Contacts of the helix formed by residues 204 - 215 (chain A) in PDB entry 1WUR
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 ASN 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A VAL* 2.8 30.0 + - + +
201A PHE 4.2 0.5 - - - +
203A GLU* 1.3 71.6 - - - +
205A GLN* 1.3 63.6 + - - +
206A LYS* 3.0 23.3 + - - +
207A THR* 3.1 24.2 + - - +
208A ARG* 3.0 23.7 + - - +
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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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203A GLU 3.5 6.2 + - - +
204A ASN* 1.3 71.6 + - - +
206A LYS* 1.3 64.1 + - + +
208A ARG* 2.7 39.2 + - - +
209A GLU* 2.9 67.8 + - - +
206B LYS* 3.6 42.4 - - + +
210B GLU* 4.6 5.2 - - - +
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Residues in contact with LYS 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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204A ASN* 3.0 10.1 + - - +
205A GLN* 1.3 76.9 - - + +
207A THR* 1.3 61.4 + - - +
209A GLU* 3.7 29.8 + - + +
210A GLU* 2.8 31.2 + - - +
206B LYS* 4.1 17.1 - - - +
205E GLN* 3.8 48.7 - - + +
206E LYS* 5.1 8.9 - - - +
208E ARG* 5.9 0.9 - - - +
209E GLU* 4.3 9.0 + - - +
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Residues in contact with THR 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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96A MET* 3.6 15.8 - - + +
124A ILE* 3.7 31.1 - - + +
200A VAL* 3.9 8.9 - - + +
201A PHE* 3.9 18.6 - - + -
204A ASN* 3.1 37.0 + - - +
206A LYS* 1.3 75.7 - - - +
208A ARG* 1.3 63.9 + - - +
210A GLU* 3.4 5.2 + - - -
211A PHE* 3.1 19.4 + - - +
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Residues in contact with ARG 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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197A MET* 3.2 35.5 - - + +
201A PHE 3.3 14.7 + - - +
202A ARG* 2.5 37.8 + - - +
203A GLU* 4.8 4.4 - - - +
204A ASN 3.0 5.9 + - - +
205A GLN* 2.7 48.1 + - - +
207A THR* 1.3 77.7 - - - +
209A GLU* 1.3 62.7 + - + +
211A PHE* 3.2 3.9 + - - +
212A LEU* 3.0 34.0 + - + +
95B GLU* 4.8 5.3 + - - -
210B GLU* 3.0 33.4 + - - +
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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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205A GLN* 2.9 51.4 + - - +
206A LYS* 3.7 28.6 + - + +
208A ARG* 1.3 76.4 - - + +
210A GLU* 1.3 58.6 + - - +
212A LEU* 3.4 8.3 + - + +
213A SER* 2.9 36.4 + - - +
216A ARG* 5.1 0.2 + - - -
206B LYS* 3.5 20.8 + - - +
209B GLU* 5.1 4.5 - - - +
210B GLU* 5.8 2.2 - - + +
209E GLU* 4.9 7.3 - - - +
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Residues in contact with GLU 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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95A GLU* 4.6 8.5 - - - +
96A MET* 4.0 21.4 - - + +
206A LYS 2.8 18.4 + - - +
207A THR* 3.6 8.1 - - - +
208A ARG 3.2 0.2 - - - -
209A GLU* 1.3 76.8 - - - +
211A PHE* 1.3 63.5 + - - +
213A SER* 3.3 6.9 + - - -
214A HIS* 3.2 35.8 + - + +
205E GLN* 4.7 6.0 - - - +
208E ARG* 3.0 35.0 + - - +
212E LEU* 4.1 25.9 - - + +
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Residues in contact with PHE 211 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A MET* 3.7 10.3 - - - +
98A VAL* 4.0 20.4 - - + -
120A HIS 3.8 14.6 - - - -
121A ILE 3.7 5.4 - - - -
122A GLY* 3.5 26.7 - - - -
170A GLY* 3.5 33.2 - - - -
171A VAL 4.2 0.2 - - - -
172A VAL* 3.9 17.5 - - + -
197A MET* 4.3 8.7 - - + -
201A PHE* 3.7 26.9 - + + -
207A THR 3.1 14.5 + - - +
208A ARG 3.5 6.1 - - - +
210A GLU* 1.3 75.4 - - - +
212A LEU* 1.3 71.6 + - + +
214A HIS* 3.0 20.4 + - - +
215A LEU* 3.5 19.7 + - + +
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Residues in contact with LEU 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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172A VAL* 3.9 27.4 - - + -
195A SER* 6.2 0.2 - - - -
197A MET* 5.8 2.2 - - - -
208A ARG* 3.0 29.7 + - + +
209A GLU* 3.9 6.7 - - + +
211A PHE* 1.3 84.4 - - + +
213A SER* 1.3 62.4 + - - +
215A LEU* 3.1 25.0 + - + +
216A ARG* 3.6 19.7 + - - +
210B GLU* 3.9 38.6 - - + +
213B SER* 6.3 1.8 - - - -
214B HIS* 4.0 24.0 - - + +
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLU* 2.9 23.5 + - - +
210A GLU* 3.6 7.4 - - - -
211A PHE 3.2 0.2 - - - -
212A LEU* 1.3 74.6 - - - +
214A HIS* 1.3 64.7 + - - +
216A ARG* 3.1 50.0 + - - +
212E LEU* 6.3 2.2 - - - -
216E ARG* 3.4 28.8 + - - -
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Residues in contact with HIS 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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96A MET* 4.2 8.8 - - - +
98A VAL* 4.1 33.8 - - + +
100A LYS* 2.9 28.1 + - - +
210A GLU* 3.2 38.5 + - + +
211A PHE 3.0 9.5 + - - +
213A SER* 1.3 78.0 - - - +
215A LEU* 1.3 62.5 + - - +
216A ARG 3.5 5.4 + - - +
172E VAL* 5.0 6.3 - - + -
193E VAL* 4.1 24.6 - - + +
195E SER* 5.5 5.1 + - - -
212E LEU* 4.1 29.4 - - + +
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Residues in contact with LEU 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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98A VAL* 4.1 13.0 - - + -
100A LYS* 4.1 22.9 - - + -
120A HIS* 3.7 48.2 - - + +
172A VAL* 3.9 26.0 - - + -
211A PHE* 3.7 19.1 - - + +
212A LEU* 3.4 16.4 - - + +
213A SER 3.1 1.0 - - - -
214A HIS* 1.3 78.3 - - - +
216A ARG* 1.3 59.4 + - + +
214B HIS* 6.2 0.7 - - + -
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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