Contacts of the helix formed by residues 210 - 219 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209L PHE* 1.3 76.1 - - - +
211L GLU* 1.3 61.3 + - - +
212L ARG 3.4 1.3 - - - -
213L ALA* 3.4 7.8 - - - +
214L ARG* 2.9 27.2 + - - +
246L PRO* 4.1 8.8 - - - +
247L LEU 3.4 22.4 + - - -
248L ASP* 4.2 12.8 - - - -
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Residues in contact with GLU 211 (chain L).
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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210L THR* 1.3 74.8 - - - +
212L ARG* 1.3 59.0 + - - +
214L ARG* 4.5 1.3 - - - +
215L GLU* 2.9 35.0 + - - +
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Residues in contact with ARG 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L THR* 3.4 0.8 - - - -
211L GLU* 1.3 77.9 - - - +
213L ALA* 1.3 54.0 + - - +
215L GLU* 4.6 2.2 - - - -
216L THR* 2.6 40.8 + - - +
248L ASP 3.3 20.5 + - - +
249L ASP* 4.5 7.4 - - + -
250L ILE 4.4 2.4 + - - -
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Residues in contact with ALA 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209L PHE* 4.0 9.9 - - + -
210L THR 3.4 22.5 + - - +
211L GLU 3.3 0.4 - - - -
212L ARG* 1.3 79.9 - - - +
214L ARG* 1.3 50.7 + - - +
217L LEU* 2.7 39.2 + - - +
247L LEU* 3.4 22.2 - - + +
248L ASP 3.7 3.5 + - - +
250L ILE* 3.9 23.0 - - + +
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Residues in contact with ARG 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L MET* 5.8 5.1 - - + +
209L PHE* 4.0 17.4 - - + +
210L THR 2.9 16.8 + - - +
211L GLU* 4.5 1.6 - - - +
213L ALA* 1.3 75.7 - - - +
215L GLU* 1.3 60.0 + - - +
217L LEU* 3.7 4.3 - - - +
218L LEU* 2.9 32.4 + - - +
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Residues in contact with GLU 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211L GLU 2.9 20.7 + - - +
212L ARG* 4.6 2.5 - - - -
214L ARG* 1.3 78.5 - - - +
216L THR* 1.3 56.3 + - - +
218L LEU* 3.6 3.6 + - - +
219L ASN* 3.1 29.6 + - - +
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Residues in contact with THR 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212L ARG* 2.6 26.5 + - - +
213L ALA 4.5 0.2 - - - -
215L GLU* 1.3 75.8 - - - +
217L LEU* 1.3 57.2 + - - +
219L ASN* 3.7 4.6 - - - +
220L TYR* 3.0 28.6 + - - +
250L ILE 3.5 23.7 - - - +
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Residues in contact with LEU 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L ILE* 4.1 10.5 - - - +
187L MET* 6.2 0.9 - - - -
190L ALA* 4.2 24.0 - - + -
213L ALA 2.7 24.3 + - - +
214L ARG* 3.7 6.3 - - - +
215L GLU 3.2 0.2 - - - -
216L THR* 1.3 76.1 - - - +
218L LEU* 1.3 64.1 + - - +
220L TYR* 3.4 18.2 + - - +
250L ILE* 4.9 8.1 - - + -
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Residues in contact with LEU 218 (chain L).
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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183L GLU* 3.3 40.0 - - - +
186L ILE* 3.9 14.0 - - + +
187L MET* 4.7 14.6 - - + +
214L ARG 2.9 16.5 + - - +
215L GLU* 4.2 3.6 - - - +
217L LEU* 1.3 76.4 - - - +
219L ASN* 1.3 59.3 + - - +
220L TYR 3.7 2.1 + - - +
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Residues in contact with ASN 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183L GLU* 5.4 1.1 - - - -
215L GLU 3.1 18.5 + - - +
216L THR* 3.7 5.4 - - - +
218L LEU* 1.3 73.8 - - - +
220L TYR* 1.3 66.0 + - - +
221L ARG* 3.8 0.9 + - - -
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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