Contacts of the helix formed by residues 195 - 204 (chain D) in PDB entry 2VCK
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 TYR 195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D LEU* 3.7 18.2 - - + -
92D TYR* 3.8 17.5 - + + -
93D PRO* 2.7 45.3 + - + +
94D LYS 4.2 1.6 + - - -
95D THR* 3.6 27.5 - - + +
99D LEU 4.4 2.8 + - - -
101D CYS* 3.6 27.1 - - - -
123D PRO* 3.8 28.0 - - + +
191D ASP 4.5 0.7 - - - -
192D THR 3.0 14.7 + - - +
194D VAL* 1.3 81.5 - - + +
196D SER* 1.3 59.7 + - - +
197D ASP 3.4 2.0 - - - -
198D PHE* 3.3 10.7 + + + +
199D ASP* 2.9 31.2 + - - +
232D TYR* 3.7 18.6 - + + -
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Residues in contact with SER 196 (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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193D THR* 3.1 22.7 + - - -
195D TYR* 1.3 78.4 - - - +
197D ASP* 1.3 66.5 + - - +
199D ASP* 3.9 1.0 - - - +
200D THR* 2.8 31.8 + - - -
232D TYR 3.3 23.4 + - - -
233D LYS* 3.0 18.5 + - - -
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Residues in contact with ASP 197 (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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123D PRO 4.3 12.0 - - - +
125D GLU* 3.7 31.4 + - + +
149D HIS* 4.0 2.8 + - + -
193D THR 4.8 0.6 + - - -
194D VAL 4.8 2.3 + - - +
195D TYR* 3.4 0.4 - - - +
196D SER* 1.3 81.6 + - - +
198D PHE* 1.3 64.4 + - - +
200D THR* 3.7 6.2 - - - -
201D TYR* 3.0 24.9 + - - +
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Residues in contact with PHE 198 (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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90D ILE* 4.0 12.1 - - + -
92D TYR* 3.8 24.7 - + - -
101D CYS* 4.3 13.2 - - + -
121D GLN* 3.6 49.4 - - + -
122D HIS 4.5 3.1 - - - -
123D PRO* 4.3 14.2 + - + -
149D HIS* 3.6 37.4 - + + +
195D TYR* 3.3 12.7 + + - +
196D SER 3.2 0.4 - - - -
197D ASP* 1.3 79.1 - - - +
199D ASP* 1.3 80.3 + - - +
201D TYR* 3.2 4.0 + - - +
202D MSE 2.9 55.4 + - + +
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Residues in contact with ASP 199 (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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73D LYS* 5.0 0.5 + - - -
92D TYR* 2.7 30.0 + - - -
195D TYR 2.9 17.2 + - - +
198D PHE* 1.3 84.0 - - - +
200D THR* 1.3 56.2 + - - +
202D MSE 4.5 0.4 - - - +
203D THR* 2.6 38.1 + - - -
230D PHE* 3.4 18.1 - - + +
231D SER 3.2 6.9 + - - -
232D TYR* 2.8 33.2 + - - +
233D LYS* 3.7 23.1 - - + +
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Residues in contact with THR 200 (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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196D SER* 2.8 24.8 + - - -
197D ASP* 3.7 6.7 - - - -
199D ASP* 1.3 75.1 - - - +
201D TYR* 1.3 64.9 + - - +
203D THR* 3.3 11.3 + - - -
204D GLU* 3.4 20.8 - - + +
233D LYS* 3.7 27.6 + - + +
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Residues in contact with TYR 201 (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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125D GLU* 4.7 4.5 - - - +
144D PHE* 3.7 27.5 - - - -
145D GLU 4.1 5.5 + - - -
148D ASN* 3.3 46.7 + - + +
149D HIS* 3.4 21.3 - + + +
150D PHE* 3.9 10.1 - + - -
197D ASP 3.0 17.7 + - - +
198D PHE 3.4 3.1 - - - +
200D THR* 1.3 78.0 - - - +
202D MSE 1.3 86.1 + - + +
204D GLU* 3.3 15.7 + - - +
205D LEU* 3.4 21.9 + - + +
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Residues in contact with MSE 202 (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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121D GLN* 3.7 20.9 - - - +
150D PHE* 4.2 0.7 - - - -
198D PHE* 2.9 44.6 + - + +
199D ASP 4.1 0.4 - - - +
201D TYR* 1.3 88.9 - - + +
203D THR* 1.3 65.6 + - - +
205D LEU* 3.0 40.0 + - + +
206D ASP 4.1 3.3 + - - +
230D PHE* 3.2 41.8 - - + -
1234D BLA 3.4 51.1 - - + +
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Residues in contact with THR 203 (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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199D ASP 2.6 22.8 + - - -
200D THR 3.6 6.5 - - - -
201D TYR 3.3 0.4 - - - -
202D MSE 1.3 77.4 - - - +
204D GLU* 1.3 69.4 + - - +
205D LEU 3.3 0.7 + - - -
206D ASP 4.3 9.0 - - - +
225D VAL* 3.9 15.6 - - + +
226D ASN* 3.9 10.3 - - - +
230D PHE* 3.2 16.4 - - - +
233D LYS* 2.9 36.5 + - - +
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Residues in contact with GLU 204 (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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200D THR* 3.4 20.1 - - + +
201D TYR* 3.3 7.8 + - - +
202D MSE 3.1 0.4 - - - -
203D THR* 1.3 90.1 - - - +
205D LEU* 1.3 64.5 + - - +
206D ASP 4.8 1.6 - - - -
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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