Contacts of the helix formed by residues 200 - 208 (chain A) in PDB entry 2W2R
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 GLN 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A TYR* 3.9 26.2 - - + +
82A ASP* 4.9 7.9 + - - +
193A MSE 5.0 1.3 - - - -
196A LYS 4.8 1.7 - - - +
197A TYR* 3.0 35.3 + - - +
199A SER* 1.3 90.9 + - - +
201A ILE* 1.3 64.7 + - - +
202A GLN 3.4 2.5 - - - -
203A LYS* 3.5 7.8 + - + +
204A GLU* 3.0 47.2 + - + +
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Residues in contact with ILE 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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110A LEU* 4.4 7.6 - - + +
190A TRP* 4.2 28.9 - - + +
193A MSE 4.1 40.2 - - + -
197A TYR 4.0 0.4 + - - -
198A GLN* 3.3 23.3 - - + +
199A SER 3.4 2.2 - - - -
200A GLN* 1.3 78.3 - - - +
202A GLN* 1.3 64.5 + - - +
204A GLU* 5.2 0.7 - - - -
205A GLY* 2.9 23.2 + - - -
212A LEU* 3.5 22.4 - - + +
220A TRP* 4.0 36.6 - - + +
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Residues in contact with GLN 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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199A SER 5.2 1.0 + - - -
200A GLN 3.4 0.4 - - - -
201A ILE* 1.3 85.0 - - - +
203A LYS* 1.3 66.2 + - - +
205A GLY* 3.4 5.9 + - - -
206A LEU* 3.5 11.1 + - - +
210A LEU 4.8 2.8 - - - +
212A LEU* 2.9 37.4 + - + +
213A SER* 4.3 5.7 - - - +
220A TRP* 3.6 32.4 - - + -
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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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82A ASP* 5.3 5.9 + - - -
200A GLN* 3.5 8.3 + - - +
201A ILE 3.3 0.2 - - - -
202A GLN* 1.3 82.2 - - - +
204A GLU* 1.3 78.7 + - - +
206A LEU* 3.3 19.3 + - - +
207A LYS* 4.1 6.9 + - - +
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Residues in contact with GLU 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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81A TYR* 4.0 20.9 - - + -
82A ASP* 3.8 16.8 - - - +
85A THR* 2.6 32.6 + - + +
110A LEU* 4.0 17.9 - - + -
200A GLN* 3.0 32.0 + - + +
203A LYS* 1.3 94.7 - - - +
205A GLY* 1.3 65.3 + - - +
207A LYS* 2.7 36.0 + - - +
208A PHE* 3.3 14.2 - - - -
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Residues in contact with GLY 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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110A LEU* 4.1 18.3 - - - +
201A ILE 2.9 18.8 + - - -
202A GLN 3.9 1.8 - - - -
203A LYS 3.2 0.4 - - - -
204A GLU* 1.3 78.4 - - - +
206A LEU* 1.3 55.4 + - - +
208A PHE* 2.9 21.4 + - - +
210A LEU* 3.1 31.8 + - - +
212A LEU* 4.4 2.7 - - - -
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Residues in contact with LEU 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 GLN 3.5 7.3 + - - +
203A LYS* 3.3 13.8 + - - +
204A GLU 3.1 0.8 - - - -
205A GLY* 1.3 76.6 - - - +
207A LYS* 1.3 62.9 + - + +
209A GLY* 3.0 11.5 + - - -
210A LEU 3.4 9.0 + - - +
211A ILE* 4.4 24.0 - - + -
226A SER* 5.0 11.7 - - - +
229A LYS* 4.6 4.5 - - - +
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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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82A ASP* 2.7 38.4 + - - +
85A THR* 3.1 9.4 + - - +
86A ALA* 3.8 19.9 - - - +
89A SER* 3.4 21.0 + - - +
203A LYS* 4.6 5.8 - - - +
204A GLU* 2.7 40.4 + - - +
206A LEU* 1.3 76.8 - - + +
208A PHE* 1.3 59.3 + - + +
209A GLY 3.3 0.4 - - - -
229A LYS* 3.3 28.0 - - - +
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Residues in contact with PHE 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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85A THR* 4.1 24.7 - - - -
88A VAL* 3.7 31.6 - - + -
89A SER* 3.8 14.6 - - - +
91A TRP* 4.3 9.2 - + - -
92A ASP* 5.8 0.7 - - - -
106A LYS* 2.8 51.1 + - + +
109A ALA* 3.8 16.4 - - + -
110A LEU* 3.7 34.8 - - + -
113A SER* 4.5 3.8 - - - -
204A GLU 3.3 18.8 - - - -
205A GLY* 2.9 8.7 + - - +
207A LYS* 1.3 79.7 - - + +
209A GLY* 1.3 57.8 + - - +
210A LEU* 3.9 13.9 - - + -
229A LYS* 4.2 6.1 - - - +
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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