Contacts of the helix formed by residues 194 - 201 (chain C) in PDB entry 2VZE
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 PHE 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C ALA* 4.4 12.8 - - + -
96C VAL* 4.5 16.2 - - + -
97C LEU* 5.4 4.9 - - + -
118C GLU* 4.0 21.1 - - + -
121C LEU* 5.1 3.8 - - + -
122C VAL* 3.8 26.5 - - + -
158C VAL* 4.8 1.6 - - + -
181C LEU* 4.1 34.8 - - + -
182C LEU 2.9 22.9 + - - +
183C VAL* 3.7 22.9 - - + -
192C LEU 3.3 1.6 + - - -
193C ASN* 1.3 72.9 + - - +
195C LYS* 1.3 63.6 + - + +
197C LEU* 3.3 2.7 + - - +
198C LEU* 2.8 61.3 + - + +
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Residues in contact with LYS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLU* 2.2 36.4 + - + +
182C LEU 4.5 0.8 + - - -
183C VAL* 4.2 17.9 - - + -
184C SER* 3.7 26.9 - - - +
185C GLU* 3.3 28.3 + - - +
193C ASN* 3.4 8.2 + - - +
194C PHE* 1.3 85.1 - - + +
196C LYS* 1.3 62.6 + - - +
198C LEU* 3.6 8.0 - - + +
199C ASN* 3.1 32.0 + - - +
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Residues in contact with LYS 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ASN* 3.2 30.8 + - + +
195C LYS* 1.3 77.1 - - - +
197C LEU* 1.3 63.9 + - + +
199C ASN* 3.3 8.2 + - - +
200C GLU* 3.3 38.5 + - + +
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Residues in contact with LEU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C VAL* 3.7 27.2 - - + +
100C ALA* 4.2 22.0 - - + -
101C CYS* 4.9 0.7 - - - -
181C LEU* 4.2 5.6 - - + -
192C LEU* 4.2 29.4 - - + -
193C ASN* 3.1 21.7 + - + +
194C PHE 3.8 2.9 - - - +
196C LYS* 1.3 75.6 - - + +
198C LEU* 1.3 66.3 + - - +
200C GLU* 3.1 23.6 + - + +
201C ALA* 3.0 23.2 + - - +
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89C ASN* 3.7 14.4 - - + +
92C GLN* 3.1 27.5 + - + +
93C ALA* 3.6 36.3 - - + +
96C VAL* 3.6 8.0 - - + +
118C GLU* 5.5 4.0 - - + +
121C LEU* 4.2 17.7 - - + -
194C PHE* 2.8 45.9 + - + +
195C LYS* 3.6 8.7 - - + +
197C LEU* 1.3 71.9 - - - +
199C ASN* 1.3 71.3 + - - +
201C ALA* 3.1 13.2 + - - +
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Residues in contact with ASN 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLN* 4.1 10.8 + - - +
195C LYS* 3.1 19.5 + - - +
196C LYS* 3.7 10.3 - - + +
197C LEU 3.3 0.6 - - - -
198C LEU* 1.3 87.5 - - - +
200C GLU* 1.3 59.9 - - + +
201C ALA 4.5 0.5 - - - +
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Residues in contact with GLU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C LYS* 3.3 27.6 - - + +
197C LEU* 3.1 29.9 + - + +
199C ASN* 1.3 79.6 - - + +
201C ALA* 1.3 62.3 + - - +
202C SER 3.9 0.7 + - - -
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Residues in contact with ALA 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLN* 2.9 51.4 + - - +
95C ASN* 3.9 12.3 - - + -
96C VAL* 3.8 7.4 - - + +
197C LEU 3.0 11.2 + - - +
198C LEU 3.1 10.4 + - - +
199C ASN 4.5 0.2 - - - +
200C GLU* 1.3 81.3 - - - +
202C SER* 1.3 61.3 + - - +
203C THR* 3.7 0.7 + - - +
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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
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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