Contacts of the helix formed by residues 338 - 346 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B GLU* 5.1 7.9 - - - +
329B ARG* 3.2 42.6 - - - +
334B TYR* 2.7 31.3 + - + +
337B GLU* 1.3 80.6 - - + +
339B PHE* 1.3 66.8 + - - +
340B PRO* 3.2 3.1 - - - -
341B ILE* 2.9 8.8 + - + -
342B GLU* 2.8 49.6 + - + +
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Residues in contact with PHE 339 (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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157B PHE* 3.8 17.9 - - + -
158B THR* 3.8 5.4 - - - -
159B SER* 4.2 2.7 - - - -
167B MET* 3.9 22.2 - - + -
175B PHE* 4.6 8.3 - + - -
232B PHE* 3.6 29.6 - + + -
236B LEU* 4.4 7.9 - - + -
334B TYR* 2.8 34.0 + + + +
335B ALA* 3.3 26.2 - - - +
338B VAL* 1.3 71.6 - - - +
340B PRO* 1.4 59.2 - - + +
342B GLU* 3.1 5.9 + - + +
343B GLU* 2.8 68.7 + - + +
350B TRP* 3.9 18.2 - + - -
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Residues in contact with PRO 340 (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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236B LEU* 4.9 4.9 - - + -
335B ALA 3.0 26.7 - - - +
336B ARG 2.9 21.5 - - - +
337B GLU 4.3 0.2 - - - -
338B VAL 3.3 2.2 - - - -
339B PHE* 1.4 85.5 - - + +
341B ILE* 1.3 66.6 + - + +
343B GLU* 3.4 5.6 + - + -
344B GLU* 2.9 25.6 + - - +
350B TRP* 4.5 13.2 - - + -
351B MET* 3.2 28.5 - - + +
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Residues in contact with ILE 341 (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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337B GLU* 3.1 24.9 - - - +
338B VAL* 2.9 8.2 + - + +
340B PRO* 1.3 80.6 - - + +
342B GLU* 1.3 66.5 + - + +
344B GLU* 3.4 16.9 + - + +
345B ALA* 3.1 24.3 + - + +
712J LEU* 5.4 13.0 - - + -
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Residues in contact with GLU 342 (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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155B ASN* 3.5 29.6 + - - +
157B PHE 4.2 7.1 - - - +
193B GLU* 5.3 5.2 - - - +
334B TYR* 2.7 25.7 + - - -
338B VAL* 2.8 33.7 + - + +
339B PHE* 3.4 8.8 - - + +
341B ILE* 1.3 79.8 - - + +
343B GLU* 1.3 64.9 + - + +
345B ALA* 3.3 6.5 + - - +
346B ASN* 3.3 27.0 + - - +
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Residues in contact with GLU 343 (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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157B PHE 4.7 0.3 - - - +
158B THR* 3.3 16.8 + - - -
159B SER* 2.4 48.9 + - - -
160B LEU* 5.4 0.2 - - - +
339B PHE* 2.8 48.0 + - + +
340B PRO 3.5 5.6 - - - +
342B GLU* 1.3 76.5 - - - +
344B GLU* 1.3 57.6 + - - +
346B ASN* 2.9 31.2 + - - +
348B LEU* 3.3 17.3 + - + +
350B TRP* 3.4 17.4 + - + +
351B MET* 3.7 13.0 - - + -
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Residues in contact with GLU 344 (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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340B PRO 2.9 15.5 + - - +
341B ILE* 3.6 21.3 - - + +
342B GLU 3.3 0.2 - - - -
343B GLU* 1.3 75.4 - - - +
345B ALA* 1.3 57.3 + - - +
347B GLY* 2.9 21.1 + - - -
348B LEU 3.5 5.9 + - - +
351B MET* 3.2 31.5 - - + +
352B LEU* 4.1 16.3 - - + +
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Residues in contact with ALA 345 (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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341B ILE* 3.1 17.6 + - + +
342B GLU* 3.8 7.0 - - - +
343B GLU 3.3 0.2 - - - -
344B GLU* 1.3 75.8 - - - +
346B ASN* 1.3 61.7 + - - +
347B GLY 3.2 1.9 + - - -
712J LEU* 6.2 4.5 - - + -
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Residues in contact with ASN 346 (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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158B THR* 4.5 9.3 + - - -
160B LEU* 4.1 30.9 - - + +
342B GLU* 3.3 19.4 + - - +
343B GLU* 2.9 15.7 + - - +
345B ALA* 1.3 79.6 - - - +
347B GLY* 1.3 59.5 + - - +
348B LEU* 3.5 10.4 + - + +
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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