Contacts of the helix formed by residues 203 - 209 (chain A) in PDB entry 3LX9
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 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A LYS* 4.6 7.6 - - - +
169A PHE 3.2 13.1 + - - -
170A ASP* 3.8 4.4 + - - -
184A TYR* 3.3 11.6 + - - -
201A SER* 5.2 0.9 + - - -
202A CYS* 1.3 72.2 - - - +
204A TRP* 1.3 65.5 + - - +
205A PRO* 3.4 2.0 - - - -
206A ALA* 3.0 15.9 + - - +
207A TYR* 3.3 24.8 - - - -
227A ARG* 4.0 15.4 - - - +
1000A A2G 2.7 34.6 + - - +
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Residues in contact with TRP 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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180A LEU* 3.6 20.9 - - + +
181A ALA* 3.7 30.5 - - + +
184A TYR* 3.2 51.2 + + + -
185A LYS* 3.9 24.7 - - + -
202A CYS* 3.2 5.0 - - + -
203A SER* 1.3 75.4 - - - +
205A PRO* 1.4 71.6 - - + +
207A TYR* 3.1 9.9 + - - -
208A MET* 3.4 31.8 + - - +
218A GLU* 4.1 27.8 - - + -
219A ILE* 3.8 31.6 - - + -
222A TYR* 4.3 18.6 - + + -
223A CYS* 4.1 11.9 - - - -
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Residues in contact with PRO 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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203A SER 3.6 4.3 - - - -
204A TRP* 1.4 97.0 - - + +
206A ALA* 1.3 58.9 + - - -
208A MET* 3.1 22.5 + - + +
209A TRP* 3.1 15.6 + - - +
214A PRO* 3.9 17.0 - - + +
216A TYR* 4.0 2.2 - - - +
219A ILE* 3.7 23.3 - - + -
226A TRP* 3.8 23.6 - - + -
227A ARG 3.3 14.4 - - - +
228A ASN* 3.6 21.7 - - - +
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Residues in contact with ALA 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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203A SER 3.0 8.3 + - - +
205A PRO* 1.3 76.6 - - - +
207A TYR* 1.3 61.4 + - + +
209A TRP* 3.6 16.0 + - - +
227A ARG 3.1 23.5 + - - +
228A ASN 3.4 23.6 + - - +
229A PHE* 3.9 13.4 - - - +
1000A A2G 4.2 15.9 - - + -
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Residues in contact with TYR 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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142A CYS* 3.4 2.9 - - - -
170A ASP* 2.6 30.9 + - - -
171A GLY* 3.3 37.0 - - - +
172A CYS* 3.4 24.1 - - - -
177A LEU* 3.6 16.0 - - + +
180A LEU* 4.2 15.9 - - + -
203A SER* 3.3 22.4 - - - -
204A TRP 3.1 8.6 + - - +
206A ALA* 1.3 76.8 - - + +
208A MET* 1.3 62.8 + - - +
209A TRP 4.4 1.8 - - - -
211A PHE* 3.7 15.1 - - - -
1000A A2G 4.0 20.3 + - + +
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Residues in contact with MET 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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177A LEU* 4.3 13.9 - - + -
180A LEU* 4.2 8.3 - - + -
204A TRP* 3.4 40.6 + - + +
205A PRO* 3.1 9.1 + - - +
207A TYR* 1.3 78.8 - - - +
209A TRP* 1.3 53.5 + - - +
211A PHE* 2.7 33.6 + - - +
212A GLN* 3.0 49.5 + - + +
213A LYS 3.8 17.7 - - - +
214A PRO* 3.8 21.8 - - + -
215A ASN 5.0 1.8 - - - +
219A ILE* 4.9 1.3 - - - -
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Residues in contact with TRP 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 PRO 3.1 14.8 + - - +
206A ALA 3.6 14.9 + - - +
207A TYR* 3.5 0.4 - - - -
208A MET* 1.3 79.5 - - - +
210A PRO* 1.4 102.0 - - + +
211A PHE* 3.4 11.1 - - - -
212A GLN 4.4 3.8 - - - -
214A PRO* 5.2 9.0 - - + -
228A ASN 4.5 7.6 - - - +
229A PHE* 4.4 15.5 - + - -
245A TRP* 3.3 41.0 - + - +
249A ASN* 4.1 6.9 + - - -
252A ARG* 3.8 28.0 - - - +
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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