Contacts of the helix formed by residues 195 - 205 (chain C) in PDB entry 3D7S
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 PRO 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C LEU 3.5 9.6 - - - +
164C LYS* 3.8 19.7 - - + +
170C HIS* 3.7 21.5 - - + +
193C ALA 3.7 2.5 - - - +
194C MET* 1.3 101.4 - - + +
196C GLN* 1.3 66.0 + - - +
197C TYR* 3.5 22.0 - - + -
198C ILE* 3.2 14.7 + - + +
199C LEU* 3.2 14.4 + - - +
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Residues in contact with GLN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C MET 3.8 1.2 + - - -
195C PRO* 1.3 72.1 - - - +
197C TYR* 1.3 52.4 + - - +
199C LEU* 2.7 46.5 + - - +
200C ASP* 2.7 45.9 + - - +
203C ASP* 5.6 1.2 + - - -
209C TRP* 5.9 0.4 - - - -
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Residues in contact with TYR 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C HIS* 3.3 37.0 - + - +
174C GLN* 3.9 14.8 + - - -
195C PRO* 3.8 19.5 - - + -
196C GLN* 1.3 78.5 - - - +
198C ILE* 1.3 90.4 + - + +
200C ASP* 3.8 10.7 + - - +
201C MET* 3.0 29.9 + - + +
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Residues in contact with ILE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C HIS* 4.0 16.4 - - + +
173C THR* 4.0 15.0 - - + -
174C GLN* 3.9 26.0 - - + -
194C MET* 3.8 31.4 - - + -
195C PRO* 3.2 10.6 + - + +
196C GLN 2.9 1.2 + - - -
197C TYR* 1.3 114.1 - - + +
199C LEU* 1.3 63.0 + - + +
201C MET* 3.1 13.4 - - + +
202C LEU* 2.7 45.3 - - + +
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C PHE* 3.7 21.8 - - + -
194C MET* 3.5 36.3 - - + +
195C PRO 3.2 11.4 - - - +
196C GLN* 2.7 34.0 + - - +
198C ILE* 1.3 72.5 - - - +
200C ASP* 1.3 51.3 + - - +
202C LEU* 2.7 12.2 + - - +
203C ASP* 2.7 37.1 + - - +
209C TRP* 3.6 39.5 + - + +
211C LEU* 5.1 7.6 - - + -
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Residues in contact with ASP 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C GLN* 2.7 52.7 + - - +
197C TYR* 3.8 8.2 + - - +
199C LEU* 1.3 71.0 - - - +
201C MET* 1.3 52.5 + - - +
203C ASP* 2.5 41.8 + - + +
204C GLU* 2.7 27.1 + - + +
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Residues in contact with MET 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLN* 4.1 40.2 - - + +
177C ALA* 3.9 10.3 - - + -
197C TYR* 3.0 19.6 + - + +
198C ILE* 3.1 26.9 + - + +
200C ASP* 1.3 75.4 - - - +
202C LEU* 1.3 72.6 + - + +
204C GLU* 3.5 16.2 + - - +
205C LYS* 3.3 52.8 + - - +
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Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C THR* 4.1 16.8 - - + -
177C ALA* 4.9 2.2 - - + -
184C PHE* 4.2 11.2 - - + -
186C PHE* 3.7 34.5 - - + -
198C ILE* 2.7 34.1 - - + +
199C LEU* 2.7 13.3 + - - +
201C MET* 1.3 91.0 - - + +
203C ASP* 1.3 61.2 + - - +
204C GLU 3.2 0.2 - - - -
205C LYS 4.0 0.2 - - - -
206C GLY 3.3 1.7 + - - -
207C ILE* 2.6 58.5 + - + +
209C TRP* 3.9 19.3 - - + -
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Residues in contact with ASP 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C GLN* 5.6 1.0 + - - -
199C LEU* 2.7 12.8 + - - +
200C ASP* 2.5 36.7 + - + +
202C LEU* 1.3 73.1 - - - +
204C GLU* 1.3 60.2 + - + +
206C GLY* 3.2 13.7 + - - -
207C ILE 5.4 0.2 - - - -
209C TRP* 3.4 24.5 + - - +
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Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C ASP* 2.7 19.7 + - + +
201C MET* 3.5 19.6 - - - +
203C ASP* 1.3 71.6 - - + +
205C LYS* 1.3 66.7 + - + +
206C GLY 2.9 9.5 + - - -
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Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ALA* 3.1 27.8 - - - +
178C LYS* 5.9 2.9 - - - -
201C MET* 3.3 46.0 + - - +
202C LEU 3.8 0.4 + - - -
203C ASP 3.6 0.2 - - - -
204C GLU* 1.3 80.9 + - + +
206C GLY* 1.3 66.3 + - - +
207C ILE* 3.6 21.7 - - + +
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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