Contacts of the strand formed by residues 204 - 210 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A VAL* 4.0 34.5 - - + -
169A ARG* 4.0 3.1 - - - +
197A LEU* 5.5 0.7 - - + -
198A LEU 3.5 5.6 - - - -
199A VAL* 4.1 9.2 - - + +
203A GLU* 1.3 78.1 - - - +
205A TRP* 1.3 63.7 + - - +
286A LYS* 3.9 5.9 - - - +
287A LEU* 2.9 45.7 + - + +
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Residues in contact with TRP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 3.3 9.5 - - - +
198A LEU* 2.9 36.8 + - + +
203A GLU* 2.7 30.9 + - + +
204A ALA* 1.3 78.6 - - - +
206A HIS* 1.3 60.9 + - - +
240A LEU* 3.9 27.5 - - + +
241A GLN* 3.5 50.5 - - + -
244A LEU* 3.7 20.4 - - + +
284A ALA* 3.9 16.2 - - + -
285A THR 3.4 7.0 - - - -
286A LYS* 3.6 52.8 - - + +
287A LEU* 4.7 0.2 - - - -
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Residues in contact with HIS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL* 4.6 0.7 - - + -
184A LEU* 4.1 7.2 - - + -
189A TYR* 3.5 27.2 - + - -
193A ARG* 4.0 13.9 - - - -
195A GLU* 2.5 45.3 + - + +
196A MSE 3.6 10.3 - - - -
197A LEU* 3.8 16.6 - - + -
205A TRP* 1.3 75.4 - - - +
207A ILE* 1.3 77.0 + - - +
208A SER* 4.6 0.7 - - - -
244A LEU* 4.2 0.7 - - - -
284A ALA* 3.2 5.7 - - - +
285A THR* 2.7 48.1 + - - +
287A LEU* 3.8 16.6 - - + -
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A PHE 3.9 0.4 - - - +
195A GLU* 3.3 6.9 - - - +
196A MSE 3.1 39.7 + - + +
206A HIS* 1.3 82.1 - - - +
208A SER* 1.3 73.3 + - - +
244A LEU* 3.8 30.1 - - + +
245A GLU* 3.9 13.9 - - + -
248A THR* 3.4 47.3 - - + +
282A PHE* 3.7 22.9 - - + +
283A SER 3.9 15.3 - - - +
284A ALA* 4.0 2.7 - - + +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ARG* 3.1 51.8 + - - +
194A PHE 3.1 12.3 + - - -
195A GLU* 3.5 3.7 - - - +
206A HIS* 4.6 1.6 - - - -
207A ILE* 1.3 81.4 - - - +
209A ARG* 1.3 64.4 + - - +
248A THR* 4.6 1.3 - - - -
282A PHE* 3.7 22.9 - - - +
283A SER 4.9 2.0 + - - +
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ARG* 3.8 4.5 - - - +
194A PHE* 2.9 86.7 + - + +
196A MSE 4.8 5.9 - - - +
208A SER* 1.3 77.4 + - - +
210A PRO* 1.3 74.0 + - + +
212A VAL* 6.2 0.4 - - - +
222A VAL* 3.9 19.6 - - - +
226A THR* 5.2 2.0 + - - +
248A THR* 3.9 25.0 + - + +
251A VAL* 3.6 27.9 - - - +
252A TYR* 3.8 29.0 - - - +
255A MSE 5.0 8.2 - - - +
282A PHE* 3.9 17.9 - - + -
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Residues in contact with PRO 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ARG* 4.8 5.4 - - + -
209A ARG* 1.3 100.4 + - + +
211A LEU* 1.3 70.3 + - - +
212A VAL* 3.7 2.8 + - - +
252A TYR* 3.7 37.2 - - + +
282A PHE* 3.5 24.2 - - + -
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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