Contacts of the strand formed by residues 204 - 210 (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 ALA 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C VAL* 4.2 32.3 - - + -
169C ARG* 4.2 3.8 - - - +
197C LEU* 5.5 0.2 - - + -
198C LEU 3.6 4.7 - - - -
199C VAL* 4.3 6.7 - - + +
203C GLU* 1.3 78.6 - - - +
205C TRP* 1.3 64.1 + - - +
286C LYS* 3.6 5.7 - - - +
287C LEU* 2.8 47.2 + - + +
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Residues in contact with TRP 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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197C LEU* 3.3 10.2 - - - +
198C LEU* 2.8 40.1 + - + +
203C GLU* 2.8 29.0 + - - +
204C ALA* 1.3 82.2 - - - +
206C HIS* 1.3 61.2 + - - +
240C LEU* 3.9 26.4 - - + +
241C GLN* 3.7 47.6 - - + -
244C LEU* 3.8 18.7 - - + +
284C ALA* 3.9 16.2 - - + -
285C THR 3.6 5.8 - - - -
286C LYS* 3.4 57.1 - - + +
287C LEU* 4.5 0.2 - - - -
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Residues in contact with HIS 206 (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* 4.7 2.7 - - + +
184C LEU* 4.4 5.4 - - + -
189C TYR* 3.5 27.7 - + - -
193C ARG* 4.5 3.6 - - - -
195C GLU* 2.5 46.6 + - + +
196C MSE 3.6 10.1 - - - -
197C LEU* 3.9 11.0 - - + -
205C TRP* 1.3 76.3 - - - +
207C ILE* 1.3 83.5 + - - +
208C SER* 4.5 4.9 - - - -
244C LEU* 4.3 1.3 - - - -
283C SER 4.5 0.2 - - - +
284C ALA* 3.4 2.6 - - - +
285C THR* 2.8 42.0 + - - +
287C LEU* 3.5 28.9 - - + +
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Residues in contact with ILE 207 (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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195C GLU* 3.5 4.9 - - - +
196C MSE 3.0 45.1 + - + +
206C HIS* 1.3 83.6 + - - +
208C SER* 1.3 78.5 + - - +
244C LEU* 3.6 24.9 - - + +
245C GLU* 4.0 13.7 - - + -
248C THR* 3.6 38.1 - - + +
282C PHE* 3.7 24.2 - - + +
283C SER 3.9 13.9 - - - +
284C ALA* 4.0 10.8 - - + +
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Residues in contact with SER 208 (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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193C ARG* 3.0 52.4 + - - +
194C PHE 3.1 13.8 + - - -
195C GLU* 4.0 5.2 - - - -
206C HIS* 4.5 2.5 - - - -
207C ILE* 1.3 82.1 - - - +
209C ARG* 1.3 72.4 + - - +
248C THR* 4.3 1.7 - - - +
282C PHE* 3.7 21.5 - - - +
283C SER 5.2 0.6 + - - -
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Residues in contact with ARG 209 (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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193C ARG* 3.9 3.1 - - - +
194C PHE* 2.9 79.3 + - + +
196C MSE 4.9 7.7 - - + +
208C SER* 1.3 81.0 + - - +
210C PRO* 1.3 85.5 + - + +
222C VAL* 4.1 10.5 - - - +
226C THR* 5.1 2.2 + - - +
248C THR* 3.4 41.0 + - + +
251C VAL* 3.6 31.5 - - - +
252C TYR* 3.7 17.7 - - - +
255C MSE 5.2 5.9 - - - +
282C PHE* 3.9 20.0 - - + -
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Residues in contact with PRO 210 (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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193C ARG* 5.1 6.5 - - + -
209C ARG* 1.3 102.0 + - + +
211C LEU* 1.3 68.3 + - - +
212C VAL* 3.7 1.7 + - - +
252C TYR* 3.5 38.2 - - + +
282C PHE* 3.4 23.6 - - + -
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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