - - - -
264A PHE* 6.2 0.2 - - - -
285C PRO* 3.3 26.1 - - - +
286C ALA* 3.5 13.4 + - - +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS* 2.8 56.8 + - - +
209A ARG* 3.8 6.3 - - - +
211A SER* 1.3 76.7 - - - +
213A ALA* 1.3 59.8 + - - +
215A GLU* 3.5 5.8 + - - +
216A SER* 3.0 29.0 + - - -
286C ALA* 3.8 20.2 - - + +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ARG* 3.6 32.8 + - - +
181A PHE* 4.0 14.4 - - + -
209A ARG 3.1 17.0 + - - +
210A LEU 3.8 2.7 - - - +
211A SER 3.3 0.4 - - - -
212A GLU* 1.3 75.2 - - - +
214A TYR* 1.3 62.7 + - - +
216A SER* 3.4 12.8 + - - -
217A LEU* 3.6 15.9 - - - +
223A ILE* 3.6 18.1 - - + +
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Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU 3.0 17.8 + - - +
211A SER* 3.7 3.6 - - - +
213A ALA* 1.3 75.1 - - - +
215A GLU* 1.3 69.6 + - - +
216A SER 3.3 0.3 + - - -
217A LEU* 3.5 27.8 + - + +
222A LYS* 6.5 0.2 - - - -
223A ILE* 3.4 12.7 - - + +
241A MSE 3.8 42.0 - - + -
242A SER* 3.7 4.9 + - - -
243A SER* 3.4 28.8 + - - -
244A ASN* 3.3 36.3 - - + -
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A SER 3.0 17.3 + - - +
212A GLU* 3.9 6.5 - - - +
214A TYR* 1.3 80.7 - - - +
216A SER* 1.3 61.6 + - - +
217A LEU 3.3 5.2 + - - +
244A ASN* 4.1 14.1 + - - +
302C PRO* 3.5 27.7 - - + +
303C ALA* 3.2 30.1 + - - +
304C THR* 4.6 9.1 + - - +
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Residues in contact with SER 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 4.6 10.0 + - - -
212A GLU* 3.0 17.1 + - - +
213A ALA* 3.7 9.1 - - - -
214A TYR 3.2 1.0 - - - -
215A GLU* 1.3 76.4 - - - +
217A LEU* 1.3 63.8 + - - +
218A PRO* 3.5 6.6 - - - +
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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