Contacts of the helix formed by residues 210 - 218 (chain N) in PDB entry 5NSS
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 210 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208N GLY 4.1 0.2 - - - -
209N PHE* 1.3 76.7 - - - +
211N GLU* 1.3 65.9 + - - +
212N ARG 3.5 2.5 - - - -
213N ALA* 4.0 5.4 - - - +
214N ARG* 3.4 21.1 + - - +
246N PRO* 4.9 10.1 - - - -
247N LEU 3.3 26.5 + - - -
248N ASP* 4.1 13.2 - - - -
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Residues in contact with GLU 211 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210N THR* 1.3 74.1 - - - +
212N ARG* 1.3 62.3 + - - +
214N ARG* 3.4 5.2 + - - +
215N GLU* 2.9 29.6 + - - +
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Residues in contact with ARG 212 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210N THR* 3.5 1.4 - - - -
211N GLU* 1.3 76.4 - - - +
213N ALA* 1.3 58.6 + - - +
215N GLU* 3.8 6.9 - - - +
216N THR* 2.9 33.6 + - - -
248N ASP* 3.2 27.5 + - + +
249N ASP* 4.2 8.9 - - + +
250N ILE 4.8 0.7 + - - -
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Residues in contact with ALA 213 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208N GLY 5.5 1.3 - - - +
209N PHE* 5.0 5.4 - - + -
210N THR 3.8 20.1 + - - +
211N GLU 3.3 0.6 - - - -
212N ARG* 1.3 77.5 - - - +
214N ARG* 1.3 54.2 + - - +
217N LEU* 2.7 39.7 + - + +
233N VAL* 6.4 1.6 - - + -
247N LEU* 4.1 9.4 - - + +
248N ASP 2.7 17.2 + - - +
250N ILE* 4.6 17.5 - - + +
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Residues in contact with ARG 214 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N GLU 5.7 3.4 - - - +
186N ILE* 6.2 2.7 - - + -
187N MET* 6.3 3.1 - - + -
209N PHE* 5.9 4.9 - - + +
210N THR 3.4 14.5 + - - +
211N GLU* 3.4 6.1 + - - +
213N ALA* 1.3 77.2 - - - +
215N GLU* 1.3 61.0 + - - +
217N LEU* 4.8 0.4 - - - -
218N LEU* 2.5 42.1 + - + +
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Residues in contact with GLU 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211N GLU 2.9 17.5 + - - +
212N ARG* 3.3 8.2 + - - +
214N ARG* 1.3 77.3 - - - +
216N THR* 1.3 52.5 + - - +
218N LEU 5.2 0.2 - - - -
219N ASN* 2.6 39.5 + - - +
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Residues in contact with THR 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212N ARG 2.9 15.2 + - - -
215N GLU* 1.3 74.8 - - - +
217N LEU* 1.3 65.2 + - - +
219N ASN* 3.6 13.7 + - - +
220N TYR* 4.1 5.9 + - - +
249N ASP* 5.8 1.1 - - - -
250N ILE 3.3 24.2 - - - -
251N ILE* 5.1 3.1 - - - -
252N ILE* 5.5 7.8 + - - +
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Residues in contact with LEU 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213N ALA* 2.7 22.6 + - + +
214N ARG* 4.8 0.4 - - - -
216N THR* 1.3 80.7 - - - +
218N LEU* 1.3 59.0 + - - +
219N ASN 3.5 0.5 + - - -
220N TYR* 3.6 14.2 + - - +
222N TRP* 5.2 5.9 - - - +
229N LEU* 5.8 11.2 - - + +
232N VAL* 5.7 8.1 - - + -
233N VAL* 5.8 7.6 - - + -
250N ILE* 4.2 13.1 + - + +
251N ILE 6.3 0.4 - - - -
252N ILE* 6.2 2.2 - - - +
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Residues in contact with LEU 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179N LEU* 4.8 7.6 - - - +
182N ARG 5.7 0.7 - - - -
183N GLU* 3.7 39.8 - - + +
186N ILE* 4.9 8.1 - - + -
214N ARG* 2.5 30.4 + - + +
217N LEU* 1.3 76.1 - - - +
219N ASN* 1.3 65.1 + - - +
220N TYR 3.5 6.7 - - - +
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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