Contacts of the helix formed by residues 317 - 325 (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 VAL 317 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G PRO* 5.4 3.4 - - + -
217G ALA* 3.1 38.3 - - + +
219G THR* 3.6 17.0 - - + +
222G THR* 4.3 17.0 - - + -
277G PHE* 4.7 6.3 - - + -
281G GLU 5.4 2.4 + - - -
282G PHE* 4.1 38.1 + - + +
284G ARG* 5.8 2.4 - - - +
316G ARG* 1.3 81.3 - - + +
318G THR* 1.3 61.4 + - - +
319G ASP* 3.1 2.7 + - - -
320G GLU* 4.1 8.5 + - - +
321G ALA 4.5 1.4 + - - -
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Residues in contact with THR 318 (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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219G THR* 3.6 24.5 - - + +
220G PHE 3.6 1.8 - - - -
221G GLU* 3.3 36.8 - - - +
222G THR* 4.2 2.0 - - + +
316G ARG* 2.7 40.1 + - - +
317G VAL* 1.3 77.8 - - + +
319G ASP* 1.3 60.4 + - - +
320G GLU 3.6 0.2 - - - -
321G ALA* 3.5 2.1 + - - +
322G ARG* 2.9 51.2 + - - +
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Residues in contact with ASP 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G ARG* 2.6 38.2 + - - +
317G VAL 3.1 2.2 - - - -
318G THR* 1.3 77.7 + - - +
320G GLU* 1.3 67.1 + - + +
322G ARG* 3.2 9.4 + - - +
323G LYS* 3.0 23.8 + - - +
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Residues in contact with GLU 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G TRP* 4.2 24.9 - - + -
214G HIS* 4.4 12.7 + - - -
215G ARG 3.7 18.8 - - - +
216G ILE* 4.1 19.5 - - + +
217G ALA 4.8 2.2 + - - +
282G PHE* 5.2 3.6 - - - -
317G VAL 4.1 6.2 + - - +
318G THR 3.6 0.2 - - - -
319G ASP* 1.3 77.4 - - + +
321G ALA* 1.3 62.4 + - - +
323G LYS* 3.3 12.0 + - + +
324G LEU* 3.1 30.7 + - + +
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Residues in contact with ALA 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G ALA* 6.4 0.2 - - - -
216G ILE* 4.9 2.2 - - - +
217G ALA 3.4 18.5 + - - +
218G LEU* 4.7 5.4 - - + -
219G THR 3.2 30.1 - - - +
220G PHE* 3.2 23.1 - - + -
317G VAL 4.5 1.2 + - - -
318G THR* 3.8 3.7 - - - +
319G ASP 3.2 0.4 - - - -
320G GLU* 1.3 80.4 - - - +
322G ARG* 1.3 62.4 + - - +
324G LEU* 3.2 12.5 + - - +
325G TRP 3.1 18.5 + - - -
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Residues in contact with ARG 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G PHE* 3.1 33.5 + - + +
221G GLU* 4.3 5.5 - - - +
316G ARG* 3.6 23.9 - - - +
318G THR* 2.9 34.0 + - - +
319G ASP* 3.7 8.7 - - - +
321G ALA* 1.3 75.8 - - - +
323G LYS* 1.3 59.8 + - - +
325G TRP 3.1 24.0 - - - +
326G SER* 3.5 14.0 + - - -
328G TRP* 3.3 39.9 - - - +
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Residues in contact with LYS 323 (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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206G ASP* 5.3 0.4 + - - -
210G LYS* 3.0 34.5 - - - +
211G TRP* 4.8 9.3 - - + -
319G ASP 3.0 16.5 + - - +
320G GLU* 3.6 12.1 - - + +
322G ARG* 1.3 77.6 - - - +
324G LEU* 1.3 62.7 + - + +
325G TRP 5.1 0.2 - - - -
326G SER* 5.3 0.7 + - - -
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Residues in contact with LEU 324 (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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199G ALA* 4.8 8.7 - - + +
202G GLN* 3.0 50.2 + - + +
203G ILE* 3.9 24.7 - - + +
206G ASP* 3.3 14.8 - - - +
211G TRP* 3.3 36.3 - - + -
216G ILE* 4.0 27.8 - - + -
218G LEU* 5.9 1.3 - - + -
320G GLU 3.1 19.8 + - - +
321G ALA* 3.6 7.6 - - - +
323G LYS* 1.3 81.4 - - + +
325G TRP* 1.3 61.3 + - + +
703O LEU* 6.0 0.3 - - - +
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Residues in contact with TRP 325 (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 4.0 2.9 + - - -
195G ASP* 3.1 31.5 + - + +
198G PRO* 3.4 38.2 - - + +
199G ALA* 4.1 16.2 - - - -
202G GLN* 6.2 0.4 - - - -
220G PHE* 3.1 44.3 - + + -
321G ALA 3.1 3.6 + - - +
322G ARG* 3.1 10.8 - - - +
323G LYS 3.4 0.2 - - - -
324G LEU* 1.3 80.9 - - - +
326G SER* 1.3 64.0 + - - +
327G GLY* 3.2 30.7 + - - -
328G TRP* 3.8 4.0 - - - -
696O ALA* 3.7 28.7 - - + -
699O LEU* 4.0 20.2 - - + -
700O PHE* 4.2 17.5 - + + -
703O LEU* 4.3 15.0 - - + -
704O HIS* 5.9 2.2 - - - -
708O ARG* 4.7 4.0 - - - -
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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