Contacts of the strand formed by residues 193 - 199 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D HIS* 5.3 3.6 - - - -
185D ALA* 5.9 2.4 + - - -
190D SER* 3.5 34.6 + - - +
191D ARG 3.3 3.4 + - - +
192D ASP* 1.3 84.5 - - + +
194D PHE* 1.3 60.8 + - - +
195D GLU* 3.7 14.1 + - + +
208D SER* 2.6 49.9 + - - +
209D ARG* 3.6 14.6 - - - +
210D PRO* 3.8 24.1 - - - +
211D LEU* 3.6 14.4 - - - +
282D PHE* 5.1 4.0 - - - -
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Residues in contact with PHE 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D LYS 3.4 25.6 - - - -
183D HIS* 3.6 34.8 - + + -
193D ARG* 1.3 70.9 - - - +
195D GLU* 1.3 60.5 - - - +
196D MSE 3.8 19.7 - - + -
207D ILE* 5.9 0.2 - - - +
208D SER* 3.2 2.4 - - - -
209D ARG* 2.9 83.4 + - + +
210D PRO 4.4 1.1 - - - +
211D LEU* 4.0 22.9 - - + +
222D VAL* 4.2 19.5 - - + -
226D THR* 5.6 1.3 - - - -
248D THR* 5.9 0.2 - - - +
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Residues in contact with GLU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D HIS* 3.7 5.0 + - - -
184D LEU* 2.9 41.3 + - + +
185D ALA 5.5 1.9 - - - +
188D GLY* 3.3 6.9 - - - -
189D TYR* 2.7 27.1 + - - +
190D SER* 2.6 40.7 + - - +
193D ARG* 3.7 10.7 + - + +
194D PHE* 1.3 78.9 - - - +
196D MSE 1.3 68.9 + - - +
206D HIS* 3.0 21.6 + - - +
207D ILE 3.2 6.1 - - - +
208D SER* 3.8 18.6 - - - +
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Residues in contact with MSE 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU* 4.4 8.3 - - + -
181D VAL 3.3 8.7 - - - +
182D LYS* 3.3 33.7 - - - +
184D LEU* 3.9 6.3 - - - -
194D PHE* 3.8 16.6 + - + -
195D GLU* 1.3 77.5 - - - +
197D LEU* 1.3 60.0 + - - +
205D TRP 4.0 0.2 - - - +
206D HIS* 3.5 7.6 - - - -
207D ILE* 2.9 38.6 + - + +
209D ARG* 5.1 4.0 - - - +
226D THR* 3.6 31.0 - - + -
244D LEU* 3.7 18.8 - - + -
247D VAL* 4.8 2.2 - - + -
248D THR* 3.3 34.8 - - + +
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Residues in contact with LEU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D VAL* 4.1 9.2 - - + +
164D ALA* 3.5 33.4 - - + -
165D VAL* 3.9 20.6 - - + +
179D VAL 4.3 0.2 - - - -
180D LEU* 3.3 7.5 - - - +
181D VAL* 2.6 47.7 + - + -
184D LEU* 4.0 16.7 - - + +
196D MSE 1.3 73.0 - - - +
198D LEU* 1.3 59.3 + - - +
199D VAL* 4.1 11.4 - - + -
205D TRP 3.2 15.9 - - - +
206D HIS* 4.0 12.3 - - + -
244D LEU* 5.3 0.7 - - - -
287D LEU* 3.9 26.7 - - + -
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Residues in contact with LEU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ILE* 3.6 29.2 - - + -
179D VAL 3.4 7.0 - - - +
180D LEU* 3.9 18.4 - - + -
197D LEU* 1.3 72.3 - - - +
199D VAL* 1.3 61.1 + - - +
200D THR* 5.6 1.0 - - - +
203D GLU 4.1 0.5 - - - +
204D ALA* 3.5 1.4 - - - -
205D TRP* 2.8 39.0 + - + +
230D LEU* 4.0 22.4 - - + -
234D LEU* 5.4 2.2 - - + -
240D LEU* 3.6 50.6 - - + +
244D LEU* 4.1 27.3 - - + +
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D VAL* 4.4 8.1 - - + +
168D ALA* 3.8 32.5 - - + -
169D ARG* 3.8 21.5 - - + +
172D ILE* 3.8 4.7 - - + +
178D ILE* 3.3 6.1 - - - +
179D VAL* 2.7 41.7 + - + +
181D VAL* 5.3 0.9 - - + -
197D LEU* 4.2 26.9 - - + -
198D LEU* 1.3 78.7 - - - +
200D THR* 1.3 78.7 + - - +
203D GLU 3.5 5.2 - - - +
204D ALA* 4.2 12.1 - - + -
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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