Contacts of the helix formed by residues 210 - 220 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209K PHE* 1.3 75.6 - - - +
211K GLU* 1.3 62.2 + - - +
212K ARG 3.4 4.7 - - - -
213K ALA* 3.5 8.3 - - - +
214K ARG* 3.0 27.4 + - - +
246K PRO* 3.6 17.0 - - - +
247K LEU 3.4 23.3 + - - -
248K ASP* 4.5 5.8 - - - -
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Residues in contact with GLU 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K THR* 1.3 76.0 - - - +
212K ARG* 1.3 58.9 + - - +
214K ARG* 3.9 2.8 - - - +
215K GLU* 2.9 31.5 + - - +
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Residues in contact with ARG 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K THR* 3.4 1.6 - - - -
211K GLU* 1.3 77.0 - - - +
213K ALA* 1.3 60.9 + - - +
215K GLU* 3.9 5.6 - - - +
216K THR* 2.9 33.3 + - - -
248K ASP* 3.3 21.5 - - - +
250K ILE 4.9 1.4 - - - +
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Residues in contact with ALA 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208K GLY 5.6 0.2 - - - +
209K PHE* 4.2 10.1 - - + -
210K THR* 3.5 16.4 + - - +
211K GLU 3.3 0.4 - - - -
212K ARG* 1.3 79.6 - - - +
214K ARG* 1.3 57.4 + - - +
217K LEU* 2.8 36.3 + - - +
247K LEU* 3.5 23.1 - - + +
248K ASP 4.1 2.8 + - - -
250K ILE* 3.8 24.6 - - + +
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Residues in contact with ARG 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209K PHE* 4.5 11.8 - - + +
210K THR 3.0 18.4 + - - +
211K GLU* 4.2 2.7 - - - +
213K ALA* 1.3 75.0 - - - +
215K GLU* 1.3 58.6 + - - +
217K LEU* 4.7 1.6 - - - -
218K LEU* 2.6 40.6 + - + +
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Residues in contact with GLU 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211K GLU 2.9 20.6 + - - +
212K ARG* 3.9 5.8 - - - +
214K ARG* 1.3 77.2 - - - +
216K THR* 1.3 52.6 + - - +
218K LEU* 5.0 0.2 - - - -
219K ASN* 2.6 41.6 + - - +
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Residues in contact with THR 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K ARG 2.9 18.5 + - - -
215K GLU* 1.3 77.8 - - - +
217K LEU* 1.3 63.8 + - - +
219K ASN* 4.2 3.5 - - - +
220K TYR* 3.7 16.5 + - - +
250K ILE 3.8 18.6 - - - -
251K ILE* 5.8 0.4 - - - -
252K ILE* 4.5 7.8 - - - +
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Residues in contact with LEU 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K ILE* 5.6 1.4 - - - +
190K ALA* 6.2 4.5 - - + -
213K ALA* 2.8 21.9 + - + +
214K ARG* 4.7 1.3 - - - -
216K THR* 1.3 78.0 - - - +
218K LEU* 1.3 61.0 + - - +
219K ASN 3.5 0.2 + - - -
220K TYR* 3.5 16.5 + - - +
222K TRP* 5.7 2.9 - - - +
232K VAL* 6.1 3.6 - - + -
250K ILE* 5.0 8.2 + - + +
251K ILE 6.2 0.2 - - - -
252K ILE* 5.0 12.2 - - + +
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Residues in contact with LEU 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K GLU* 5.4 8.8 - - - +
186K ILE* 4.3 25.6 - - + +
214K ARG* 2.6 27.1 + - + +
217K LEU* 1.3 76.5 - - - +
219K ASN* 1.3 64.9 + - - +
220K TYR 3.4 7.8 + - - +
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Residues in contact with ASN 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K GLU 2.6 24.4 + - - +
216K THR* 4.2 5.2 - - - +
217K LEU 3.3 0.2 - - - -
218K LEU* 1.3 77.4 - - - +
220K TYR* 1.3 61.1 + - - +
221K ARG 3.9 0.3 + - - -
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Residues in contact with TYR 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216K THR 3.7 10.0 + - - +
217K LEU 3.5 13.4 + - - +
218K LEU 3.2 11.1 - - - +
219K ASN* 1.3 81.4 - - - +
221K ARG* 1.3 65.3 + - - +
222K TRP* 3.2 12.2 + - + +
252K ILE* 4.4 17.5 - - + -
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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