Contacts of the helix formed by residues 338 - 346 (chain D) in PDB entry 2VUU
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 338 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329D ARG* 3.3 46.4 - - - +
333D GLU 4.4 1.3 - - - +
334D TYR* 2.6 31.9 + - + +
337D GLU* 1.3 78.8 - - + +
339D PHE* 1.3 67.5 + - - +
340D PRO* 3.2 3.1 - - - -
341D ILE* 2.8 18.6 + - + +
342D GLU* 2.9 38.1 + - + +
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Residues in contact with PHE 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D PHE* 3.8 6.7 - - + -
158D THR* 3.7 16.8 - - - -
159D SER 4.2 1.3 - - - -
167D MET* 3.7 31.4 - - + -
175D PHE* 4.7 3.4 - + - -
232D PHE* 3.5 26.7 - + - -
236D LEU* 4.2 13.5 - - + -
334D TYR* 2.9 42.7 + + + -
335D ALA* 3.2 18.2 - - - +
338D VAL* 1.3 71.7 - - - +
340D PRO* 1.3 64.8 - - - +
342D GLU* 3.1 3.5 + - + +
343D GLU* 2.9 59.7 + - + +
350D TRP* 4.3 16.4 - + - -
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Residues in contact with PRO 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D LEU* 4.2 14.6 - - + -
335D ALA 2.8 26.0 - - - +
336D ARG 3.1 22.7 - - - +
337D GLU 4.3 0.2 - - - -
338D VAL 3.3 3.8 - - - +
339D PHE* 1.3 82.9 - - + +
341D ILE* 1.3 62.8 + - + +
343D GLU 3.3 0.2 + - - -
344D GLU* 2.9 32.0 + - - +
350D TRP* 4.3 18.2 - - + -
351D MET* 3.3 20.2 - - + +
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D ARG 5.8 0.2 - - - +
337D GLU* 2.9 25.6 - - - +
338D VAL* 2.8 11.9 + - + +
340D PRO* 1.3 74.6 - - + +
342D GLU* 1.3 62.5 + - + +
344D GLU* 3.6 17.0 - - - +
345D ALA* 2.9 30.9 + - + +
712L LEU* 5.5 11.4 - - + -
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Residues in contact with GLU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ASN* 3.8 19.6 - - - +
157D PHE 4.3 4.8 - - - +
193D GLU* 5.1 8.8 - - - +
334D TYR* 2.4 32.2 + - - -
338D VAL* 2.9 36.3 + - + +
339D PHE* 3.6 6.7 - - + +
341D ILE* 1.3 73.4 - - + +
343D GLU* 1.3 70.5 + - + +
345D ALA* 3.0 16.4 + - - +
346D ASN* 3.1 23.5 + - - +
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Residues in contact with GLU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D PHE 5.1 0.2 - - - +
158D THR* 3.2 23.0 + - - -
159D SER* 2.6 35.1 + - - -
160D LEU* 4.0 0.9 - - - +
339D PHE* 2.9 39.8 + - + +
340D PRO 3.4 7.2 - - - +
342D GLU* 1.3 75.8 - - - +
344D GLU* 1.3 55.4 + - - +
346D ASN* 2.6 37.9 + - - +
348D LEU* 3.4 21.9 + - + +
350D TRP* 3.5 33.4 + - + +
351D MET* 3.8 2.0 - - + -
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Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D PRO 2.9 14.3 + - - +
341D ILE* 3.6 23.8 + - - +
343D GLU* 1.3 76.0 - - - +
345D ALA* 1.3 61.8 + - - +
346D ASN 3.0 1.1 + - - -
347D GLY* 3.2 10.7 + - - -
348D LEU 3.6 15.0 - - - +
351D MET* 3.3 22.0 - - + +
352D LEU* 4.2 23.4 - - + +
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Residues in contact with ALA 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D ILE* 2.9 20.8 + - + +
342D GLU* 3.0 8.5 + - - +
344D GLU* 1.3 77.5 - - - +
346D ASN* 1.3 59.9 + - - +
347D GLY 3.3 3.1 + - - -
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Residues in contact with ASN 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D THR* 4.5 8.5 + - - -
160D LEU* 4.5 27.6 - - + +
342D GLU* 3.1 24.5 + - - +
343D GLU* 2.6 17.4 + - - +
345D ALA* 1.3 80.6 - - - +
347D GLY* 1.3 59.8 + - - +
348D LEU* 3.3 8.1 + - - +
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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