Contacts of the helix formed by residues 330 - 338 (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 ASP 330 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ASN* 3.9 2.0 - - - -
221D GLU* 3.1 16.6 - - - +
328D TRP* 3.5 25.4 + - + -
329D ARG* 1.3 76.0 - - - +
331D MET* 1.3 65.3 - - - +
332D GLU* 3.7 18.0 + - - +
333D GLU* 3.1 24.3 + - - +
334D TYR* 3.0 18.0 + - - +
680L THR* 4.8 3.4 - - - +
682L PRO* 6.1 0.5 - - - +
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Residues in contact with MET 331 (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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154D ASN* 3.1 44.0 - - + +
157D PHE* 4.3 2.2 - - + -
189D TRP* 3.5 34.8 - - + -
221D GLU* 2.7 9.1 + - - +
223D LEU* 3.7 23.8 - - + -
228D VAL* 4.3 11.2 - - + -
231D ALA* 4.1 14.8 - - + -
232D PHE* 3.5 34.8 - - + -
330D ASP* 1.3 73.5 - - - +
332D GLU* 1.3 54.7 + - - +
334D TYR* 3.0 5.3 + - - +
335D ALA* 2.6 37.5 + - - +
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Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D ALA* 4.2 12.7 - - + +
234D ARG* 2.8 37.6 + - - +
235D ALA* 3.6 19.1 - - + +
330D ASP* 3.4 14.9 + - - +
331D MET* 1.3 78.2 - - - +
333D GLU* 1.3 58.8 + - - +
335D ALA* 4.4 4.9 - - - -
336D ARG* 2.9 36.5 + - + +
237H ASN* 4.2 12.2 + - - +
680L THR* 4.0 16.9 + - + +
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Residues in contact with GLU 333 (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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194D HIS* 4.5 8.5 + - - -
328D TRP 4.6 2.6 - - - +
329D ARG* 3.4 39.6 + - + +
330D ASP* 3.1 23.6 + - - +
332D GLU* 1.3 75.0 - - - +
334D TYR* 1.3 59.2 + - - +
336D ARG* 4.3 0.4 - - - -
337D GLU* 2.7 46.5 + - + +
676L CYS* 5.6 1.2 - - - -
678L THR* 3.3 18.7 + - - +
680L THR* 3.3 45.4 - - + +
681L THR* 5.0 3.5 + - - -
682L PRO* 5.3 3.8 - - - +
694L CYS* 5.9 1.4 - - - +
708L ARG* 5.8 0.5 + - - -
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Residues in contact with TYR 334 (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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154D ASN* 3.7 34.1 - - + +
155D ASN* 3.5 27.9 - - + -
157D PHE* 3.7 10.5 + - + -
191D ASP* 3.8 18.8 - - - +
232D PHE* 4.3 6.3 - + - -
329D ARG* 4.1 4.9 - - - +
330D ASP 3.0 13.2 + - - +
331D MET* 3.4 13.7 - - - +
333D GLU* 1.3 76.6 - - - +
335D ALA* 1.3 65.4 + - - +
338D VAL* 2.6 54.6 + - + -
339D PHE* 2.9 39.2 + + + -
342D GLU* 2.4 32.3 + - - -
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Residues in contact with ALA 335 (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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232D PHE* 3.8 35.9 - - + -
235D ALA* 3.6 20.0 - - + -
236D LEU* 3.6 8.3 - - + +
331D MET 2.6 21.1 + - - +
332D GLU* 4.4 0.7 - - - -
334D TYR* 1.3 81.8 - - - +
336D ARG* 1.3 53.1 + - - +
339D PHE* 3.2 9.2 - - - +
340D PRO* 2.8 31.0 - - - +
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Residues in contact with ARG 336 (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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235D ALA* 3.6 29.9 + - + +
236D LEU* 5.0 1.3 - - - -
332D GLU* 2.9 23.6 + - + +
333D GLU 3.8 1.8 - - - +
335D ALA* 1.3 76.6 - - - +
337D GLU* 1.3 82.3 + - - +
340D PRO* 3.1 25.3 - - - +
679L GLN* 2.6 39.4 + - - +
680L THR* 3.9 12.2 + - + +
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Residues in contact with GLU 337 (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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329D ARG* 5.7 1.3 - - - +
333D GLU* 2.7 33.7 + - + +
336D ARG* 1.3 107.6 + - - +
338D VAL* 1.3 62.2 + - + +
340D PRO* 4.3 0.4 - - - -
341D ILE* 2.9 28.7 - - - +
677L PHE 4.3 2.8 - - - +
678L THR* 3.5 23.3 - - - +
679L GLN* 3.6 21.5 + - - -
680L THR* 2.7 24.7 + - - +
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Residues in contact with VAL 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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