Contacts of the strand formed by residues 193 - 199 (chain C) in PDB entry 1VI9
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 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C HIS* 5.4 4.0 - - - -
185C ALA* 5.8 3.3 + - - -
189C TYR* 3.3 21.6 - - - +
190C SER* 3.3 30.4 + - - +
191C ARG* 4.1 3.5 - - - +
192C ASP* 1.3 86.0 - - + +
194C PHE* 1.3 64.1 + - - +
195C GLU* 2.5 44.0 + - - +
206C HIS* 4.8 3.2 - - - -
208C SER* 3.0 28.9 + - - +
209C ARG 4.0 8.3 - - - +
210C PRO* 5.1 3.6 - - + -
211C LEU* 3.8 9.2 - - - +
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Residues in contact with PHE 194 (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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182C LYS 3.3 27.8 - - - -
183C HIS* 3.3 39.7 - + + -
193C ARG* 1.3 71.7 - - - +
195C GLU* 1.3 60.4 + - - +
196C MSE 3.9 16.6 - - + +
208C SER* 3.1 4.8 + - - -
209C ARG* 2.9 90.6 + - + +
210C PRO 4.5 1.3 - - - +
211C LEU* 3.6 26.8 - - + +
222C VAL* 5.1 9.6 - - + -
226C THR* 6.1 0.4 - - - -
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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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161C VAL* 5.1 0.2 - - - -
183C HIS* 3.9 4.5 + - - -
184C LEU* 3.2 39.3 + - + +
185C ALA 5.5 1.7 - - - +
188C GLY* 3.4 6.1 - - - -
189C TYR* 2.7 37.4 + - - -
190C SER 3.6 8.5 + - - +
193C ARG* 2.5 36.5 + - - +
194C PHE* 1.3 73.6 - - - +
196C MSE 1.3 68.8 + - - +
206C HIS* 2.5 39.0 + - + +
207C ILE 3.5 4.3 - - - +
208C SER* 4.0 3.6 - - - -
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Residues in contact with MSE 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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180C LEU* 4.6 7.0 - - + -
181C VAL 3.4 8.3 - - - +
182C LYS* 3.4 29.2 - - - +
184C LEU* 4.2 3.6 - - - -
194C PHE* 3.9 15.9 - - + -
195C GLU* 1.3 81.9 - - - +
197C LEU* 1.3 63.6 + - - +
206C HIS* 3.6 6.6 - - - -
207C ILE* 3.0 41.4 + - + +
209C ARG* 4.9 6.7 - - + +
226C THR* 4.0 27.4 - - + -
244C LEU* 3.9 16.1 - - + +
247C VAL* 4.9 3.1 - - + -
248C THR* 3.4 37.7 - - + +
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Residues in contact with LEU 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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161C VAL* 4.1 7.2 - - + +
164C ALA* 3.6 32.8 - - + -
165C VAL* 3.9 21.8 - - + +
179C VAL 3.5 0.2 - - - +
180C LEU* 3.3 10.4 - - - +
181C VAL* 2.8 47.3 + - + -
184C LEU* 4.0 16.4 - - + +
196C MSE 1.3 77.0 - - - +
198C LEU* 1.3 60.2 + - - +
199C VAL* 4.0 8.7 - - + -
205C TRP 3.3 16.2 - - - +
206C HIS* 3.9 13.7 - - + -
244C LEU* 5.1 1.3 - - - -
287C LEU* 3.7 26.7 - - + -
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Residues in contact with LEU 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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178C ILE* 3.7 20.6 - - + -
179C VAL 3.4 13.9 - - - +
180C LEU* 3.9 20.2 - - + -
197C LEU* 1.3 72.7 - - - +
199C VAL* 1.3 61.7 + - - +
200C THR* 4.4 0.8 + - - -
203C GLU 4.6 0.2 - - - -
204C ALA* 3.6 1.2 - - - -
205C TRP* 2.8 41.3 + - + +
230C LEU* 4.1 22.2 - - + -
234C LEU* 5.2 0.9 - - + -
240C LEU* 3.5 52.5 - - + +
243C ALA* 4.8 1.6 - - + -
244C LEU* 4.2 27.7 - - + +
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Residues in contact with VAL 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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165C VAL* 4.4 15.3 - - + -
168C ALA* 4.1 28.9 - - + -
169C ARG* 3.8 21.1 - - + +
172C ILE* 3.9 4.1 - - + +
178C ILE* 3.5 5.4 - - - +
179C VAL* 2.8 43.8 + - + +
181C VAL* 5.2 0.4 - - + -
197C LEU* 4.2 20.0 - - + -
198C LEU* 1.3 79.7 - - - +
200C THR* 1.3 79.0 + - - +
203C GLU 3.3 8.5 - - - +
204C ALA* 4.3 13.2 - - + -
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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