Contacts of the strand formed by residues 206 - 211 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200P ILE* 3.7 3.5 - - - +
201P MET* 3.1 38.9 + - + -
203P ASN* 3.9 10.3 + - - +
205P ASP* 1.3 104.2 + - + +
207P ILE* 1.3 67.6 + - - +
218P MET* 4.4 27.5 - - + +
219P TRP 3.2 16.5 + - - +
220P GLU* 3.7 26.5 - - + -
221P VAL* 3.2 2.1 - - - +
227P VAL* 4.7 10.5 - - + +
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Residues in contact with ILE 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166P ALA* 4.3 9.9 - - + -
174P ILE* 4.7 6.3 - - + -
176P LEU* 4.5 18.6 - - + -
188P MET* 4.6 16.4 - - + -
198P VAL* 3.4 25.8 - - + -
199P SER 3.3 9.4 - - - +
200P ILE* 3.8 24.0 - - + -
206P HIS* 1.3 77.8 - - - +
208P VAL* 1.3 69.1 + - - +
218P MET* 3.1 7.8 - - - +
219P TRP* 2.7 51.9 + - + +
221P VAL* 4.2 18.4 - - + -
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Residues in contact with VAL 208 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198P VAL* 3.2 5.2 - - - +
199P SER* 2.8 43.6 + - - +
201P MET* 3.4 35.2 - - + -
207P ILE* 1.3 79.5 - - - +
209P SER* 1.3 64.5 + - - +
216P ILE* 3.6 23.1 - - + -
217P LYS 3.3 9.9 - - - +
218P MET* 3.7 15.9 - - + -
230P PHE* 5.4 0.7 - - + -
240P VAL* 4.0 16.3 - - + +
242P PRO* 5.0 0.7 - - + -
249P ILE* 4.1 13.7 - - + -
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Residues in contact with SER 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174P ILE* 3.6 20.4 - - - -
191P HIS* 2.7 21.7 + - - -
195P VAL* 4.2 4.9 - - - -
197P SER 3.1 12.1 - - - -
198P VAL* 4.7 1.8 - - - -
208P VAL* 1.3 75.7 - - - +
210P ALA* 1.3 62.3 + - - +
216P ILE* 3.1 24.1 - - - +
217P LYS 3.0 13.9 + - - -
219P TRP* 2.7 26.0 + - - -
240P VAL* 3.5 3.8 - - - -
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Residues in contact with ALA 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191P HIS* 4.6 0.7 - - - -
195P VAL* 3.4 6.3 - - - +
196P SER 2.8 30.7 + - - -
197P SER* 3.0 10.9 + - - +
209P SER* 1.3 75.5 - - - +
211P SER* 1.3 57.8 + - - +
215P THR 3.4 6.5 - - - +
216P ILE* 4.5 1.3 - - + -
237P VAL* 3.5 33.7 - - + +
239P MET 4.4 5.6 - - - +
240P VAL* 3.3 20.4 - - + -
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Residues in contact with SER 211 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191P HIS* 3.3 20.5 - - - +
193P HIS 3.2 11.1 + - - -
194P ASN 2.5 22.5 + - - -
195P VAL* 4.6 0.2 - - - -
196P SER 4.4 0.7 - - - +
210P ALA* 1.3 77.8 - - - +
212P ARG* 1.3 59.0 + - - +
213P ASP* 3.0 31.2 + - - +
214P LYS 3.1 10.0 + - - -
215P THR 3.2 5.4 + - - -
236P TRP* 3.7 7.0 - - - -
237P VAL* 2.9 23.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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