Contacts of the helix formed by residues 317 - 325 (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 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B PRO* 5.6 3.1 - - + -
217B ALA* 3.4 33.5 - - + +
219B THR* 3.6 10.8 + - - +
222B THR* 4.0 26.0 - - + -
277B PHE* 4.8 9.6 - - + -
282B PHE* 4.8 20.2 - - + +
316B ARG* 1.3 82.8 - - + +
318B THR* 1.3 61.8 + - + +
319B ASP 2.6 17.7 + - - -
320B GLU* 3.6 12.1 + - - +
321B ALA 4.5 2.6 + - - -
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 3.7 12.6 - - - +
220B PHE 4.1 2.9 - - - -
221B GLU* 3.8 28.3 - - - +
222B THR* 4.1 11.9 - - + -
316B ARG* 3.6 27.0 + - - +
317B VAL* 1.3 76.1 - - + +
319B ASP* 1.3 65.3 + - - +
320B GLU 3.6 0.4 - - - -
321B ALA* 3.5 2.7 + - - +
322B ARG* 2.8 67.7 + - - +
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Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 2.6 44.8 + - - +
317B VAL 2.6 6.1 + - - -
318B THR* 1.3 81.3 + - - +
320B GLU* 1.3 67.0 + - + +
322B ARG* 3.3 5.3 + - - +
323B LYS* 3.0 28.0 + - + +
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TRP* 3.9 27.7 - - + -
215B ARG 5.8 3.1 - - - +
216B ILE* 4.5 18.4 - - + -
217B ALA* 5.5 3.1 - - + +
317B VAL 3.6 7.1 + - - +
319B ASP* 1.3 77.2 - - + +
321B ALA* 1.3 64.9 + - - +
323B LYS* 3.1 21.0 + - - +
324B LEU* 3.1 27.3 + - - +
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Residues in contact with ALA 321 (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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199B ALA* 6.4 0.2 - - - -
216B ILE* 5.1 2.2 - - - -
217B ALA 3.4 18.6 + - - +
218B LEU* 4.7 3.8 - - + -
219B THR 3.0 30.1 - - - +
220B PHE* 3.1 24.6 - - + -
317B VAL 4.5 0.8 + - - +
318B THR 3.5 4.2 + - - +
319B ASP 3.3 0.4 - - - -
320B GLU* 1.3 80.0 - - - +
322B ARG* 1.3 62.1 + - - +
324B LEU* 3.1 12.0 + - - +
325B TRP 3.1 18.7 + - - -
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Residues in contact with ARG 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 2.6 33.0 + - + +
221B GLU* 3.5 18.0 - - - +
316B ARG* 3.8 16.6 - - - +
318B THR* 2.8 47.2 + - - +
319B ASP* 3.9 5.6 - - - +
321B ALA* 1.3 72.7 - - - +
323B LYS* 1.3 59.6 + - - +
324B LEU 3.4 0.2 - - - -
325B TRP 3.1 23.5 - - - +
326B SER* 3.6 13.0 + - - -
328B TRP* 3.2 38.9 - - - +
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Residues in contact with LYS 323 (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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210B LYS* 5.5 7.9 - - - +
319B ASP* 3.0 15.1 + - + +
320B GLU* 3.1 25.4 + - - +
322B ARG* 1.3 78.1 - - - +
324B LEU* 1.3 60.1 + - + +
325B TRP 3.8 0.3 + - - -
326B SER* 5.2 1.2 + - - -
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Residues in contact with LEU 324 (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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198B PRO 4.8 0.2 - - - +
199B ALA* 4.8 9.9 - - + +
202B GLN* 3.3 43.6 + - + +
203B ILE* 3.8 27.8 - - + -
206B ASP* 3.4 25.6 - - - +
210B LYS* 5.7 1.1 - - - +
211B TRP* 4.1 20.2 - - + +
216B ILE* 3.9 28.5 - - + -
218B LEU* 6.2 1.3 - - + -
320B GLU* 3.1 18.7 + - - +
321B ALA* 3.7 7.2 - - - +
323B LYS* 1.3 80.2 - - + +
325B TRP* 1.3 62.1 + - + +
703J LEU* 5.9 1.7 - - - +
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Residues in contact with TRP 325 (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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194B HIS* 4.5 4.5 - + - -
195B ASP* 2.9 50.9 + - + +
198B PRO* 3.5 32.5 - - + -
199B ALA* 4.2 15.7 - - - +
220B PHE* 3.5 16.9 - + + -
321B ALA 3.1 10.3 + - - +
322B ARG* 3.1 14.9 - - - +
324B LEU* 1.3 81.8 - - - +
326B SER* 1.3 57.2 + - - +
327B GLY* 3.3 27.8 + - - -
328B TRP* 3.7 11.4 - - - -
696J ALA* 3.8 27.8 - - + -
699J LEU* 3.4 29.2 - - + -
700J PHE* 4.2 19.1 - + + -
703J LEU* 4.5 9.0 - - + -
704J HIS* 5.9 2.9 - - - -
708J ARG* 4.7 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
------------------------------------------------------------
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