Contacts of the helix formed by residues 330 - 338 (chain H) 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 ASP 330 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154H ASN* 4.0 1.6 - - - -
221H GLU* 3.2 20.1 - - - +
328H TRP* 3.6 27.1 + - + -
329H ARG* 1.3 79.2 - - - +
331H MET* 1.3 59.5 + - - +
332H GLU* 3.7 18.7 + - - +
333H GLU* 3.0 22.8 + - - +
334H TYR* 3.0 21.5 + - - +
680P THR* 5.0 2.4 - - - +
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Residues in contact with MET 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H ASN* 3.1 33.1 - - - +
157H PHE* 4.0 3.6 - - + -
189H TRP* 3.4 36.3 - - + -
221H GLU* 2.7 17.1 + - - +
223H LEU* 3.6 13.9 - - + -
228H VAL* 3.8 18.2 - - + +
231H ALA* 3.8 20.2 - - + -
232H PHE* 3.6 28.0 - - + -
330H ASP* 1.3 70.7 - - - +
332H GLU* 1.3 56.7 + - - +
334H TYR* 4.0 10.5 - - - -
335H ALA* 2.7 38.6 + - - +
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Residues in contact with GLU 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ASN* 3.4 27.3 - - - +
231H ALA* 4.4 26.0 - - + +
234H ARG* 3.4 33.7 + - - +
235H ALA* 3.6 8.8 - - + +
330H ASP* 3.4 16.2 + - - +
331H MET* 1.3 78.0 - - - +
333H GLU* 1.3 58.5 + - - +
335H ALA* 4.5 1.1 - - - -
336H ARG* 3.0 45.2 + - - +
680P THR* 4.8 10.7 - - + +
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Residues in contact with GLU 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H HIS* 4.5 7.3 + - - -
328H TRP 4.3 3.3 - - - +
329H ARG* 3.3 43.0 + - - +
330H ASP* 3.0 19.7 + - - +
332H GLU* 1.3 73.7 - - - +
334H TYR* 1.3 58.1 + - - +
337H GLU* 2.7 48.4 + - + +
678P THR* 3.4 15.8 + - - +
680P THR* 3.1 43.1 - - + +
681P THR* 4.8 0.7 + - - -
682P PRO* 5.2 6.8 - - - +
694P CYS* 5.6 2.3 - - - -
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Residues in contact with TYR 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H ASN* 3.0 39.3 - - + +
155H ASN* 3.3 20.0 - - + -
157H PHE 3.5 4.5 + - - -
191H ASP* 3.8 19.3 - - - +
232H PHE* 3.9 17.9 - + - -
329H ARG* 4.0 8.7 - - - +
330H ASP 3.0 14.3 + - - +
331H MET* 3.4 16.8 - - - +
333H GLU* 1.3 77.0 - - - +
335H ALA* 1.3 69.7 + - - +
338H VAL* 2.6 67.4 + - + +
339H PHE* 2.9 26.6 + + + -
342H GLU* 2.5 21.5 + - - -
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Residues in contact with ALA 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H PHE* 3.7 36.8 - - + -
235H ALA* 3.4 20.9 - - + -
236H LEU* 3.9 4.9 - - + +
331H MET 2.7 21.2 + - - +
334H TYR* 1.3 73.9 - - - +
336H ARG* 1.3 51.9 + - - +
339H PHE* 3.0 14.6 - - - +
340H PRO* 2.7 34.5 - - - +
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Residues in contact with ARG 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ARG 5.3 2.4 + - - -
237D ASN* 4.1 17.4 + - - -
234H ARG 2.6 31.3 + - - -
235H ALA* 3.0 33.8 + - + +
236H LEU* 5.1 0.4 - - - -
237H ASN* 4.2 12.1 + - - +
332H GLU* 3.0 28.9 + - - +
333H GLU 4.0 0.9 - - - +
335H ALA* 1.3 77.2 - - - +
337H GLU* 1.3 69.4 + - - +
340H PRO* 3.2 22.7 - - - +
679P GLN* 6.2 0.4 - - - -
680P THR* 3.1 26.5 + - - +
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Residues in contact with GLU 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329H ARG* 5.7 1.1 - - - +
333H GLU* 2.7 29.6 + - + +
336H ARG* 1.3 84.7 - - - +
338H VAL* 1.3 63.5 + - + +
340H PRO* 4.3 0.7 - - - -
341H ILE* 3.5 20.1 - - - +
677P PHE 4.1 4.7 - - - +
678P THR* 3.1 36.8 - - - +
679P GLN* 3.3 27.7 + - - +
680P THR* 3.1 23.2 + - - +
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Residues in contact with VAL 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193H GLU* 5.8 2.9 - - - +
329H ARG* 3.3 46.0 - - - +
334H TYR* 2.6 38.8 + - + +
337H GLU* 1.3 78.4 - - + +
339H PHE* 1.3 66.1 + - - +
340H PRO* 3.2 2.7 - - - -
341H ILE* 2.9 17.5 + - + +
342H GLU* 3.0 33.2 + - + +
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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