Contacts of the helix formed by residues 196 - 205 (chain M) 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 ARG 196 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193M LYS 3.8 0.4 + - - -
194M ASP* 2.8 13.2 + - + +
195M LEU* 1.3 78.4 - - - +
197M ASP* 1.3 53.5 + - - +
198M CYS 3.0 1.6 - - - -
199M LEU* 2.7 6.5 + - - +
200M LEU* 2.4 37.9 + - - +
220M ILE* 3.8 28.4 - - + +
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Residues in contact with ASP 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M ALA* 3.9 27.2 - - + +
194M ASP* 4.2 8.1 - - + +
196M ARG* 1.3 77.5 - - - +
198M CYS* 1.3 56.8 + - - +
200M LEU* 3.7 9.8 - - - +
201M ILE* 2.9 28.4 + - - +
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Residues in contact with CYS 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M GLY* 5.1 6.0 - - - -
190M VAL 4.7 11.7 - - - +
191M ALA 3.7 22.2 - - - +
192M ALA* 3.7 8.0 - - + +
193M LYS 4.2 9.4 + - - +
195M LEU* 5.2 4.5 - - - -
196M ARG 3.0 0.6 - - - -
197M ASP* 1.3 78.6 - - - +
199M LEU* 1.3 57.6 + - - +
201M ILE* 3.3 6.3 + - - +
202M GLN* 2.9 27.2 + - - +
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Residues in contact with LEU 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M LEU 3.7 16.7 + - - +
196M ARG* 2.7 15.3 + - - +
198M CYS* 1.3 73.3 - - - +
200M LEU* 1.3 58.3 + - - +
202M GLN* 3.7 8.2 - - - +
203M LEU* 2.9 28.2 + - - +
220M ILE* 4.7 15.5 - - + +
253M ILE* 6.5 0.4 - - + -
256M LEU* 5.8 8.1 - - + -
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Residues in contact with LEU 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M ARG 2.4 24.9 + - - +
197M ASP* 3.7 11.2 - - - +
199M LEU* 1.3 71.5 - - - +
201M ILE* 1.3 60.4 + - - +
203M LEU* 3.2 6.9 + - - +
204M SER* 2.9 28.6 + - - -
217M ARG* 5.9 4.0 - - + +
220M ILE* 5.1 12.0 - - + +
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Residues in contact with ILE 201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183M GLN* 5.7 8.3 - - + -
184M ARG* 5.9 6.7 - - + +
188M VAL 4.2 11.0 - - - +
189M GLY* 5.6 3.4 - - - -
192M ALA* 6.2 0.7 - - + -
197M ASP 2.9 18.3 + - - +
198M CYS* 3.7 7.0 - - - +
200M LEU* 1.3 76.5 - - - +
202M GLN* 1.3 59.4 + - - +
204M SER* 2.7 22.8 + - - +
205M GLN* 3.5 9.5 + - - +
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Residues in contact with GLN 202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M VAL* 4.4 14.8 + - + +
189M GLY* 5.5 2.0 - - - -
198M CYS 2.9 17.6 + - - +
199M LEU* 3.7 9.2 - - - +
200M LEU 3.2 0.2 - - - -
201M ILE* 1.3 78.9 - - - +
203M LEU* 1.3 59.4 + - - +
204M SER 3.6 0.2 + - - -
205M GLN* 3.6 11.6 + - - +
206M PHE* 3.6 11.8 + - - +
256M LEU* 5.8 7.9 - - + -
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Residues in contact with LEU 203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199M LEU 2.9 17.7 + - - +
200M LEU* 3.2 7.6 + - - +
202M GLN* 1.3 76.1 - - - +
204M SER* 1.3 63.5 + - - +
205M GLN 3.3 0.2 - - - -
206M PHE* 3.3 19.9 + - + +
207M ALA* 3.7 8.3 + - - +
213M LEU* 6.0 3.8 - - + +
217M ARG* 4.5 22.0 - - + -
220M ILE* 5.4 5.2 - - + -
253M ILE* 5.8 8.5 - - + -
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Residues in contact with SER 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200M LEU 2.9 12.2 + - - -
201M ILE* 2.7 28.9 + - - +
203M LEU* 1.3 80.1 - - - +
205M GLN* 1.3 57.6 + - - +
207M ALA* 3.3 23.3 - - - +
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Residues in contact with GLN 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M ARG* 6.3 3.8 - - + -
188M VAL* 5.2 15.3 - - + +
201M ILE 3.5 10.6 + - - +
202M GLN* 3.6 6.9 + - - +
203M LEU 3.3 0.4 - - - -
204M SER* 1.3 79.4 + - - +
206M PHE* 1.3 57.6 + - - +
207M ALA 3.2 4.1 + - - +
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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