Contacts of the helix formed by residues 142 - 146 (chain B) in PDB entry 3V4R
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 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 5.0 3.1 - - + -
64B ALA 4.4 3.0 + - - -
141B SER* 1.4 66.5 - - - +
143B SER* 1.4 53.7 + - - +
144B CYS* 3.0 11.7 - - - -
145B ILE* 3.0 29.9 + - + +
146B TYR* 3.4 9.0 - - + -
346B GLN* 3.4 33.4 - - + +
347B VAL* 3.6 36.1 - - + -
350B MET* 4.3 16.4 - - + -
5C G 3.8 31.9 - - + +
6C T 3.8 11.0 - - - +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.5 13.8 - - - -
90B VAL* 4.0 4.0 - - - -
91B SER 4.0 9.0 - - - -
123B ARG* 2.9 23.1 + - - -
141B SER* 2.8 17.3 + - - -
142B VAL* 1.4 76.0 - - - +
144B CYS* 1.3 58.5 + - - +
145B ILE 3.3 1.1 + - - -
146B TYR* 3.5 21.6 + - - +
148B LEU* 4.3 3.3 - - - +
6C T 3.6 12.0 - - - -
7C T 2.7 26.2 + - - -
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Residues in contact with CYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.5 9.6 - - + -
63B ILE* 3.8 33.0 - - - -
89B PHE* 4.0 8.8 - - - -
140B ALA* 4.1 9.2 - - + -
141B SER 3.1 22.4 + - - +
142B VAL* 3.0 4.0 - - - -
143B SER* 1.3 76.7 - - - +
145B ILE* 1.4 69.7 + - - +
146B TYR 3.5 0.7 - - - -
324B THR* 3.6 17.7 - - - -
325B LEU* 3.6 31.1 + - + -
326B LEU* 3.9 9.5 - - + +
347B VAL* 6.4 0.7 - - - -
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Residues in contact with ILE 145 (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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63B ILE* 5.6 0.2 - - + -
142B VAL* 3.0 26.8 + - + +
144B CYS* 1.4 88.9 - - - +
146B TYR* 1.3 61.2 + - + +
324B THR* 3.4 14.4 - - - +
326B LEU* 4.0 8.7 - - + -
347B VAL* 4.2 17.3 - - + +
350B MET* 3.8 24.0 - - + -
376B PRO* 3.4 27.9 - - + +
377B LEU* 2.9 49.1 + - + +
382B PHE* 3.8 32.1 - - + -
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Residues in contact with TYR 146 (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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142B VAL 3.4 22.2 - - - -
143B SER* 3.5 10.9 + - - +
145B ILE* 1.3 80.6 - - + +
147B GLY* 1.3 69.1 + - - +
148B LEU* 3.3 16.5 - - - +
324B THR* 3.3 13.5 - - - +
350B MET* 3.8 26.3 + - + +
354B ASP* 5.2 4.2 - - + +
357B ARG* 5.8 0.9 + - - -
375B ARG 4.9 1.1 - - - -
376B PRO* 3.7 42.4 - - + +
6C T 3.5 48.6 + - + +
7C T 3.5 46.4 + + - +
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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