Contacts of the strand formed by residues 215 - 220 (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 THR 215 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191P HIS* 4.2 1.9 - - - -
210P ALA* 3.4 4.9 - - - +
211P SER* 3.2 24.5 + - - -
213P ASP* 3.1 37.0 + - - +
214P LYS* 1.3 80.7 + - - +
216P ILE* 1.3 65.7 + - - +
217P LYS* 3.7 14.1 - - + -
229P THR* 2.8 38.6 - - + -
230P PHE 4.1 4.7 - - - +
231P THR* 5.7 3.8 - - - +
237P VAL* 3.7 2.8 - - - +
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Residues in contact with ILE 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208P VAL* 3.6 22.7 - - + -
209P SER 3.1 16.4 - - - +
215P THR* 1.3 80.5 - - - +
217P LYS* 1.3 61.4 + - - +
229P THR* 3.3 1.9 - - - +
230P PHE* 2.7 58.4 + - + +
233P HIS* 4.2 7.0 - - + +
237P VAL* 4.0 13.9 - - + -
240P VAL* 3.6 11.9 - - + -
249P ILE* 5.0 2.5 - - + -
251P SER* 3.5 17.7 - - - +
261P TRP* 3.4 43.3 - - + +
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Residues in contact with LYS 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190P GLY* 4.3 17.2 + - - -
191P HIS* 2.9 37.2 - - + +
192P ASP* 6.0 0.2 + - - -
207P ILE 3.6 0.3 - - - +
208P VAL* 3.3 7.6 - - - +
209P SER* 3.0 29.6 + - - -
213P ASP* 4.7 3.1 - - - -
215P THR* 3.7 6.1 - - + -
216P ILE* 1.3 74.3 - - - +
218P MET* 1.3 61.9 + - - +
219P TRP* 3.4 29.1 - - + +
226P CYS* 3.4 20.1 - - - +
228P LYS 3.5 4.0 - - - -
229P THR* 3.3 33.6 + - + -
230P PHE* 5.1 0.2 - - - -
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Residues in contact with MET 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201P MET* 4.2 7.2 - - - +
206P HIS* 4.4 30.1 - - + +
207P ILE 3.1 9.2 - - - +
208P VAL* 3.7 26.9 - - + -
217P LYS* 1.3 73.8 - - - +
219P TRP* 1.3 59.4 + - - +
226P CYS* 3.7 0.7 - - - -
227P VAL* 2.8 39.8 + - + +
228P LYS* 2.9 47.5 + - + +
230P PHE* 4.2 10.1 - - + -
249P ILE* 5.6 0.2 - - + -
263P VAL* 3.6 30.3 - - + -
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Residues in contact with TRP 219 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174P ILE* 3.2 21.2 - - + +
188P MET* 3.3 46.4 - - + -
189P HIS 3.6 36.3 - - - -
190P GLY* 3.6 7.6 - - - -
191P HIS* 3.8 18.8 - + - -
206P HIS* 3.2 8.7 - - - -
207P ILE* 2.7 55.2 + - + +
209P SER* 2.7 25.0 + - - -
217P LYS* 3.4 18.1 - - + +
218P MET* 1.3 76.8 - - - +
220P GLU* 1.3 63.1 + - - +
221P VAL 3.4 0.3 + - - -
224P GLY 3.9 14.8 - - - -
225P TYR 3.1 6.1 - - - +
226P CYS* 3.9 24.0 - - + -
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Residues in contact with GLU 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188P MET* 5.1 0.2 - - - +
205P ASP 4.2 3.1 - - - +
206P HIS* 3.7 23.3 - - + -
219P TRP* 1.3 72.8 - - - +
221P VAL* 1.3 62.4 + - - +
222P GLN* 4.6 10.1 - - + +
223P THR* 2.8 39.8 - - + +
224P GLY* 2.8 32.2 + - - -
225P TYR* 2.8 20.4 + - + +
227P VAL* 3.7 21.8 - - + +
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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