Contacts of the helix formed by residues 273 - 280 (chain B) in PDB entry 2VZE
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 LEU 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 4.0 11.7 - - + -
119B TRP* 4.3 6.3 - - + -
120B TRP* 3.8 31.6 - - + +
123B ILE* 4.2 13.9 - - + -
124B LEU* 4.2 10.8 - - + -
127B ILE* 5.5 1.1 - - + -
268B ASN 3.2 7.8 + - - +
269B ILE* 3.4 28.5 - - + +
272B SER* 1.3 80.4 - - - +
274B MET* 1.3 82.6 + - + +
275B GLU 3.6 0.9 - - - -
276B PRO* 3.5 2.5 - - - +
277B TRP* 3.3 61.5 + - + +
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Residues in contact with MET 274 (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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46B PHE* 3.6 36.8 - - + -
127B ILE* 4.5 12.1 - - + -
133B PHE* 5.7 0.2 - - + -
235B TYR 5.6 0.2 - - - +
238B LEU* 3.6 38.8 - - + +
239B GLY* 3.7 21.5 - - - +
242B ALA* 3.5 17.2 - - + +
269B ILE* 3.0 35.2 + - + +
270B LEU* 3.6 7.2 + - - +
273B LEU* 1.3 85.4 - - + +
275B GLU* 1.3 60.6 + - - +
278B ALA* 2.8 32.8 + - - +
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ALA* 4.7 3.9 - - - +
245B ASP* 4.2 1.4 - - - +
246B ALA* 3.5 16.3 + - - +
247B GLY* 2.9 25.1 + - - -
248B TRP* 3.5 13.9 + - - +
249B THR* 2.7 45.8 + - + +
251B LEU* 4.4 3.6 - - + -
257B MET* 4.2 10.3 - - + -
270B LEU 3.1 17.1 + - - +
271B CYS* 3.7 10.1 - - + +
274B MET* 1.3 78.4 - - - +
276B PRO* 1.3 75.3 - - + +
278B ALA* 3.3 12.0 + - - +
279B LEU* 3.5 16.7 + - - +
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Residues in contact with PRO 276 (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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251B LEU* 3.6 25.4 - - + -
257B MET* 4.9 4.7 - - + -
271B CYS 3.0 26.5 - - - +
272B SER 3.5 15.5 - - - +
273B LEU 3.5 10.5 - - - +
275B GLU* 1.3 86.3 - - + +
277B TRP* 1.3 61.3 + - + +
279B LEU 3.2 2.6 + - - -
280B GLY 3.1 6.9 + - - -
281B ALA* 2.8 39.4 + - + +
282B CYS 4.2 4.0 - - - +
283B THR* 3.7 17.9 - - - +
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Residues in contact with TRP 277 (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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46B PHE* 4.1 9.2 - + + -
50B VAL* 3.3 6.7 - - - +
51B LEU* 4.0 24.7 - - + -
54B TRP* 2.9 30.1 + - - -
68B ALA* 2.8 24.7 + - - +
69B LEU* 4.1 7.2 - - + -
83B PHE* 3.8 10.3 - + + -
86B LEU* 3.5 30.1 - - + -
120B TRP* 3.7 23.3 - + + -
124B LEU* 3.8 21.5 - - + -
273B LEU* 3.3 50.0 + - + +
275B GLU 3.2 0.6 - - - -
276B PRO* 1.3 77.6 - - + +
278B ALA* 1.3 60.3 + - - +
280B GLY 3.6 1.3 + - - +
281B ALA 3.4 16.6 + - - -
283B THR* 3.7 25.4 - - + +
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Residues in contact with ALA 278 (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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46B PHE* 4.1 2.2 - - + -
50B VAL* 3.8 15.1 - - + +
54B TRP* 3.4 18.0 + - - -
242B ALA 4.3 1.8 - - - +
243B LYS* 4.2 20.9 - - + +
246B ALA* 3.4 28.9 - - + +
274B MET 2.8 19.3 + - - +
275B GLU 3.5 2.5 - - - +
277B TRP* 1.3 77.9 - - - +
279B LEU* 1.3 57.2 + - - +
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Residues in contact with LEU 279 (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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54B TRP* 3.5 14.3 - - - -
246B ALA* 3.9 21.5 - - + +
247B GLY* 3.7 22.0 - - - +
251B LEU* 3.6 38.6 - - + +
252B GLN* 5.4 1.8 - - - -
253B ALA* 3.3 30.1 - - - +
275B GLU* 3.5 22.4 + - - +
276B PRO 3.2 6.8 + - - +
278B ALA* 1.3 77.0 - - - +
280B GLY* 1.3 57.7 + - - +
281B ALA* 4.3 7.0 - - + +
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Residues in contact with GLY 280 (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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54B TRP* 3.5 30.4 - - - +
63B ARG* 3.1 16.1 + - - -
66B SER* 4.8 0.9 - - - -
67B PRO 4.5 1.0 - - - +
83B PHE* 3.3 25.7 - - - -
253B ALA 3.0 13.5 - - - +
276B PRO 3.1 2.6 + - - -
277B TRP 3.6 0.4 + - - -
278B ALA 3.5 0.6 - - - -
279B LEU* 1.3 77.4 - - - +
281B ALA* 1.3 60.1 + - - +
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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