Contacts of the strand formed by residues 206 - 211 (chain D) in PDB entry 1VYH
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 HIS 206 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D ILE* 3.7 2.4 - - - +
201D MET* 3.1 43.3 + - + +
203D ASN* 3.8 11.8 + - - +
205D ASP* 1.3 102.2 + - + +
207D ILE* 1.3 63.7 + - - +
218D MET* 3.5 30.6 - - + +
219D TRP 3.2 13.4 + - - +
220D GLU* 3.7 28.1 - - + -
221D VAL* 3.2 8.4 - - - +
227D VAL* 4.9 7.8 - - + +
228D LYS* 6.3 0.2 - - - -
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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
----------------------------------------------------------
166D ALA* 4.3 7.6 - - + -
174D ILE* 4.4 2.2 - - + -
176D LEU* 3.8 29.2 - - + -
188D MET* 3.8 16.6 - - + -
198D VAL* 3.8 23.1 - - + -
199D SER 3.4 5.6 - - - +
200D ILE* 3.6 31.2 - - + -
206D HIS* 1.3 72.0 - - - +
208D VAL* 1.3 65.7 + - - +
218D MET* 3.2 6.7 - - - +
219D TRP* 2.7 59.2 + - + +
221D VAL* 3.7 26.5 - - + -
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Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D VAL* 3.1 7.1 - - - +
199D SER* 2.8 43.3 + - - +
201D MET* 3.2 34.8 - - + -
207D ILE* 1.3 73.6 - - - +
209D SER* 1.3 66.2 + - - +
216D ILE* 3.5 28.3 - - + -
217D LYS 3.3 4.7 - - - +
218D MET* 3.4 19.7 - - + -
230D PHE* 5.8 0.2 - - + -
240D VAL* 3.8 17.2 - - + +
249D ILE* 3.6 13.7 - - + -
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Residues in contact with SER 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ILE* 3.4 20.9 - - - -
191D HIS* 2.8 24.0 + - - -
195D VAL* 4.1 1.8 - - - -
197D SER 3.1 11.7 - - - -
198D VAL* 4.1 2.9 - - - -
208D VAL* 1.3 77.6 - - - +
210D ALA* 1.3 62.5 + - - +
216D ILE* 3.2 10.9 - - - +
217D LYS* 3.0 25.3 + - - +
219D TRP* 2.7 25.4 + - - -
240D VAL* 3.7 3.6 - - - -
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D HIS* 4.3 1.6 - - - -
195D VAL* 3.5 6.2 - - - +
196D SER 2.9 24.1 + - - -
197D SER* 3.0 14.5 + - - -
209D SER* 1.3 73.7 - - - +
211D SER* 1.3 61.0 + - - +
215D THR 3.3 6.7 - - - +
216D ILE* 4.6 2.2 - - + -
237D VAL* 3.9 32.5 - - + +
239D MET 4.5 1.3 - - - -
240D VAL* 3.2 25.1 - - + -
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Residues in contact with SER 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D HIS* 3.3 29.6 - - - -
193D HIS 3.3 9.5 + - - -
194D ASN 2.7 22.4 + - - -
195D VAL* 4.3 0.2 - - - +
196D SER 4.4 0.7 - - - +
210D ALA* 1.3 77.4 - - - +
212D ARG* 1.3 62.8 + - - +
213D ASP* 2.8 23.3 + - - +
214D LYS 3.1 10.9 + - - -
215D THR 3.1 5.9 + - - -
236D TRP* 4.2 0.4 - - - -
237D VAL* 3.0 29.5 + - - +
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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
------------------------------------------------------------
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