Contacts of the helix formed by residues 330 - 338 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ASN* 4.0 2.2 - - - -
221G GLU* 3.2 19.4 - - - +
328G TRP* 3.5 26.9 + - + -
329G ARG* 1.3 77.6 - - - +
331G MET* 1.3 63.9 + - - +
332G GLU* 3.8 14.1 - - - +
333G GLU* 2.9 24.1 + - - +
334G TYR* 3.0 18.0 + - - +
680O THR* 5.2 1.4 - - - +
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Residues in contact with MET 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ASN* 2.9 39.4 - - - +
157G PHE* 4.1 4.0 - - + -
189G TRP* 3.5 36.3 - - + -
221G GLU* 2.7 16.4 + - - +
223G LEU* 3.7 15.5 - - + -
228G VAL* 4.0 18.4 - - + +
231G ALA* 4.2 12.1 - - + -
232G PHE* 3.8 32.1 - - + -
330G ASP* 1.3 73.9 - - - +
332G GLU* 1.3 53.5 + - - +
334G TYR* 3.4 5.0 - - - +
335G ALA* 2.7 38.3 + - - +
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Residues in contact with GLU 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ASN* 3.4 20.4 + - - -
231G ALA* 4.2 18.3 - - + +
234G ARG* 3.5 25.5 + - - +
235G ALA* 3.5 13.0 - - + +
330G ASP* 3.3 14.4 + - - +
331G MET* 1.3 78.6 - - - +
333G GLU* 1.3 58.4 + - - +
335G ALA 3.4 0.2 + - - -
336G ARG* 2.9 68.8 + - - +
680O THR* 4.8 5.6 - - + +
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Residues in contact with GLU 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G HIS* 4.4 8.9 + - - -
328G TRP 4.6 2.3 - - - +
329G ARG* 3.2 42.2 + - + +
330G ASP* 2.9 17.4 + - - +
332G GLU* 1.3 75.8 - - - +
334G TYR* 1.3 55.9 + - - +
337G GLU* 2.6 46.3 + - + +
676O CYS* 5.6 0.9 - - - -
678O THR* 3.2 21.5 + - - +
680O THR* 3.3 36.3 - - + +
681O THR* 5.0 3.7 + - - -
682O PRO* 5.2 4.5 - - - +
694O CYS* 5.6 2.3 - - - +
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Residues in contact with TYR 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ASN* 3.3 35.0 - - + +
155G ASN* 3.3 22.6 - - + -
157G PHE* 3.4 12.7 + - + -
191G ASP* 3.7 20.9 - - - +
232G PHE* 4.0 12.1 - + - -
329G ARG* 4.0 4.7 - - - +
330G ASP 3.0 14.0 + - - +
331G MET* 3.4 15.5 - - - +
333G GLU* 1.3 76.7 - - - +
335G ALA* 1.3 71.6 + - - +
338G VAL* 2.6 61.3 + - + -
339G PHE* 2.8 27.9 + + + -
342G GLU* 2.3 33.8 + - - -
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Residues in contact with ALA 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G PHE* 3.7 33.4 - - + -
235G ALA* 3.3 21.8 - - + -
236G LEU* 3.6 5.8 - - + +
331G MET 2.7 21.3 + - - +
334G TYR* 1.3 76.5 - - - +
336G ARG* 1.3 53.4 + - - +
339G PHE* 3.0 14.5 - - - +
340G PRO* 2.7 32.9 - - - +
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Residues in contact with ARG 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234G ARG* 3.2 40.4 + - - +
235G ALA* 3.4 31.3 + - + +
236G LEU* 5.1 0.2 - - - -
332G GLU* 2.9 56.7 + - - +
333G GLU 4.0 0.9 - - - +
335G ALA* 1.3 77.3 - - - +
337G GLU* 1.3 78.8 + - - +
340G PRO* 3.3 23.3 - - - +
679O GLN* 6.3 0.2 - - - -
680O THR* 3.6 19.4 + - - +
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Residues in contact with GLU 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G ARG* 5.7 0.7 - - - +
333G GLU* 2.6 30.3 + - + +
336G ARG* 1.3 87.6 - - - +
338G VAL* 1.3 61.1 + - + +
340G PRO* 4.4 0.7 - - - -
341G ILE* 3.6 19.3 - - - +
677O PHE 4.4 3.3 - - - +
678O THR* 3.4 24.7 - - - +
679O GLN* 3.6 33.2 + - - +
680O THR* 2.6 30.5 + - - +
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Residues in contact with VAL 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G ARG* 2.9 46.7 - - - +
333G GLU 4.6 0.4 - - - +
334G TYR* 2.6 43.4 + - + +
337G GLU* 1.3 77.9 - - + +
339G PHE* 1.3 68.0 + - - +
340G PRO* 3.2 2.7 - - - -
341G ILE* 2.8 18.4 + - + +
342G GLU* 2.9 29.5 + - + +
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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