Contacts of the strand formed by residues 204 - 210 (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 ALA 204 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D VAL* 4.1 28.7 - - + -
169D ARG* 4.0 9.8 - - - +
197D LEU* 5.3 0.4 - - + -
198D LEU 3.5 4.9 - - - -
199D VAL* 4.2 8.3 - - + -
203D GLU* 1.3 78.4 - - - +
205D TRP* 1.3 58.3 + - - +
286D LYS* 3.6 5.8 - - - +
287D LEU* 2.7 49.2 + - + +
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Residues in contact with TRP 205 (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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197D LEU* 3.2 8.6 - - - +
198D LEU* 2.8 48.5 + - + +
203D GLU* 2.6 33.1 + - + +
204D ALA* 1.3 77.9 - - - +
206D HIS* 1.3 60.1 + - - +
240D LEU* 4.3 20.3 - - + +
241D GLN* 3.2 54.5 - - + -
244D LEU* 4.0 17.8 - - + +
284D ALA* 4.0 15.7 - - + -
285D THR 3.3 6.5 - - - -
286D LYS* 3.4 53.8 - - + +
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Residues in contact with HIS 206 (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* 4.4 2.5 - - + -
184D LEU* 3.9 12.6 - - + -
189D TYR* 3.4 29.7 - + - -
195D GLU* 3.0 30.1 + - - +
196D MSE 3.5 10.5 - - - -
197D LEU* 4.0 10.8 - - + -
204D ALA 4.2 0.4 - - - -
205D TRP* 1.3 75.0 - - - +
207D ILE* 1.3 93.2 + - - +
208D SER* 4.1 10.3 - - - -
244D LEU* 4.5 0.7 - - - -
284D ALA* 3.4 1.6 - - - -
285D THR* 2.7 44.9 + - - +
287D LEU* 3.8 22.2 - - + -
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Residues in contact with ILE 207 (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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194D PHE 5.9 0.2 - - - +
195D GLU* 3.2 3.5 - - - -
196D MSE 2.9 45.2 + - + +
206D HIS* 1.3 84.1 + - - +
208D SER* 1.3 76.7 + - - +
244D LEU* 3.8 24.0 - - + +
245D GLU* 4.1 11.7 - - - -
248D THR* 3.4 42.6 - - + +
282D PHE* 3.6 23.8 - - + +
283D SER 4.1 7.2 - - - +
284D ALA* 4.0 18.4 - - + +
285D THR* 5.8 0.2 - - - -
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Residues in contact with SER 208 (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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193D ARG* 2.6 52.2 + - - +
194D PHE 3.2 7.2 - - - -
195D GLU* 3.8 13.7 - - - -
206D HIS* 4.1 8.9 + - - -
207D ILE* 1.3 81.4 - - - +
209D ARG* 1.3 62.9 + - - +
248D THR* 5.0 0.9 - - - -
282D PHE* 3.8 18.0 - - - +
283D SER 5.2 1.4 + - - +
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Residues in contact with ARG 209 (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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193D ARG* 3.6 12.4 - - - +
194D PHE* 2.9 90.2 + - + +
196D MSE 5.1 5.1 - - - +
208D SER* 1.3 76.9 + - - +
210D PRO* 1.3 75.5 + - + +
212D VAL* 6.1 0.6 - - - +
222D VAL* 4.2 4.0 - - - +
226D THR* 5.5 1.2 + - - -
248D THR* 3.3 35.6 + - + +
251D VAL* 3.7 29.6 - - - +
252D TYR* 3.6 31.8 - - - +
255D MSE 4.7 7.9 - - - +
282D PHE* 3.9 18.2 - - + -
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Residues in contact with PRO 210 (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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192D ASP 4.9 0.2 - - - +
193D ARG* 3.9 21.1 - - - +
194D PHE* 4.4 0.9 - - - +
209D ARG* 1.3 107.2 + - + +
211D LEU* 1.3 69.7 + - - +
212D VAL* 3.6 1.6 + - - +
252D TYR* 3.8 29.5 - - + +
282D PHE* 3.3 24.7 - - + -
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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