Contacts of the helix formed by residues 182 - 189 (chain L) 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 ARG 182 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176L ARG* 3.6 28.2 - - - +
180L ILE 3.6 0.6 + - - -
181L VAL* 1.3 77.5 - - + +
183L SER* 1.3 59.4 + - - +
185L TYR* 3.0 44.9 - - - +
186L GLU* 2.6 42.6 + - - +
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Residues in contact with SER 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K ASN* 4.7 5.9 + - - -
181L VAL* 3.2 16.8 - - - +
182L ARG* 1.3 79.0 - - - +
184L LEU* 1.3 62.4 + - - +
186L GLU* 3.3 16.4 + - - +
187L ASP* 2.7 35.4 + - - +
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Residues in contact with LEU 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K LEU* 3.7 27.4 - - + -
105K MET* 4.1 22.0 - - + -
108K ASN* 3.2 32.8 - - - +
159L LYS* 3.6 20.9 - - - +
163L LEU* 4.6 1.4 - - + +
180L ILE* 3.8 35.2 - - + -
181L VAL* 3.3 19.9 + - + +
183L SER* 1.3 78.8 + - - +
185L TYR* 1.3 63.6 + - - +
186L GLU 3.2 0.2 - - - -
187L ASP* 3.4 8.9 + - + +
188L LEU* 3.2 27.4 + - - +
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Residues in contact with TYR 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175L TYR* 3.0 29.6 - - + -
176L ARG* 3.0 53.6 + - - +
178L LEU 2.6 25.1 + - - -
179L ASP* 4.8 0.3 - - - -
180L ILE* 3.6 32.5 + - + -
181L VAL 3.4 1.3 + - - -
182L ARG* 3.0 43.9 + - - +
184L LEU* 1.3 77.4 - - - +
186L GLU* 1.3 64.3 + - - +
188L LEU* 3.5 6.1 + - - +
189L GLU* 3.2 29.2 + - - +
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Residues in contact with GLU 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176L ARG* 4.0 6.2 + - - -
182L ARG* 2.6 44.8 + - - +
183L SER* 3.3 15.7 + - - +
184L LEU 3.2 0.2 - - - -
185L TYR* 1.3 80.7 - - - +
187L ASP* 1.3 60.5 + - - +
189L GLU* 3.2 11.8 + - - +
190L ASP* 3.0 30.8 + - - +
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Residues in contact with ASP 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159L LYS* 3.1 26.1 + - - +
163L LEU* 4.1 23.9 - - + +
167L ARG* 2.8 23.4 + - - -
183L SER* 2.7 22.1 + - - +
184L LEU* 3.4 14.6 - - - +
185L TYR 3.4 0.4 - - - -
186L GLU* 1.3 77.1 - - - +
188L LEU* 1.3 58.3 + - - +
190L ASP* 3.6 11.9 + - - +
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Residues in contact with LEU 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K LEU* 5.3 2.2 - - + -
163L LEU* 3.8 19.7 - - + +
166L VAL* 3.9 22.9 - - + -
167L ARG* 3.0 46.0 + - + +
175L TYR* 3.6 30.6 - - + +
178L LEU* 3.6 30.1 - - + -
180L ILE* 4.0 16.4 - - + -
184L LEU 3.2 16.1 + - - +
185L TYR* 3.7 4.5 - - - +
186L GLU 3.2 0.2 - - - -
187L ASP* 1.3 73.9 - - - +
189L GLU* 1.3 60.7 + - - +
190L ASP 3.1 5.2 + - - -
191L HIS* 3.3 10.9 + - - -
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Residues in contact with GLU 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L PRO 5.3 3.3 - - - +
175L TYR* 3.8 21.5 - - + +
176L ARG* 3.0 43.3 + - - +
185L TYR 3.2 12.3 + - - +
186L GLU* 3.2 10.9 + - - +
188L LEU* 1.3 75.2 - - - +
190L ASP* 1.3 57.7 + - - +
191L HIS* 3.0 19.8 + - - +
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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