Contacts of the helix formed by residues 184 - 190 (chain A) in PDB entry 1VAV
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 ASP 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A TYR* 5.0 1.0 + - - -
136A GLU* 3.5 36.7 + - - +
137A ARG* 3.8 21.4 - - + +
182A GLN 3.7 1.8 + - - -
183A LEU* 1.3 77.4 - - - +
185A PRO* 1.3 78.7 - - - +
186A GLN* 2.9 43.1 + - - +
187A TRP* 3.1 23.5 + - + +
188A ALA 4.3 0.7 + - - -
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Residues in contact with PRO 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TYR* 5.3 2.5 - - - +
183A LEU 3.5 4.2 - - - +
184A ASP* 1.3 96.1 - - - +
186A GLN* 1.3 62.4 + - + +
187A TRP 3.1 1.8 + - - -
188A ALA* 3.2 23.4 + - + +
189A TYR* 3.6 9.9 - - - -
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Residues in contact with GLN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.7 25.9 + - - +
138A PRO* 3.7 29.4 - - + +
139A ASP* 4.5 10.9 + - - +
184A ASP* 2.9 17.7 + - - +
185A PRO* 1.3 78.4 - - + +
187A TRP* 1.3 59.4 + - - +
188A ALA 3.3 0.4 - - - -
189A TYR* 3.5 31.4 + - + +
190A GLN* 3.1 25.5 + - - +
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Residues in contact with TRP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TYR* 3.8 9.1 - - - -
105A SER* 3.9 27.6 - - - -
114A ALA 4.7 0.4 - - - -
115A PRO 4.6 0.2 - - - -
116A LEU* 3.4 40.6 - - + +
135A ARG* 3.7 19.6 + - + -
136A GLU 2.8 28.7 + - - -
137A ARG* 3.7 4.8 - - - +
138A PRO* 3.3 38.4 - - + -
183A LEU* 4.0 28.5 - - + +
184A ASP* 3.1 30.2 + - + +
186A GLN* 1.3 73.8 - - - +
188A ALA* 1.3 65.1 + - - +
189A TYR 3.1 4.8 + - - -
190A GLN* 3.2 26.3 + - + +
192A LEU* 3.9 24.5 - - + +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ARG* 3.6 21.7 + - - +
76A TYR* 3.3 33.6 + - + +
77A ALA* 5.5 6.6 - - + +
185A PRO* 3.2 17.4 + - + +
187A TRP* 1.3 79.2 - - - +
189A TYR* 1.3 60.2 + - + +
190A GLN 3.6 0.7 - - - -
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Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ARG* 3.7 29.4 + - - +
109A ASN* 2.6 49.9 + - + +
185A PRO 3.6 21.3 - - - -
186A GLN* 3.5 29.8 + - + +
187A TRP 3.1 0.6 - - - -
188A ALA* 1.3 80.3 - - + +
190A GLN* 1.3 78.4 + - - +
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Residues in contact with GLN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A TRP 3.7 6.4 - - - +
75A ARG* 3.7 12.0 - - - +
105A SER* 4.0 14.7 + - - +
108A SER* 4.4 4.0 - - - +
109A ASN* 2.9 47.2 - - - +
110A SER* 3.7 14.1 + - - +
138A PRO* 4.1 13.6 - - + +
186A GLN* 3.1 25.6 + - - +
187A TRP* 3.2 34.5 + - + +
189A TYR* 1.3 89.7 - - - +
191A GLY* 1.3 62.7 + - - +
192A LEU* 3.4 8.3 + - + +
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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