Contacts of the helix formed by residues 194 - 202 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85I LEU* 6.1 0.9 - - + -
87I VAL* 4.8 5.4 - - + -
95I PRO* 4.4 25.4 - - + -
118I LEU* 3.7 36.6 - - + -
120I ARG* 3.9 28.9 - - + +
125I HIS* 4.7 16.4 - - + -
193I ASN* 1.3 69.7 + - - +
195I GLN* 1.3 61.1 + - - +
196I LYS 3.1 1.6 - - - -
197I ASP* 3.2 7.5 + - - +
198I LEU* 2.9 29.0 + - + +
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Residues in contact with GLN 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I GLY 5.1 3.8 + - - -
94I GLU* 4.2 13.0 + - - +
95I PRO* 3.7 26.3 - - + +
193I ASN* 3.2 9.2 + - - +
194I VAL* 1.3 77.4 - - - +
196I LYS* 1.3 57.0 + - - +
198I LEU* 3.1 21.0 + - - +
199I GLU* 2.8 54.9 + - - +
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Residues in contact with LYS 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I ASP* 5.5 8.3 - - - +
193I ASN* 2.9 33.4 + - + +
195I GLN* 1.3 77.6 - - - +
197I ASP* 1.3 58.3 + - - +
199I GLU* 3.3 22.4 + - - +
200I ARG* 2.9 75.9 + - + +
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Residues in contact with ASP 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I LEU* 6.0 1.6 - - + -
120I ARG* 2.6 32.4 + - - +
125I HIS 5.5 0.9 - - - +
127I GLY* 5.4 1.7 + - - -
134I GLU* 6.5 1.3 - - + -
192I PRO* 5.7 2.6 - - - +
193I ASN 3.0 24.4 + - - +
194I VAL* 3.2 5.4 + - + +
196I LYS* 1.3 75.7 - - - +
198I LEU* 1.3 62.8 + - + +
200I ARG* 3.2 12.3 - - - +
201I LEU* 2.9 36.1 + - + +
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Residues in contact with LEU 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I LEU* 3.4 27.7 - - + +
89I LEU* 3.7 38.4 - - + -
93I GLY 4.4 7.4 - - - +
95I PRO* 3.9 17.9 - - + -
118I LEU* 4.1 15.5 - - + -
135I LEU* 5.0 0.9 - - + -
194I VAL* 2.9 19.3 + - + +
195I GLN* 3.4 23.3 - - - +
197I ASP* 1.3 75.4 - - + +
199I GLU* 1.3 56.5 + - - +
200I ARG 3.1 0.2 + - - -
201I LEU* 3.3 9.3 + - + +
202I THR* 2.7 39.4 + - - +
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Residues in contact with GLU 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195I GLN* 2.8 45.0 + - - +
196I LYS* 3.5 30.9 + - - +
198I LEU* 1.3 76.2 - - - +
200I ARG* 1.3 63.9 + - - +
202I THR* 3.7 6.1 - - - -
203I GLN* 2.9 30.8 + - - +
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Residues in contact with ARG 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196I LYS* 2.9 80.1 + - + +
197I ASP* 3.2 14.8 - - - +
198I LEU 3.0 0.2 - - - -
199I GLU* 1.3 83.1 + - - +
201I LEU* 1.3 67.0 + - + +
203I GLN* 3.1 26.1 + - - +
204I GLU* 3.6 4.4 + - - +
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Residues in contact with LEU 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I LEU* 4.2 15.5 - - + -
118I LEU* 5.7 1.3 - - + -
134I GLU* 4.2 29.8 - - + +
135I LEU* 3.9 38.6 - - + -
197I ASP* 2.9 25.5 + - + +
198I LEU* 3.8 9.0 - - + +
200I ARG* 1.3 72.0 - - + +
202I THR* 1.3 63.8 + - - +
204I GLU* 3.0 25.4 + - + +
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Residues in contact with THR 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I LEU* 3.7 26.2 - - + +
198I LEU* 2.7 23.9 + - - +
199I GLU* 3.7 7.1 - - - -
201I LEU* 1.3 73.6 - - - +
203I GLN* 1.3 52.6 + - - +
204I GLU* 2.5 22.9 + - - -
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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