Contacts of the helix formed by residues 187 - 195 (chain D) in PDB entry 1Y1V
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 187 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D ASP* 1.3 84.7 + - - +
188D ALA* 1.3 67.6 + - + +
189D ASP* 3.8 17.7 - - + +
190D GLU* 3.3 24.0 - - - +
191D ALA 3.4 3.3 + - - -
208D GLU* 3.5 12.1 - - - +
211D LEU* 3.5 8.5 - - - +
167G TYR* 4.1 13.8 + - - +
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Residues in contact with ALA 188 (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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187D THR* 1.3 72.5 - - + +
189D ASP* 1.3 56.5 + - - +
191D ALA* 2.5 25.8 + - - +
192D LYS* 2.6 21.4 + - + -
204D ASP* 3.9 38.8 - - + +
207D LEU* 4.2 22.0 - - + -
208D GLU* 2.9 18.1 + - - +
211D LEU* 4.6 3.4 - - - -
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Residues in contact with ASP 189 (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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187D THR* 4.2 11.1 - - + +
188D ALA* 1.3 76.1 - - - +
190D GLU* 1.3 56.8 + - - +
192D LYS* 4.5 6.5 - - - +
193D THR* 2.8 48.2 + - - -
204D ASP* 5.3 1.2 + - - -
167G TYR* 3.6 23.2 - - - +
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Residues in contact with GLU 190 (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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184D ALA 3.6 5.6 - - - +
185D CYS* 2.7 18.1 - - - -
186D ASP* 2.6 45.6 + - - +
187D THR* 3.3 16.1 + - - +
188D ALA 3.0 0.6 - - - -
189D ASP* 1.3 80.5 - - - +
191D ALA* 1.3 59.8 + - - +
193D THR* 4.0 0.5 - - - -
194D LEU* 2.9 40.8 + - + +
144G ARG* 4.8 6.4 + - - -
167G TYR* 3.2 44.8 - - + +
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Residues in contact with ALA 191 (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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180D LEU* 4.3 14.1 - - + -
185D CYS* 3.5 22.6 - - + -
187D THR 3.4 6.7 + - - +
188D ALA 2.5 12.7 + - - +
190D GLU* 1.3 70.8 - - - +
192D LYS* 1.3 52.7 + - - +
193D THR 2.9 5.1 + - - -
194D LEU* 3.1 1.7 + - - -
195D ILE* 2.6 44.7 + - + +
198D LEU* 4.3 2.9 - - + -
207D LEU* 4.0 18.4 - - + -
211D LEU* 4.1 7.9 - - + -
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Residues in contact with LYS 192 (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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188D ALA 2.6 23.4 + - - +
189D ASP* 3.7 5.4 - - - +
191D ALA* 1.3 72.1 - - - +
193D THR* 1.3 58.6 + - - +
195D ILE 3.8 10.1 - - - -
196D PRO* 3.6 18.4 - - - +
198D LEU* 3.8 9.0 - - + -
199D ASN* 3.1 59.2 + - - +
202D ILE* 3.3 21.2 + - + -
204D ASP* 2.4 35.6 + - - +
207D LEU* 3.6 22.0 - - + -
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Residues in contact with THR 193 (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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189D ASP* 2.8 31.7 + - - -
190D GLU 4.0 1.1 - - - -
192D LYS* 1.3 77.9 + - - +
194D LEU* 1.3 78.9 + - + +
195D ILE 3.2 1.1 + - - -
196D PRO* 3.5 13.4 - - - +
146G LYS* 6.0 0.7 + - - -
165G GLU* 6.0 2.9 - - + -
166G ASP* 4.5 11.2 - - + +
167G TYR* 4.1 20.5 - - + -
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Residues in contact with LEU 194 (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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179D GLN* 5.6 0.7 - - - +
183D LEU* 4.8 8.3 - - + -
184D ALA 5.0 0.2 - - - +
185D CYS* 4.6 7.9 - - - -
190D GLU* 2.9 31.4 - - + +
191D ALA 3.1 3.0 + - - +
193D THR* 1.3 88.8 - - + +
195D ILE* 1.3 67.2 + - + +
196D PRO* 3.2 7.8 - - - +
84G GLY 4.5 2.9 - - - +
86G VAL* 3.1 49.4 + - + +
144G ARG* 3.8 28.9 - - - +
166G ASP 4.4 0.2 - - - +
167G TYR* 4.0 20.4 - - + +
168G LEU* 4.2 11.2 - - + -
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Residues in contact with ILE 195 (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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175D PHE* 5.1 4.9 - - + +
176D GLU* 4.3 13.5 - - + +
179D GLN* 3.6 39.0 - - + +
180D LEU* 3.8 33.4 - - + +
183D LEU* 5.0 7.2 - - + -
185D CYS* 5.8 1.8 - - - -
191D ALA* 2.6 18.7 + - - +
192D LYS 3.7 5.1 - - - +
194D LEU* 1.3 89.3 - - + +
196D PRO* 1.3 59.5 - - - +
197D SER* 3.4 17.3 - - - +
198D LEU* 3.0 37.1 + - + +
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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
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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