Contacts of the helix formed by residues 324 - 329 (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 THR 324 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B CYS 3.6 10.5 - - - -
145B ILE* 3.4 20.2 - - - +
146B TYR 3.3 22.0 - - - +
147B GLY* 4.6 0.4 - - - +
148B LEU* 4.0 5.6 - - - -
322B PRO* 4.0 4.9 + - + +
323B TYR* 1.3 77.4 - - - +
325B LEU* 1.3 65.1 + - - +
326B LEU* 3.5 22.7 + - - +
327B ASP* 2.7 30.0 + - - +
328B TYR* 3.5 9.9 - - - -
377B LEU* 3.7 25.1 - - + +
385B HIS* 4.7 1.7 + - - -
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Residues in contact with LEU 325 (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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61B LEU* 4.1 18.8 - - + -
89B PHE* 3.7 41.7 - - + -
127B THR* 3.6 34.3 - - + +
138B ILE* 4.1 17.0 - - + -
140B ALA* 4.7 0.2 - - + -
144B CYS* 3.6 26.7 + - + +
148B LEU* 3.5 9.7 - - - +
324B THR* 1.3 73.6 - - - +
326B LEU* 1.3 56.8 + - - +
328B TYR* 2.9 36.0 + - + +
329B PHE* 3.6 15.5 - - + -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.5 31.6 - - + -
144B CYS* 3.9 9.4 - - + +
145B ILE* 4.0 9.2 - - + -
324B THR* 3.0 8.4 - - - +
325B LEU* 1.3 76.7 - - - +
327B ASP* 1.3 57.5 + - - +
328B TYR 3.4 0.2 - - - -
329B PHE* 3.5 24.3 + - - +
333B PHE* 3.9 21.5 - - + -
335B ILE* 4.9 3.6 - - + -
377B LEU* 3.9 22.4 - - + -
382B PHE* 3.8 33.4 - - + -
385B HIS* 3.8 32.1 + - + +
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Residues in contact with ASP 327 (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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151B PRO* 4.2 16.3 - - + +
322B PRO 3.9 4.2 - - - +
323B TYR* 3.3 29.4 - - + -
324B THR* 2.7 37.4 + - - +
326B LEU* 1.3 71.4 - - - +
328B TYR* 1.3 63.8 + - - +
329B PHE 3.2 8.7 + - - +
385B HIS* 3.3 24.7 + - - -
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Residues in contact with TYR 328 (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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127B THR* 3.9 29.4 - - + -
130B LEU* 3.7 29.8 - - + +
148B LEU* 4.4 17.0 - - + +
149B GLY* 2.8 37.0 + - - -
151B PRO* 3.6 30.3 - - + -
154B TYR* 3.7 42.1 - + - +
324B THR 3.5 17.7 - - - -
325B LEU* 2.9 20.0 + - + +
327B ASP* 1.3 75.4 - - - +
329B PHE* 1.4 61.6 + - + +
330B PRO* 4.1 1.4 - - - +
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Residues in contact with PHE 329 (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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59B PRO* 4.1 9.0 - - + -
60B THR 3.6 26.9 - - - -
61B LEU* 3.6 37.9 - - + -
130B LEU* 5.3 4.9 - - + -
136B VAL* 5.2 3.4 - - + -
138B ILE* 3.6 26.5 - - + -
325B LEU* 3.6 32.3 - - + -
326B LEU* 3.5 18.0 + - - +
327B ASP* 3.2 9.3 - - - +
328B TYR* 1.4 81.1 - - + +
330B PRO* 1.4 76.6 - - + +
331B ASP 3.8 0.3 + - - -
333B PHE* 3.5 35.3 - + + -
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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