Contacts of the helix formed by residues 202 - 214 (chain A) in PDB entry 1YAA
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 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A THR* 1.3 77.7 + - - +
203A GLU* 1.3 71.8 + - - +
205A TRP* 3.4 3.0 + - - +
206A VAL* 3.3 26.0 + - - +
238A TYR* 3.5 39.3 + - - -
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Residues in contact with GLU 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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201A THR* 3.2 27.2 + - + +
202A SER* 1.3 85.3 - - - +
204A GLN* 1.3 62.1 + - + +
206A VAL* 3.4 20.7 + - - +
207A GLN* 3.6 15.5 + - - +
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Residues in contact with GLN 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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168A LEU* 3.6 27.0 + - - +
170A LEU* 3.5 36.9 - - + +
199A ASP 4.8 1.2 - - - +
200A PRO* 3.9 10.9 - - + +
201A THR* 3.0 39.2 + - + +
203A GLU* 1.3 76.9 - - + +
205A TRP* 1.3 64.7 + - - +
207A GLN* 3.1 14.2 + - - +
208A ILE* 3.1 26.6 + - - +
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Residues in contact with TRP 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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160A TYR* 6.4 0.9 - + - -
173A PHE* 5.4 2.0 - + - -
188A LEU* 4.1 31.2 - - + -
189A HIS 3.3 27.8 - - - -
190A SER 4.1 6.9 + - - -
199A ASP* 5.3 2.4 - - - +
200A PRO* 3.2 51.4 + - + +
201A THR 3.0 10.7 + - - -
202A SER 3.6 8.5 - - - +
204A GLN* 1.3 75.6 - - - +
206A VAL* 1.3 57.7 + - - +
208A ILE* 3.3 28.0 + - + +
209A VAL* 2.9 42.1 + - + +
221A PHE* 4.4 4.0 - + - -
238A TYR* 4.0 20.2 - + + -
239A ALA* 3.4 32.1 - - + +
242A LEU* 4.1 5.4 - - + -
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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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202A SER 3.3 15.9 + - - +
203A GLU* 3.5 12.6 - - - +
204A GLN 3.2 0.4 - - - -
205A TRP* 1.3 78.8 - - - +
207A GLN* 1.3 59.1 + - + +
209A VAL* 4.0 0.7 - - - +
210A ASP* 2.9 42.1 + - - +
238A TYR* 3.5 16.8 - - - +
242A LEU* 3.9 14.1 - - + +
243A LYS* 3.7 20.9 - - - +
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Residues in contact with GLN 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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170A LEU* 3.2 31.1 - - - +
174A LEU* 3.6 18.1 - - + +
203A GLU* 3.6 9.9 + - - +
204A GLN* 3.1 21.9 + - - +
206A VAL* 1.3 77.1 - - + +
208A ILE* 1.3 63.6 + - - +
210A ASP* 3.5 6.3 + - - +
211A ALA* 3.1 24.3 + - - +
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Residues in contact with ILE 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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170A LEU* 4.1 7.0 - - + -
173A PHE* 3.4 43.1 - - + -
174A LEU* 3.9 24.9 - - + -
177A ILE* 4.0 8.8 - - + +
188A LEU* 4.8 1.3 - - + -
200A PRO* 3.9 26.2 - - + -
204A GLN 3.1 16.0 + - - +
205A TRP* 3.7 26.0 - - + +
207A GLN* 1.3 77.1 - - - +
209A VAL* 1.3 61.6 + - + +
211A ALA* 3.4 3.8 + - - +
212A ILE* 3.1 34.5 + - + +
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Residues in contact with VAL 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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188A LEU* 6.0 1.1 - - + -
205A TRP* 2.9 33.6 + - + +
206A VAL 4.0 2.7 - - - +
208A ILE* 1.3 75.1 - - + +
210A ASP* 1.3 58.8 + - - +
212A ILE* 3.3 11.3 + - + +
213A ALA* 2.9 26.9 + - - +
221A PHE* 4.9 6.1 - - + -
239A ALA 4.7 4.3 - - - +
242A LEU* 4.2 39.9 - - + +
243A LYS* 3.9 35.0 - - + -
244A LEU* 4.6 9.3 - - + +
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Residues in contact with ASP 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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206A VAL* 2.9 26.8 + - - +
207A GLN* 3.8 7.0 - - - +
208A ILE 3.4 0.2 - - - -
209A VAL* 1.3 75.5 - - - +
211A ALA* 1.3 58.4 + - - +
213A ALA* 3.4 7.3 + - - +
214A SER* 2.8 33.2 + - - +
243A LYS* 3.1 33.0 + - - +
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Residues in contact with ALA 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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174A LEU* 3.4 33.0 - - + -
177A ILE* 3.7 16.3 - - + +
178A GLN* 4.9 13.6 + - - +
207A GLN 3.1 7.0 + - - +
208A ILE 3.6 4.5 - - - +
210A ASP* 1.3 75.6 - - - +
212A ILE* 1.3 64.3 + - - +
214A SER* 3.4 7.0 + - - -
215A LYS* 3.2 29.3 + - - +
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Residues in contact with ILE 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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177A ILE* 4.0 21.1 - - + -
186A PHE* 4.4 17.0 - - + -
188A LEU* 3.9 28.9 - - + -
208A ILE* 3.1 26.8 + - + +
209A VAL* 3.3 10.7 + - + +
211A ALA* 1.3 74.3 - - - +
213A ALA* 1.3 64.3 + - - +
215A LYS 3.4 1.0 + - - -
216A ASN* 3.2 2.9 + - - -
217A HIS* 3.0 61.9 + - + +
218A ILE 4.9 0.2 - - - -
219A ALA* 4.6 7.6 - - + +
244A LEU* 4.3 19.1 - - + -
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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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209A VAL* 2.9 19.3 + - + +
210A ASP* 3.5 9.0 - - - +
212A ILE* 1.3 77.7 - - - +
214A SER* 1.3 61.4 + - - +
216A ASN* 3.3 14.2 + - - -
243A LYS* 4.7 7.9 - - + +
244A LEU* 3.7 22.2 - - + -
247A VAL* 3.6 22.4 - - + +
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Residues in contact with SER 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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178A GLN* 5.1 7.2 - - - -
182A GLU* 4.5 6.1 - - - +
210A ASP* 2.8 21.8 + - - +
211A ALA* 3.5 9.5 - - - -
212A ILE 3.3 0.2 - - - -
213A ALA* 1.3 75.5 - - - +
215A LYS* 1.3 64.2 + - - +
216A ASN* 3.8 4.3 + - - +
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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