Contacts of the helix formed by residues 198 - 210 (chain A) in PDB entry 1YQA
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A SER* 1.3 74.7 - - - +
199A ARG* 1.3 61.6 + - - +
200A ILE* 3.2 14.6 + - - +
201A VAL* 3.0 22.5 + - - +
202A LEU* 2.8 26.2 + - - +
244A GLY 3.6 21.4 + - - -
245A ILE* 4.0 4.0 - - - +
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Residues in contact with ARG 199 (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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198A SER* 1.3 74.9 + - - +
200A ILE* 1.3 58.6 + - + +
202A LEU* 3.7 2.4 - - - +
203A LYS* 2.7 46.7 + - + +
223A PHE* 3.6 24.9 - - + -
224A ASN* 3.6 33.1 + - - +
227A ILE* 5.0 7.4 - - + -
238A GLN* 5.4 0.4 - - - +
242A PRO* 3.3 30.8 + - - +
243A SER* 3.4 26.6 + - - +
244A GLY 4.4 5.5 + - - +
246A ILE* 3.4 22.7 - - + +
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Residues in contact with ILE 200 (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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198A SER* 3.2 9.7 + - - +
199A ARG* 1.3 81.4 - - + +
201A VAL* 1.3 60.3 + - + +
203A LYS* 3.8 22.7 - - + +
204A LYS* 2.8 37.9 + - + +
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Residues in contact with VAL 201 (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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191A LEU* 4.0 20.9 - - + -
192A ASN* 5.7 2.0 - - - +
197A SER* 4.0 10.8 - - - -
198A SER* 3.0 30.0 + - - +
200A ILE* 1.3 79.8 - - + +
202A LEU* 1.3 57.1 + - - +
204A LYS* 3.4 14.2 - - + +
205A TYR* 3.0 29.8 + - - +
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Residues in contact with LEU 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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184A ILE* 3.5 28.0 - - + -
187A SER* 3.7 12.8 - - - +
188A MET* 4.5 7.9 - - + -
191A LEU* 3.5 23.8 - - + -
197A SER* 4.1 5.8 + - - +
198A SER 2.8 19.5 + - - +
199A ARG* 3.7 2.9 - - - +
201A VAL* 1.3 70.5 - - - +
203A LYS* 1.3 54.1 + - - +
205A TYR* 3.0 3.1 + - - +
206A VAL* 2.7 53.0 + - + +
223A PHE* 3.2 24.5 - - + -
227A ILE* 4.5 0.4 - - + -
246A ILE* 3.9 29.4 - - + -
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Residues in contact with LYS 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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199A ARG* 2.7 31.7 + - - +
200A ILE* 3.8 23.6 - - + +
202A LEU* 1.3 72.1 - - - +
204A LYS* 1.3 55.7 + - - +
206A VAL* 3.7 3.1 - - - +
207A LYS* 2.8 52.3 + - + +
219A PHE* 4.3 4.5 - - + -
220A ASP* 2.7 51.5 + - - +
223A PHE* 3.6 20.1 - - + -
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Residues in contact with LYS 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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191A LEU* 6.0 0.4 - - - -
200A ILE* 2.8 20.9 + - + +
201A VAL* 3.4 19.1 - - + +
203A LYS* 1.3 78.8 - - - +
205A TYR* 1.3 79.6 + - + +
207A LYS* 4.0 4.5 - - - +
208A ASP* 3.1 35.6 + - + +
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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
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171A LYS* 5.3 6.8 + - - +
172A ALA 4.7 5.5 + - - -
174A SER* 4.5 2.6 + - - -
187A SER* 3.6 26.7 - - - -
190A GLN* 3.9 32.8 - - + +
191A LEU* 3.7 28.0 - - + -
201A VAL 3.0 17.0 + - - +
202A LEU* 3.0 5.2 + - + +
204A LYS* 1.3 91.5 - - - +
206A VAL* 1.3 54.6 + - - +
208A ASP* 3.2 6.8 + - - +
209A THR* 2.7 64.5 + - + +
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Residues in contact with VAL 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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183A MET* 4.7 9.6 - - + +
184A ILE* 4.6 5.8 - - + -
187A SER* 3.7 13.9 - - - +
202A LEU* 2.7 44.0 + - + +
203A LYS* 3.7 3.4 - - - +
205A TYR* 1.3 71.7 - - - +
207A LYS* 1.3 53.4 + - - +
209A THR* 3.8 5.2 - - - -
210A TYR* 2.7 51.6 + - + +
213A VAL* 3.5 9.2 - - + -
219A PHE* 3.3 31.0 - - + -
223A PHE* 3.9 12.3 - - + -
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Residues in contact with LYS 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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203A LYS* 2.8 34.3 + - + +
204A LYS* 4.2 4.9 - - - +
206A VAL* 1.3 73.0 - - - +
208A ASP* 1.3 61.1 + - - +
210A TYR 3.1 15.6 - - - +
211A PRO* 3.9 2.9 - - - +
213A VAL* 2.8 32.0 + - - +
214A GLY* 3.5 26.4 + - - +
216A ALA 3.1 15.4 + - - -
217A SER* 4.9 0.8 - - - +
219A PHE* 3.4 20.1 - - + -
220A ASP* 3.4 31.2 + - - +
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Residues in contact with ASP 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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204A LYS* 3.1 28.8 + - + +
205A TYR* 3.2 10.3 + - + +
207A LYS* 1.3 79.0 - - - +
209A THR* 1.3 71.2 + - - +
211A PRO* 4.4 8.7 - - - +
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Residues in contact with THR 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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173A SER* 6.2 0.4 - - - -
174A SER* 3.2 41.1 + - - +
175A PRO 4.5 2.8 - - - +
205A TYR* 2.7 57.9 + - + +
206A VAL* 3.8 0.2 - - - -
208A ASP* 1.3 80.8 - - - +
210A TYR* 1.3 76.1 + - - +
211A PRO* 3.1 10.7 - - - +
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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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174A SER* 3.5 11.7 - - - -
175A PRO* 3.4 33.7 - - + +
176A SER* 4.5 5.6 - - - -
178A LEU* 4.0 6.1 - - + +
183A MET* 3.2 63.0 + - + -
186A LYS* 3.3 24.6 - - - +
187A SER* 4.8 2.5 - - - -
206A VAL* 2.7 34.4 + - + +
207A LYS 3.1 7.4 - - - +
209A THR* 1.3 95.5 - - - +
211A PRO* 1.3 66.8 - - - +
212A ILE* 3.1 6.5 - - + -
213A VAL* 3.0 34.4 + - + +
214A GLY 3.1 0.3 + - - -
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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