Contacts of the helix formed by residues 204 - 215 (chain A) in PDB entry 1QDE
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 PRO 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ASP* 3.8 11.4 - - + +
202A THR* 3.0 29.8 - - - +
203A MET* 1.3 83.4 - - - +
205A ASN* 1.3 52.0 + - - +
206A ASP* 2.9 12.6 - - + +
207A VAL* 2.7 39.8 + - + +
208A LEU* 2.7 20.6 - - - +
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Residues in contact with ASN 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 MET 3.5 1.4 + - - -
204A PRO* 1.3 71.3 - - - +
206A ASP* 1.3 60.7 + - - +
208A LEU* 3.4 14.6 + - - +
209A GLU* 3.1 23.0 + - - +
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Residues in contact with ASP 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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175A LEU* 4.1 30.2 - - + +
180A LYS* 3.4 33.2 + - - +
184A TYR* 5.3 0.2 + - - -
204A PRO* 2.8 9.6 + - + +
205A ASN* 1.3 77.5 - - - +
207A VAL* 1.3 65.6 + - + +
209A GLU* 3.2 12.4 - - - +
210A VAL* 3.2 25.2 + - - +
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Residues in contact with VAL 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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171A ALA* 4.6 0.2 - - + -
172A ASP* 3.8 25.8 - - + +
175A LEU* 4.1 13.5 - - + -
198A LEU* 3.8 32.0 - - + +
200A SER* 4.0 3.4 - - - +
203A MET* 4.1 23.6 - - + -
204A PRO* 2.7 43.8 + - + +
206A ASP* 1.3 68.9 - - + +
208A LEU* 1.3 64.9 + - - +
209A GLU 3.1 0.2 + - - -
210A VAL* 3.2 5.1 + - - +
211A THR* 3.0 26.9 + - - +
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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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62A LEU* 4.9 10.3 - - + -
203A MET* 2.9 44.0 - - + +
204A PRO 2.7 33.0 - - - +
205A ASN* 3.5 14.1 - - - +
207A VAL* 1.3 77.0 - - - +
209A GLU* 1.3 56.3 + - - +
211A THR* 3.2 8.5 - - + -
212A THR* 2.9 36.4 + - + +
220A ARG* 5.5 4.7 - - - +
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Residues in contact with GLU 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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180A LYS* 2.8 30.1 + - - -
184A TYR* 3.6 11.4 + - - +
205A ASN 3.1 13.6 + - - +
206A ASP* 3.2 17.0 - - - +
208A LEU* 1.3 74.2 - - - +
210A VAL* 1.3 66.2 + - - +
212A THR* 2.9 21.7 + - - +
213A LYS* 3.0 13.2 + - + +
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Residues in contact with VAL 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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168A LEU* 4.7 4.7 - - + -
175A LEU* 3.6 24.9 - - + -
180A LYS* 5.7 0.7 - - + -
183A ILE* 5.4 1.3 - - + -
184A TYR* 4.1 26.7 - - + +
187A PHE* 3.9 18.8 - - + -
196A VAL* 6.2 0.2 - - + -
198A LEU* 4.3 16.8 - - + -
206A ASP* 3.2 14.2 + - - +
207A VAL 3.2 5.8 + - - +
209A GLU* 1.3 76.2 - - - +
211A THR* 1.3 58.0 + - - +
213A LYS* 3.3 2.0 + - - -
214A PHE* 2.9 51.1 + - + +
215A MET* 5.0 1.6 - - + +
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Residues in contact with THR 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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62A LEU* 3.9 30.7 - - + +
198A LEU* 4.0 5.7 - - - +
207A VAL* 3.0 14.8 + - - +
208A LEU* 3.2 14.0 - - + +
210A VAL* 1.3 79.4 - - - +
212A THR* 1.3 62.4 + - + +
215A MET* 3.2 58.6 + - + +
218A PRO* 4.5 4.1 - - + +
220A ARG* 4.2 18.6 - - - +
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Residues in contact with THR 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* 2.9 20.7 + - + +
209A GLU* 2.9 18.2 + - - +
211A THR* 1.3 80.8 - - + +
213A LYS* 1.3 59.5 + - - +
214A PHE 3.6 0.2 - - - -
215A MET 4.2 7.9 - - - +
220A ARG* 5.5 7.0 - - - +
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Residues in contact with LYS 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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184A TYR* 3.8 29.6 - - + +
209A GLU* 3.0 18.7 + - + +
210A VAL* 3.9 3.6 - - - +
212A THR* 1.3 81.1 + - - +
214A PHE* 1.3 93.1 + - + +
215A MET 5.1 0.4 - - - -
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Residues in contact with PHE 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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60A ASP* 3.8 6.2 - - - +
184A TYR* 3.8 29.6 - + - -
187A PHE* 3.4 70.9 - + + -
188A THR* 5.3 7.2 - - + -
196A VAL* 3.8 13.4 - - + +
210A VAL* 2.9 31.1 + - + +
213A LYS* 1.3 118.6 - - + +
215A MET* 1.3 64.3 + - + +
216A ARG* 4.7 8.7 + - - +
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Residues in contact with MET 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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60A ASP* 3.2 12.1 - - + +
61A VAL 4.2 16.2 - - - +
62A LEU* 4.3 4.7 - - + -
196A VAL* 4.1 22.2 - - + +
198A LEU* 3.4 38.1 - - + -
210A VAL* 5.2 1.3 - - + +
211A THR* 3.2 46.3 + - + +
212A THR* 4.2 8.7 - - - +
213A LYS 5.1 0.5 - - - -
214A PHE* 1.3 83.1 - - + +
216A ARG* 1.3 64.3 + - - +
217A ASN 4.1 1.1 + - - -
218A PRO* 3.9 31.9 - - + +
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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