Contacts of the helix formed by residues 318 - 325 (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 THR 318 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H THR* 3.6 15.3 - - + +
220H PHE 4.1 0.7 - - - -
221H GLU* 3.9 24.9 - - - +
222H THR* 4.1 13.7 - - + -
316H ARG* 3.0 34.6 + - - +
317H VAL* 1.3 82.5 - - + +
319H ASP* 1.3 68.2 + - - +
320H GLU 3.7 0.4 - - - -
321H ALA* 3.5 3.8 + - - +
322H ARG* 3.0 55.6 + - - +
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Residues in contact with ASP 319 (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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315H GLN* 2.9 39.7 + - - +
316H ARG* 3.3 19.4 + - - +
317H VAL 3.2 1.0 - - - -
318H THR* 1.3 80.8 + - - +
320H GLU* 1.3 66.9 + - + +
322H ARG* 3.1 8.3 + - - +
323H LYS* 3.0 38.2 + - - +
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Residues in contact with GLU 320 (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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211H TRP* 3.5 34.1 - - + -
214H HIS* 4.0 14.0 + - - -
215H ARG 3.6 18.7 - - - +
216H ILE* 4.0 18.4 - - + +
217H ALA* 4.3 3.6 + - - +
282H PHE* 4.6 6.9 - - - -
317H VAL 4.6 5.3 + - - +
318H THR 3.7 0.2 - - - -
319H ASP* 1.3 77.5 - - + +
321H ALA* 1.3 64.9 + - - +
323H LYS* 3.1 29.7 + - - +
324H LEU* 3.1 19.5 + - - +
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Residues in contact with ALA 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H ALA* 6.4 0.2 - - - -
216H ILE* 4.7 2.2 - - - +
217H ALA 3.5 18.0 + - - +
218H LEU* 4.8 2.7 - - + -
219H THR 3.1 28.5 - - - +
220H PHE* 3.5 24.9 - - + -
317H VAL 4.9 0.6 + - - -
318H THR 3.5 4.4 - - - +
319H ASP 3.2 0.2 - - - -
320H GLU* 1.3 79.4 - - - +
322H ARG* 1.3 64.8 + - - +
324H LEU* 3.0 23.1 + - - +
325H TRP 3.1 10.7 + - - -
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Residues in contact with ARG 322 (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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220H PHE* 2.8 34.0 + - + +
221H GLU* 3.8 15.4 - - - +
222H THR 5.0 0.4 - - - +
316H ARG* 4.6 15.2 - - - +
318H THR* 3.0 38.4 + - - +
319H ASP* 3.7 6.1 - - - +
321H ALA* 1.3 74.8 - - - +
323H LYS* 1.3 62.8 + - + +
325H TRP 3.2 23.1 - - - +
326H SER* 3.5 13.4 + - - -
328H TRP* 3.5 36.5 - - - +
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Residues in contact with LYS 323 (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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202H GLN* 5.5 0.7 - - - +
211H TRP* 6.4 2.7 - - + -
319H ASP* 3.0 32.7 + - - +
320H GLU* 3.1 19.5 + - + +
322H ARG* 1.3 78.5 - - + +
324H LEU* 1.3 62.8 + - + +
325H TRP* 4.7 0.2 - - - -
326H SER* 5.1 1.4 + - - -
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Residues in contact with LEU 324 (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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198H PRO 5.1 0.2 - - - +
199H ALA* 4.8 9.4 - - + +
202H GLN* 3.2 40.0 + - + +
203H ILE* 3.8 31.0 - - + -
206H ASP* 3.3 26.2 - - - +
211H TRP* 3.4 24.7 - - + +
216H ILE* 4.1 24.9 - - + -
218H LEU* 6.1 1.6 - - + -
320H GLU 3.1 18.6 + - - +
321H ALA* 3.0 9.1 + - - +
323H LYS* 1.3 79.5 - - + +
325H TRP* 1.3 63.6 + - + +
326H SER 4.3 0.2 - - - -
703P LEU* 5.7 1.9 - - - +
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Residues in contact with TRP 325 (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* 4.1 2.9 + + - -
195H ASP* 2.7 46.4 + - + +
198H PRO* 3.5 36.1 - - + +
199H ALA* 4.1 16.4 - - + -
220H PHE* 3.3 29.2 - + + -
321H ALA 3.1 3.9 + - - +
322H ARG* 3.2 8.4 - - - +
323H LYS 3.4 0.2 - - - -
324H LEU* 1.3 82.2 - - - +
326H SER* 1.3 63.8 + - - +
327H GLY* 3.4 26.0 - - - -
328H TRP* 3.6 9.3 - - - -
696P ALA* 3.8 27.8 - - + -
699P LEU* 3.9 21.5 - - + -
700P PHE* 4.1 18.4 - + + -
703P LEU* 4.6 12.1 - - + -
704P HIS* 5.4 3.4 - - - -
708P ARG* 4.8 3.4 - - - -
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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