Contacts of the helix formed by residues 201 - 214 (chain A) in PDB entry 5E97
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 SER 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A TRP* 3.4 40.1 + - - -
200A ASN* 1.3 71.5 + - - +
202A SER* 1.3 58.1 + - - +
203A ASN 3.4 2.5 - - - -
204A ALA* 3.3 4.2 + - - +
205A GLN* 2.8 29.9 + - - +
248A GLN* 5.9 3.1 - - - -
252A LEU* 3.6 20.5 - - - +
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Residues in contact with SER 202 (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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200A ASN* 3.0 18.9 + - - -
201A SER* 1.3 78.0 + - - +
203A ASN* 1.3 64.7 + - - +
205A GLN* 3.3 9.1 + - - +
206A LEU* 3.1 26.6 + - - +
602A NAG 3.5 26.8 + - - -
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Residues in contact with ASN 203 (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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165A TYR* 4.5 2.9 + - - -
189A ASN* 5.7 1.2 - - - +
192A LEU* 3.6 25.2 - - + +
200A ASN 4.6 1.6 + - - -
201A SER 3.4 0.6 - - - -
202A SER* 1.3 80.9 + - - +
204A ALA* 1.3 64.8 + - - +
206A LEU* 3.0 28.8 + - - +
207A LEU* 3.0 11.8 + - - +
102B LEU 4.8 1.0 - - - +
103B ILE* 3.5 18.6 - - + +
104B PHE* 2.8 54.1 + - - +
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Residues in contact with ALA 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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188A LEU* 4.1 29.6 - - + +
192A LEU* 5.5 0.6 - - - +
199A TRP* 3.6 36.3 - - + -
200A ASN 5.3 0.6 + - - -
201A SER* 3.3 6.2 + - - +
203A ASN* 1.3 78.3 + - - +
205A GLN* 1.3 58.2 + - - +
207A LEU* 3.1 3.8 + - - +
208A LEU* 2.7 37.8 + - + +
249A LEU* 5.2 0.7 - - + -
252A LEU* 5.1 2.2 - - + -
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Residues in contact with GLN 205 (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* 2.8 20.2 + - - +
202A SER* 3.5 10.3 - - - +
203A ASN 3.2 0.2 - - - -
204A ALA* 1.3 72.6 - - - +
206A LEU* 1.3 64.0 + - + +
208A LEU* 4.3 15.8 - - - +
209A ASP* 3.0 60.6 + - - +
252A LEU* 3.2 37.4 + - + +
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Residues in contact with LEU 206 (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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202A SER 3.1 18.4 + - - +
203A ASN* 3.0 25.1 + - - +
205A GLN* 1.3 78.7 - - + +
207A LEU* 1.3 62.3 + - - +
209A ASP* 3.4 7.8 + - + +
210A TYR* 3.1 23.0 + - - +
104B PHE* 3.7 14.8 - - + +
106B PRO* 4.3 24.9 - - + -
107B LYS* 6.2 0.7 - - - +
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Residues in contact with LEU 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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165A TYR* 3.6 10.1 - - + +
170A VAL* 3.8 29.6 - - + -
186A PHE* 3.6 33.4 - - + -
188A LEU* 3.7 16.2 - - + -
203A ASN 3.0 10.7 + - - +
204A ALA* 3.1 8.7 + - - +
206A LEU* 1.3 75.4 - - - +
208A LEU* 1.3 59.5 + - - +
210A TYR* 3.3 2.3 + - + +
211A CYS* 2.9 43.9 + - - -
220A TRP* 3.8 11.9 - - + -
104B PHE* 3.6 29.3 - - + -
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Residues in contact with LEU 208 (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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188A LEU* 5.1 4.0 - - + -
204A ALA* 2.7 26.8 + - + +
205A GLN* 3.8 15.0 - - - +
207A LEU* 1.3 73.4 - - - +
209A ASP* 1.3 58.8 + - - +
211A CYS* 3.8 4.1 - - - +
212A SER* 2.8 33.1 + - - -
220A TRP* 3.4 42.2 - - + +
249A LEU* 4.6 5.8 - - + -
252A LEU* 3.8 38.8 - - + +
253A LEU* 3.7 21.5 - - + -
256A SER* 5.3 7.9 - - - -
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Residues in contact with ASP 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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205A GLN* 3.0 47.1 + - - +
206A LEU* 3.7 9.3 - - + +
208A LEU* 1.3 76.9 - - - +
210A TYR* 1.3 57.7 + - - +
212A SER* 3.2 8.4 + - - -
213A SER* 2.9 29.6 + - - -
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Residues in contact with TYR 210 (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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167A ARG* 3.5 42.0 - - + +
170A VAL* 4.1 22.4 - - + -
171A ASP* 2.7 38.3 + - - -
206A LEU 3.1 16.1 + - - +
207A LEU* 3.6 4.5 - - + +
209A ASP* 1.3 77.6 - - - +
211A CYS* 1.3 65.4 + - - +
213A SER* 2.6 28.1 + - - -
214A LYS* 3.2 39.8 + - + +
216A TYR* 4.4 0.9 - + - -
104B PHE* 3.9 22.4 - + + -
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Residues in contact with CYS 211 (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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170A VAL* 4.0 15.7 - - - -
186A PHE* 6.4 0.4 - - - -
207A LEU* 2.9 41.6 + - - +
208A LEU 3.8 3.6 - - - +
210A TYR* 1.3 70.8 - - - +
212A SER* 1.3 66.1 + - - +
214A LYS* 3.2 5.7 + - - -
216A TYR* 3.1 40.8 + - + +
218A ILE* 3.7 30.7 - - + -
220A TRP* 4.0 16.8 - - + -
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Residues in contact with SER 212 (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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208A LEU 2.8 18.0 + - - -
209A ASP* 3.4 8.1 - - - -
211A CYS* 1.3 75.4 - - - +
213A SER* 1.3 62.3 + - - +
215A GLY* 3.1 15.1 + - - -
256A SER* 4.3 7.3 - - - -
257A THR* 2.7 46.1 + - - +
258A PHE* 4.3 14.9 - - - -
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Residues in contact with SER 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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209A ASP 2.9 13.3 + - - -
210A TYR* 2.6 28.3 + - - -
212A SER* 1.3 76.1 - - - +
214A LYS* 1.3 68.3 + - - +
215A GLY 3.5 0.4 + - - -
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Residues in contact with LYS 214 (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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171A ASP* 4.6 4.9 + - - -
210A TYR* 3.4 47.8 + - + +
211A CYS 3.2 3.1 + - - +
212A SER 3.2 0.6 - - - -
213A SER* 1.3 85.4 - - - +
215A GLY* 1.3 61.9 + - - +
216A TYR* 3.5 43.6 + - + -
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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