Contacts of the helix formed by residues 194 - 202 (chain C) in PDB entry 1VCB
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 VAL 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C LEU* 5.9 1.3 - - + -
87C VAL* 4.8 6.5 - - + -
95C PRO* 4.3 26.9 - - + -
118C LEU* 4.1 31.0 - - + -
120C ARG* 4.1 26.2 - - + +
125C HIS* 4.3 20.0 - - + -
193C ASN* 1.3 71.4 + - - +
195C GLN* 1.3 61.5 + - - +
197C ASP* 3.2 8.3 + - - +
198C LEU* 2.9 27.9 + - + +
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Residues in contact with GLN 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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93C GLY 5.3 2.6 + - - -
94C GLU* 4.0 14.2 + - - +
95C PRO* 3.7 23.5 - - + +
193C ASN* 3.1 8.5 + - - +
194C VAL* 1.3 77.6 - - - +
196C LYS* 1.3 57.9 + - - +
198C LEU* 3.2 21.6 + - - +
199C GLU* 2.9 56.4 + - - +
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Residues in contact with LYS 196 (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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190C ASP* 6.0 2.7 - - - +
193C ASN* 2.8 33.0 + - + +
195C GLN* 1.3 78.0 - - - +
197C ASP* 1.3 59.0 + - - +
199C GLU* 3.2 24.6 + - - +
200C ARG* 2.9 72.9 + - + +
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Residues in contact with ASP 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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118C LEU* 6.0 1.8 - - + -
120C ARG* 2.7 33.9 + - - +
125C HIS 5.2 1.7 - - - +
127C GLY* 5.4 1.7 + - - -
192C PRO* 5.8 1.4 - - - +
193C ASN 3.0 25.0 + - - +
194C VAL* 3.6 4.9 - - + +
196C LYS* 1.3 75.6 - - - +
198C LEU* 1.3 61.7 + - + +
200C ARG* 3.2 11.8 + - - +
201C LEU* 2.9 38.1 + - + +
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Residues in contact with LEU 198 (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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63C LEU* 3.9 23.0 - - + +
89C LEU* 3.9 26.9 - - + -
93C GLY 4.3 6.3 - - - +
95C PRO* 3.4 34.8 - - + -
118C LEU* 4.0 15.9 - - + -
194C VAL* 2.9 21.7 + - + +
195C GLN* 3.5 21.8 - - - +
197C ASP* 1.3 74.3 - - - +
199C GLU* 1.3 56.3 + - - +
200C ARG 3.1 0.3 + - - -
201C LEU* 3.2 9.0 + - + +
202C THR* 2.7 39.8 + - - +
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Residues in contact with GLU 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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195C GLN* 2.9 44.3 + - - +
196C LYS* 3.5 30.9 + - - +
198C LEU* 1.3 77.2 - - - +
200C ARG* 1.3 65.4 + - - +
202C THR* 3.7 6.4 - - - -
203C GLN* 2.9 30.5 + - - +
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Residues in contact with ARG 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* 2.9 79.8 + - + +
197C ASP* 3.2 15.5 - - - +
199C GLU* 1.3 82.0 + - - +
201C LEU* 1.3 68.3 + - + +
203C GLN* 3.0 26.6 + - - +
204C GLU* 3.6 3.9 - - - +
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Residues in contact with LEU 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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63C LEU* 4.0 18.6 - - + -
118C LEU* 5.3 2.7 - - + -
134C GLU* 4.1 30.7 - - + +
135C LEU* 4.1 34.8 - - + -
197C ASP* 2.9 26.2 + - + +
198C LEU* 3.8 10.8 - - + +
200C ARG* 1.3 71.9 - - + +
202C THR* 1.3 63.7 + - - +
204C GLU* 3.0 25.3 + - + +
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Residues in contact with THR 202 (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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63C LEU* 3.9 24.9 - - + +
198C LEU* 2.7 24.6 + - - +
199C GLU* 3.7 7.1 - - - -
201C LEU* 1.3 73.4 - - - +
203C GLN* 1.3 53.1 + - - +
204C GLU* 2.5 22.3 + - - -
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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