Contacts of the helix formed by residues 205 - 214 (chain A) in PDB entry 2NA1
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 THR 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ALA 2.9 15.9 + - - -
169A ALA* 3.0 25.2 + - - -
170A MET 3.4 5.2 - - - -
171A THR* 4.2 2.7 - - - +
203A TYR 3.1 4.0 + - - -
204A TYR* 1.3 78.0 - - - +
206A LEU* 1.3 62.4 + - - +
207A MET* 3.3 22.0 - - + +
208A ASP* 2.8 53.7 + - - +
209A ILE* 3.0 15.6 + - - +
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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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131A ILE* 3.5 29.6 - - + +
133A LEU* 3.8 19.3 - - + -
166A CYS* 3.4 33.4 - - - -
167A PRO 3.6 8.1 - - - +
168A ALA* 3.1 8.3 + - - +
170A MET* 2.9 22.3 + - + +
171A THR* 5.6 0.9 - - - -
172A VAL 6.1 0.2 - - - +
175A LEU* 3.9 24.5 - - + -
205A THR* 1.3 71.9 - - - +
207A MET* 1.3 58.6 + - - +
209A ILE* 3.3 20.9 + - + +
210A ALA* 2.9 26.5 + - - +
221A LEU* 4.2 12.8 - - + +
223A LEU* 4.3 2.7 - - + -
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Residues in contact with MET 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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125A ILE 4.7 5.8 - - - +
126A THR 3.4 12.3 - - - +
127A ASP* 3.3 41.7 - - + -
129A GLU* 5.5 0.2 - - + -
131A ILE* 5.2 2.2 - - + -
168A ALA* 3.1 34.1 + - + +
169A ALA* 4.5 0.7 - - - +
205A THR* 3.4 12.8 - - + -
206A LEU* 1.3 76.1 - - - +
208A ASP* 1.3 54.1 + - - +
210A ALA* 2.8 8.3 + - - +
211A TYR* 2.7 36.6 + - + +
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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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203A TYR* 4.1 4.9 - - - +
204A TYR* 3.7 14.2 - - + -
205A THR* 2.8 49.3 + - - +
207A MET* 1.3 71.0 - - - +
209A ILE* 1.3 53.0 + - - +
211A TYR* 3.1 7.3 + - - +
212A ILE* 2.6 54.7 + - + +
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Residues in contact with ILE 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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172A VAL* 4.2 12.3 - - + +
175A LEU* 5.6 0.2 - - + -
195A TYR* 4.0 18.2 - - + -
200A LEU* 3.6 27.8 - - + -
204A TYR* 4.2 15.3 - - + -
205A THR 3.0 14.3 + - - +
206A LEU* 3.5 27.6 - - + +
207A MET 3.1 0.2 - - - -
208A ASP* 1.3 77.2 - - - +
210A ALA* 1.3 64.0 + - - +
212A ILE* 4.4 3.4 - - - -
213A TYR* 2.8 47.6 + - + +
221A LEU* 4.1 13.9 - - + +
223A LEU* 4.3 9.2 - - + -
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Residues in contact with ALA 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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131A ILE* 4.6 7.4 - - + -
206A LEU 2.9 13.0 + - - +
207A MET* 2.8 11.4 + - - +
209A ILE* 1.3 75.0 - - - +
211A TYR* 1.3 54.1 + - - +
214A THR* 2.8 30.5 + - - -
215A TRP* 3.0 47.8 + - + +
221A LEU* 4.5 5.8 - - + +
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Residues in contact with TYR 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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207A MET* 2.7 17.1 + - + +
208A ASP* 3.5 9.9 - - - +
210A ALA* 1.3 70.8 - - - +
212A ILE* 1.3 73.6 + - + +
214A THR* 3.4 11.7 + - - +
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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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204A TYR* 3.8 43.5 - - + +
208A ASP* 2.6 37.8 + - + +
209A ILE* 3.8 3.8 - - - +
211A TYR* 1.3 85.0 - - + +
213A TYR* 1.4 90.9 + - + +
214A THR* 3.3 3.2 + - - +
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Residues in contact with TYR 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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195A TYR* 3.5 64.5 + + + -
196A GLU* 4.1 6.3 - - - -
198A GLU* 3.2 37.1 + - - +
199A PRO 5.1 1.0 + - - -
200A LEU* 3.8 23.0 - - + +
204A TYR* 5.4 2.6 - + - -
209A ILE* 2.8 32.4 + - + +
210A ALA* 5.5 0.2 - - - -
212A ILE* 1.4 96.3 - - + +
214A THR* 1.3 80.4 + - - +
215A TRP* 3.1 4.2 + - + +
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Residues in contact with THR 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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210A ALA 2.8 9.4 + - - -
211A TYR* 3.4 8.0 + - - +
212A ILE 3.3 5.5 - - - +
213A TYR* 1.3 94.5 - - - +
215A TRP* 1.3 65.7 + - - +
216A ARG* 3.5 16.7 + - - +
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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