Contacts of the strand formed by residues 215 - 220 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H HIS* 4.3 1.5 - - - -
210H ALA* 3.4 3.6 - - - -
211H SER* 3.1 25.7 + - - -
213H ASP* 3.2 34.5 + - - +
214H LYS* 1.3 80.3 + - - +
216H ILE* 1.3 78.6 + - - +
217H LYS* 4.0 8.5 - - + -
229H THR* 2.9 36.3 - - + -
230H PHE 4.1 6.7 - - - +
231H THR* 5.7 2.1 - - - +
237H VAL* 3.9 2.9 - - - +
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Residues in contact with ILE 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208H VAL* 3.8 22.0 - - + -
209H SER 3.2 17.9 - - - +
210H ALA* 4.2 0.7 - - + -
215H THR* 1.3 81.7 - - - +
217H LYS* 1.3 62.0 + - - +
229H THR* 3.3 2.3 - - - +
230H PHE* 2.7 58.3 + - + +
233H HIS* 4.1 9.9 - - + -
237H VAL* 4.1 9.4 - - + -
240H VAL* 3.9 13.5 - - + -
249H ILE* 5.1 3.4 - - + -
251H SER* 3.4 34.3 - - - +
261H TRP* 3.7 23.1 - - + +
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Residues in contact with LYS 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H GLY* 4.3 11.4 + - - -
191H HIS* 3.4 46.0 - - + +
192H ASP* 5.8 1.8 - - - -
207H ILE 3.6 0.9 - - - +
208H VAL* 3.4 5.4 - - - +
209H SER* 3.0 32.9 + - - -
213H ASP* 4.7 2.7 - - - -
215H THR* 4.4 3.1 - - - -
216H ILE* 1.3 73.2 - - - +
218H MET* 1.3 62.5 + - - +
219H TRP* 3.8 24.5 - - + +
226H CYS* 3.4 25.0 - - - +
228H LYS 3.4 2.5 - - - +
229H THR* 3.3 34.6 + - + +
230H PHE* 5.0 0.4 - - - -
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Residues in contact with MET 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H MET* 4.0 25.4 - - - +
206H HIS* 4.1 30.5 - - + +
207H ILE 3.2 5.6 - - - +
208H VAL* 4.3 9.6 - - + -
217H LYS* 1.3 78.6 - - - +
219H TRP* 1.3 56.4 + - - +
226H CYS* 4.6 0.2 - - - -
227H VAL* 2.7 40.2 + - + +
228H LYS* 2.9 46.7 + - + +
230H PHE* 4.0 15.0 - - + -
249H ILE* 5.5 0.2 - - + -
263H VAL* 3.8 23.8 - - + +
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Residues in contact with TRP 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H ILE* 3.4 24.5 - - + +
188H MET* 3.7 44.4 - - + -
189H HIS 3.4 38.6 - - - -
190H GLY* 3.6 6.1 - - - -
191H HIS* 4.1 7.9 - + - -
206H HIS* 3.2 10.8 + - - -
207H ILE* 2.8 55.7 + - + +
209H SER* 2.7 25.9 + - - -
217H LYS* 3.7 26.3 - - + +
218H MET* 1.3 73.2 - - - +
220H GLU* 1.3 62.8 + - - +
224H GLY 3.8 12.6 - - - -
225H TYR 3.1 5.6 - - - +
226H CYS* 3.8 26.0 - - + -
227H VAL* 4.2 0.2 - - - -
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Residues in contact with GLU 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H MET* 5.5 0.3 - - - +
205H ASP 4.4 2.5 - - - +
206H HIS* 3.8 24.6 - - + -
219H TRP* 1.3 70.0 - - - +
221H VAL* 1.3 58.9 + - - +
222H GLN* 4.9 8.8 - - + +
223H THR* 2.8 35.5 + - + +
224H GLY* 2.8 34.1 + - - -
225H TYR* 2.8 27.6 + - + +
227H VAL* 3.7 20.7 - - + +
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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
------------------------------------------------------------
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