Contacts of the helix formed by residues 147 - 151 (chain B) in PDB entry 1VQ7
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 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR* 5.3 1.6 - - - -
77B PRO* 5.2 2.7 - - + +
78B PRO 4.0 21.1 + - - +
79B MET* 5.0 0.7 - - - -
80B ARG* 4.3 32.3 - - + +
106B HIS* 3.8 26.5 - - + +
145B HIS* 4.5 10.8 - - + +
146B THR* 1.3 80.0 - - - +
148B PRO* 1.3 55.5 - - - +
149B ASP* 3.1 2.5 - - + +
150B ALA* 2.8 51.5 + - + +
151B VAL* 3.9 4.9 + - - +
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Residues in contact with PRO 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.4 33.4 - - + +
106B HIS* 5.5 0.9 - - + -
146B THR* 3.2 15.9 - - - +
147B VAL* 1.3 85.5 - - - +
149B ASP* 1.3 53.8 + - + +
150B ALA 2.9 0.2 - - - -
151B VAL* 2.8 38.0 + - + +
154B VAL* 4.1 4.4 - - + +
156B LYS* 2.7 35.7 - - + +
157B LYS* 4.1 5.8 - - - +
158B LYS 3.6 20.6 - - - +
159B PRO* 3.7 9.6 - - + -
160B ASP* 4.4 1.1 - - - +
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28520 A 4.7 4.5 + - - -
106B HIS* 4.7 8.6 + - + +
107B SER* 5.5 0.9 + - - -
108B GLU* 3.0 29.4 - - - +
147B VAL* 3.1 8.0 - - + -
148B PRO* 1.3 80.5 - - - +
150B ALA* 1.3 58.6 + - - +
151B VAL 3.1 5.7 + - - +
152B PRO* 4.8 1.4 - - - +
154B VAL 5.6 0.9 - - - -
156B LYS 4.0 3.7 + - - -
157B LYS* 4.4 24.3 - - - +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 4.4 19.9 - - + +
78B PRO* 6.2 0.4 - - + -
147B VAL* 2.8 34.8 + - + +
149B ASP* 1.3 80.5 - - - +
151B VAL* 1.3 58.0 + - - +
152B PRO* 3.5 9.7 - - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 4.3 16.6 - - + -
75B GLU* 3.3 33.2 - - + +
77B PRO* 3.7 29.6 - - + -
147B VAL 4.4 5.2 - - - +
148B PRO 2.8 18.1 + - - +
149B ASP* 4.3 4.1 - - - +
150B ALA* 1.3 80.2 - - - +
152B PRO* 1.3 66.3 - - - +
153B SER 4.0 1.1 - - - +
154B VAL* 3.2 34.2 + - + +
287B TYR* 3.4 13.0 - - - +
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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