Contacts of the helix formed by residues 317 - 325 (chain E) 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 317 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188E PRO* 5.2 3.8 - - + -
217E ALA* 3.2 40.0 - - + +
219E THR* 3.9 15.2 - - + +
222E THR* 4.1 20.0 - - + -
277E PHE* 4.5 6.3 - - + -
281E GLU 5.4 2.0 - - - +
282E PHE* 3.9 36.5 - - + +
283E SER 5.7 1.0 + - - -
316E ARG* 1.3 75.3 - - + +
318E THR* 1.3 65.2 + - + +
319E ASP 3.3 1.0 + - - -
320E GLU* 4.4 7.7 + - - +
321E ALA 4.8 0.7 + - - -
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Residues in contact with THR 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E THR* 3.4 18.2 - - + +
220E PHE 3.6 0.4 - - - -
221E GLU* 3.4 34.5 - - - +
222E THR* 3.9 20.2 - - + -
316E ARG* 3.5 19.7 + - - +
317E VAL* 1.3 76.8 - - - +
319E ASP* 1.3 66.4 + - - +
320E GLU 3.5 0.4 - - - -
321E ALA* 3.2 4.6 + - - +
322E ARG* 2.8 52.0 + - - +
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Residues in contact with ASP 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E ARG* 2.9 36.7 + - - +
317E VAL 3.3 1.0 - - - -
318E THR* 1.3 82.3 + - - +
320E GLU* 1.3 65.9 + - - +
322E ARG* 3.1 11.7 + - - +
323E LYS* 2.9 25.0 + - - +
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Residues in contact with GLU 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E TRP* 3.7 36.9 - - + -
214E HIS* 4.5 8.3 + - - -
215E ARG 3.7 18.5 - - - +
216E ILE* 4.1 17.0 - - + +
217E ALA 4.9 2.4 + - - +
282E PHE* 5.3 2.8 - - - -
317E VAL 4.4 6.0 + - - +
318E THR 3.5 0.6 - - - -
319E ASP* 1.3 77.1 - - - +
321E ALA* 1.3 63.6 + - - +
323E LYS* 3.2 8.6 + - + +
324E LEU* 3.1 26.3 + - - +
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Residues in contact with ALA 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E ALA* 6.3 0.2 - - - -
216E ILE* 4.9 2.4 - - + +
217E ALA 3.5 18.4 + - - +
218E LEU* 4.7 4.7 - - + -
219E THR 3.4 27.6 - - - +
220E PHE* 3.2 26.7 - - + -
317E VAL 4.8 0.4 + - - -
318E THR 3.2 3.4 + - - +
320E GLU* 1.3 78.7 - - - +
322E ARG* 1.3 63.3 + - - +
324E LEU* 3.0 22.6 + - - +
325E TRP 3.0 10.6 + - - -
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Residues in contact with ARG 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E PHE* 2.9 34.7 + - + +
221E GLU* 3.9 4.6 - - - +
316E ARG* 3.6 23.4 - - - +
318E THR* 2.8 39.3 + - - +
319E ASP* 3.6 10.1 + - - +
321E ALA* 1.3 72.2 - - - +
323E LYS* 1.3 58.7 + - - +
325E TRP 3.1 14.9 - - - +
326E SER* 3.0 24.6 + - - -
328E TRP* 3.4 40.9 - - - +
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Residues in contact with LYS 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E GLN* 5.4 0.5 - - - +
211E TRP* 6.4 3.4 - - + -
319E ASP 2.9 16.6 + - - +
320E GLU* 3.4 9.2 - - - +
321E ALA 3.1 0.2 - - - -
322E ARG* 1.3 77.5 - - - +
324E LEU* 1.3 60.9 + - + +
326E SER* 4.6 4.3 + - - -
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Residues in contact with LEU 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E ALA* 4.8 10.3 - - + +
202E GLN* 3.1 45.3 + - + +
203E ILE* 3.7 36.8 - - + +
206E ASP* 3.6 24.0 - - - +
211E TRP* 3.7 17.5 - - + -
216E ILE* 4.1 23.8 - - + -
218E LEU* 5.6 0.9 - - + -
320E GLU 3.1 17.3 + - - +
321E ALA* 3.0 10.2 + - - +
323E LYS* 1.3 81.3 - - + +
325E TRP* 1.3 62.6 + - + +
326E SER* 4.3 0.4 - - - -
702M LEU* 5.7 1.9 - - - +
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Residues in contact with TRP 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E HIS* 4.1 1.9 + + - -
195E ASP* 3.1 42.8 + - + -
198E PRO* 3.4 39.4 - - + +
199E ALA* 4.2 15.0 - - - +
220E PHE* 3.5 19.4 - + + -
321E ALA 3.0 9.3 + - - +
322E ARG* 3.1 11.6 - - - +
324E LEU* 1.3 81.7 - - - +
326E SER* 1.3 66.0 + - - +
327E GLY* 3.4 26.8 + - - -
328E TRP* 3.7 7.8 - - - -
695M ALA* 3.6 29.2 - - + -
698M LEU* 3.5 24.7 - - + -
699M PHE* 4.0 14.6 - + + -
702M LEU* 4.2 16.2 - - + -
703M HIS* 6.0 0.9 - - - -
707M ARG* 4.8 5.6 - - - -
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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