Contacts of the helix formed by residues 198 - 208 (chain B) in PDB entry 2VPI
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 ASN 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.6 20.4 - - + +
144B GLN* 6.1 0.2 - - - +
147B GLU* 2.9 31.8 + - - +
148B VAL 4.8 0.4 + - - -
196B THR* 3.4 2.9 - - - +
197B GLU* 1.3 96.4 - - - +
199B GLY* 1.3 63.2 + - - +
200B LYS* 3.3 3.4 - - - +
201B VAL* 3.3 25.9 + - + +
202B ILE* 3.5 19.5 + - + +
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Residues in contact with GLY 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PRO* 3.2 29.2 - - - +
196B THR* 3.1 24.8 + - - +
197B GLU 3.5 0.8 + - - -
198B ASN* 1.3 75.2 - - - +
200B LYS* 1.3 65.1 + - - +
202B ILE* 3.3 6.1 + - - +
203B LEU* 3.1 27.6 + - - +
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 2.6 54.0 + - - +
47B GLU* 3.3 25.8 + - - +
48B LEU* 3.4 30.1 - - + +
191B PRO 4.2 1.1 + - - +
197B GLU 5.3 0.4 + - - -
198B ASN* 3.3 1.3 - - - +
199B GLY* 1.3 74.2 - - - +
201B VAL* 1.3 60.9 + - + +
203B LEU* 3.5 8.5 + - + +
204B LYS* 2.9 31.5 + - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG 3.7 21.5 - - - +
142B GLY* 4.8 7.4 - - - +
143B LEU* 3.8 16.8 - - + -
198B ASN* 3.3 29.1 + - + +
199B GLY 3.3 0.6 - - - -
200B LYS* 1.3 76.3 - - + +
202B ILE* 1.3 59.3 + - - +
204B LYS* 3.3 12.8 + - + +
205B ASN* 2.9 36.6 + - - +
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 5.3 4.0 - - + -
139B LEU* 3.5 44.8 - - + +
140B PHE* 4.0 3.8 - - + -
143B LEU* 3.7 30.3 - - + -
147B GLU* 6.4 0.7 - - + -
149B VAL* 5.6 1.6 - - + -
187B ALA* 5.7 1.1 - - + -
189B PHE* 3.8 33.0 - - + -
191B PRO* 4.1 18.4 - - + -
196B THR* 4.8 2.2 - - + -
198B ASN 3.7 15.0 - - - +
199B GLY* 3.3 12.9 + - - +
201B VAL* 1.3 77.4 - - - +
203B LEU* 1.3 57.4 + - - +
205B ASN* 3.4 4.0 + - - +
206B PHE* 3.0 23.0 + - - +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ILE* 5.6 3.8 - - + -
44B ARG* 3.8 31.2 - - + -
45B VAL* 5.8 2.9 - - + -
48B LEU* 4.0 13.5 - - + -
73B ILE* 5.1 11.2 - - + -
101B LEU* 3.9 25.4 - - + -
103B ILE* 4.9 5.2 - - + -
191B PRO* 3.8 26.9 - - + +
192B GLU* 4.1 6.7 - - + +
199B GLY 3.1 19.1 + - - +
200B LYS* 3.8 10.3 - - + +
202B ILE* 1.3 72.4 - - - +
204B LYS* 1.3 60.6 + - - +
206B PHE* 3.4 4.3 + - + +
207B LEU* 2.9 41.3 + - + +
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.7 25.7 - - + +
200B LYS 2.9 18.6 + - - +
201B VAL* 3.5 11.9 - - + +
203B LEU* 1.3 73.8 - - - +
205B ASN* 1.3 62.8 + - - +
207B LEU* 4.9 1.1 - - - -
208B TYR* 2.9 75.2 + - + +
209B ASP* 4.6 1.1 - - - +
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Residues in contact with ASN 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B SER 3.4 16.8 - - - +
139B LEU* 2.7 33.1 + - - +
140B PHE* 4.0 1.2 - - - +
141B ARG* 2.8 32.9 + - - +
201B VAL* 2.9 27.9 + - - +
202B ILE* 3.5 3.8 - - - +
204B LYS* 1.3 74.3 - - - +
206B PHE* 1.3 58.4 + - - +
209B ASP* 3.0 27.4 + - - +
210B ILE* 2.9 29.4 + - - +
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Residues in contact with PHE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ALA* 4.0 17.7 - - + -
72B ILE 3.5 11.9 - - - -
73B ILE* 3.9 11.9 - - + -
99B PRO* 3.8 20.4 - - + -
100B VAL 3.5 13.7 - - - -
101B LEU* 3.3 54.7 - - + -
139B LEU* 3.7 18.8 - - + -
185B TYR* 4.6 5.2 - + - -
202B ILE 3.0 11.7 + - - +
203B LEU* 3.8 4.0 - - + +
204B LYS 3.3 0.2 - - - -
205B ASN* 1.3 76.6 - - - +
207B LEU* 1.3 75.1 + - + +
210B ILE* 3.4 23.7 - - + +
211B ALA* 2.8 30.2 + - + +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.7 35.9 - - + -
45B VAL* 4.2 26.7 - - + -
48B LEU* 3.7 25.6 - - + -
50B VAL* 4.3 15.7 - - + -
73B ILE* 4.4 7.2 - - + -
203B LEU* 2.9 28.6 + - + +
204B LYS* 4.9 0.4 - - - -
206B PHE* 1.3 90.7 - - + +
208B TYR* 1.3 68.0 + - + +
211B ALA* 3.5 5.9 - - - +
212B GLY 3.3 5.5 + - - -
213B CYS* 2.9 28.7 + - + +
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Residues in contact with TYR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 2.6 41.0 + - + +
49B PHE* 4.5 3.1 - - - -
50B VAL* 3.9 11.0 - - + -
204B LYS* 2.9 53.9 + - + +
207B LEU* 1.3 78.4 - - + +
209B ASP* 1.3 69.5 + - - +
210B ILE 3.6 0.2 - - - -
212B GLY* 2.9 27.9 + - - -
213B CYS 3.5 17.6 - - - +
215B GLY* 3.4 29.1 + - - -
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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