Contacts of the helix formed by residues 210 - 219 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209G PHE* 1.3 75.2 - - - +
211G GLU* 1.3 63.4 + - - +
212G ARG 3.4 1.1 - - - -
213G ALA* 3.4 7.6 - - - +
214G ARG* 2.9 27.0 + - - +
246G PRO* 4.1 9.0 - - - +
247G LEU 3.4 22.6 + - - -
248G ASP* 4.2 12.6 - - - -
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Residues in contact with GLU 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G THR* 1.3 75.8 - - - +
212G ARG* 1.3 58.9 + - - +
214G ARG* 4.5 1.1 - - - +
215G GLU* 2.9 35.1 + - - +
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Residues in contact with ARG 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G THR* 3.4 0.6 - - - -
211G GLU* 1.3 78.4 - - - +
213G ALA* 1.3 54.7 - - - +
215G GLU* 4.6 1.8 - - - -
216G THR* 2.6 40.4 + - - +
248G ASP 3.3 19.4 + - - +
249G ASP* 4.5 8.1 - - + -
250G ILE 4.4 2.2 + - - -
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Residues in contact with ALA 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209G PHE* 4.0 10.5 - - + -
210G THR 3.4 22.3 + - - +
211G GLU 3.3 0.4 - - - -
212G ARG* 1.3 79.2 - - - +
214G ARG* 1.3 51.6 + - - +
217G LEU* 2.7 38.7 + - - +
247G LEU* 3.4 22.2 - - + +
248G ASP 3.7 3.3 + - - +
250G ILE* 3.9 23.3 - - + +
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Residues in contact with ARG 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G MET* 5.8 4.8 - - + +
209G PHE* 4.0 17.2 - - + +
210G THR 2.9 17.5 + - - +
211G GLU* 4.5 1.1 - - - +
213G ALA* 1.3 74.4 - - - +
215G GLU* 1.3 61.4 + - - +
217G LEU* 3.7 4.2 - - - +
218G LEU* 2.9 32.7 + - - +
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Residues in contact with GLU 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211G GLU 2.9 21.9 + - - +
212G ARG* 4.6 2.0 - - - -
214G ARG* 1.3 79.0 - - - +
216G THR* 1.3 56.1 + - - +
218G LEU* 3.6 3.3 + - - +
219G ASN* 3.1 30.0 + - - +
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Residues in contact with THR 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G ARG* 2.6 26.2 + - - -
213G ALA 4.5 0.2 - - - -
215G GLU* 1.3 76.3 - - - +
217G LEU* 1.3 57.9 + - - +
219G ASN* 3.7 4.8 - - - +
220G TYR* 3.0 28.6 + - - +
250G ILE 3.5 24.0 - - - +
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Residues in contact with LEU 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G ILE* 4.1 11.5 - - - +
187G MET* 6.2 0.9 - - - -
190G ALA* 4.2 24.5 - - + +
213G ALA 2.7 24.0 + - - +
214G ARG* 3.7 6.5 - - - +
215G GLU 3.2 0.2 - - - -
216G THR* 1.3 76.1 - - - +
218G LEU* 1.3 63.5 + - - +
220G TYR* 3.4 18.7 + - - +
250G ILE* 4.9 7.6 - - + -
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Residues in contact with LEU 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G GLU* 3.3 40.5 - - - +
186G ILE* 3.9 13.3 - - + +
187G MET* 4.7 14.6 - - + +
214G ARG 2.9 17.0 + - - +
215G GLU* 4.2 3.4 - - - +
217G LEU* 1.3 77.6 - - - +
219G ASN* 1.3 58.7 + - - +
220G TYR 3.7 2.1 + - - +
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Residues in contact with ASN 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G GLU* 5.4 1.3 - - - -
215G GLU 3.1 19.1 + - - +
216G THR* 3.7 5.4 - - - +
218G LEU* 1.3 75.1 - - - +
220G TYR* 1.3 66.5 + - - +
221G ARG 3.8 0.2 + - - -
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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