Contacts of the strand formed by residues 194 - 203 (chain C) in PDB entry 5O67
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 GLU 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344B LYS* 5.0 10.1 - - - +
358B VAL* 4.1 12.4 - - + +
178C THR* 4.2 15.9 - - + -
179C TYR 3.5 6.5 - - - -
180C GLN* 3.5 25.1 - - + +
193C SER* 1.3 77.3 - - - +
195C GLU* 1.3 64.8 + - - +
196C SER* 5.7 0.7 - - - +
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Residues in contact with GLU 195 (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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178C THR* 3.6 2.3 - - - +
179C TYR* 3.2 37.2 + - - +
194C GLU* 1.3 79.3 - - - +
196C SER* 1.3 70.9 + - - +
197C VAL* 4.8 0.2 - - - +
245C ARG* 3.2 45.5 + - - -
253C TYR* 4.9 9.0 + - - +
254C VAL* 4.4 29.4 - - + +
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Residues in contact with SER 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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176C GLU* 6.6 0.4 - - - -
177C SER 3.4 6.5 - - - -
178C THR* 3.4 23.3 + - - +
194C GLU* 5.7 0.3 - - - +
195C GLU* 1.3 78.8 + - - +
197C VAL* 1.3 71.4 + - - +
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Residues in contact with VAL 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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176C GLU* 3.5 2.1 - - - +
177C SER 3.0 30.7 + - - +
179C TYR* 4.2 20.2 - - + -
195C GLU 4.8 0.4 - - - +
196C SER* 1.3 82.2 - - - +
198C SER* 1.3 73.2 + - - +
254C VAL* 4.1 17.5 - - + -
255C PRO 3.8 26.0 - - - +
256C GLU 4.8 2.2 - - - +
257C SER* 4.2 10.8 - - - +
258C LEU* 4.0 25.1 - - + -
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Residues in contact with SER 198 (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 TYR* 4.8 5.6 - - - -
175C ARG 3.3 15.0 - - - -
176C GLU* 4.2 12.1 - - - -
197C VAL* 1.3 84.4 - - - +
199C ARG* 1.3 64.9 + - - +
200C ASP* 4.2 8.2 + - - -
257C SER* 5.2 3.3 - - - -
258C LEU* 4.1 7.4 + - - +
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Residues in contact with ARG 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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173C VAL 4.3 5.6 - - - +
174C TYR* 3.1 18.4 - - - -
175C ARG* 3.1 27.6 + - + +
198C SER* 1.3 79.0 - - - +
200C ASP* 1.3 65.4 + - - +
202C THR* 3.2 25.9 + - - +
236C LYS* 3.6 41.2 - - - +
241C ILE* 5.8 0.8 - - - +
257C SER* 4.1 18.1 + - - -
258C LEU* 3.2 35.6 + - + +
260C THR* 4.0 16.0 + - - +
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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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173C VAL 3.8 0.9 - - - +
174C TYR* 4.0 14.9 - - - -
198C SER* 4.2 7.2 + - - -
199C ARG* 1.3 78.0 + - - +
201C PRO* 1.4 66.2 - - + +
202C THR* 2.2 30.5 + - - -
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Residues in contact with PRO 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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172C VAL* 4.1 15.5 - - + -
173C VAL 3.7 10.7 - - - +
174C TYR* 4.3 17.5 - - + -
200C ASP* 1.4 92.7 - - + +
202C THR* 1.3 59.1 + - - +
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Residues in contact with THR 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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172C VAL* 3.6 9.9 - - - +
173C VAL* 3.1 29.8 + - - +
199C ARG* 3.2 23.1 + - - +
200C ASP 2.2 30.7 + - - -
201C PRO* 1.3 71.0 + - - +
203C ILE* 1.3 72.5 - - - +
204C GLY 3.5 0.3 + - - -
236C LYS* 3.4 37.9 - - + +
260C THR* 4.1 6.6 - - - +
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Residues in contact with ILE 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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170C VAL* 4.1 22.9 - - + -
171C PRO 3.6 10.3 - - - +
172C VAL* 4.6 9.9 - - + +
202C THR* 1.3 76.9 - - - +
204C GLY* 1.3 74.0 + - - +
206C VAL* 4.2 12.1 - - + -
234C THR* 4.1 9.7 - - - +
235C GLY* 3.6 6.6 - - - -
236C LYS* 4.8 0.7 + - - -
260C THR* 3.0 15.0 - - - +
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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