Contacts of the helix formed by residues 146 - 153 (chain B) in PDB entry 4BVH
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 ALA 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B GLY* 1.3 72.0 - - - -
147B GLY* 1.3 61.5 + - - +
149B SER* 3.1 14.8 + - - -
150B THR* 3.3 13.5 + - - +
154B ILE 4.9 0.7 - - - +
155B PRO 4.7 0.4 - - - +
156B ASP* 3.6 29.6 - - + -
157B PHE* 4.2 5.2 - - + -
229B ASN* 3.0 14.0 + - - +
319B GLY 3.2 0.6 + - - -
1392B OCZ 4.0 21.0 + - + +
1393B AR6 2.8 22.0 + - - +
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Residues in contact with GLY 147 (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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146B ALA* 1.3 79.5 - - - +
148B ILE* 1.3 58.4 + - - +
149B SER 3.1 0.9 - - - -
150B THR* 3.3 14.8 + - - -
151B PRO* 3.5 5.0 - - - +
319B GLY* 2.8 22.6 + - - -
366B VAL* 3.6 9.8 - - - +
1393B AR6 3.4 38.8 - - - -
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Residues in contact with ILE 148 (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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144B VAL* 3.7 29.6 - - + -
145B GLY 3.0 16.8 + - - +
147B GLY* 1.3 76.3 - - - +
149B SER* 1.3 54.3 + - - +
151B PRO* 3.5 4.4 - - - +
207B ASN* 2.7 34.5 + - - +
209B THR* 3.5 28.5 - - + -
210B HIS* 3.5 30.5 - - + +
213B LEU* 4.6 5.6 - - + -
229B ASN* 3.5 10.5 - - - +
234B GLU* 4.1 2.7 - - - +
318B LEU* 3.5 36.8 - - + +
319B GLY* 3.9 0.8 - - - -
366B VAL* 4.4 9.0 - - + -
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Residues in contact with SER 149 (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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146B ALA 3.1 8.3 + - - -
148B ILE* 1.3 77.8 - - - +
150B THR* 1.3 64.2 + - - +
151B PRO* 3.2 2.2 - - - -
152B SER* 3.0 18.7 + - - -
154B ILE* 3.4 23.5 + - - +
207B ASN* 4.1 4.0 - - - +
210B HIS* 3.4 21.2 + - - -
229B ASN* 3.4 7.5 + - - -
231B ASP* 2.6 30.6 + - - -
233B LEU* 3.9 2.4 - - - +
1392B OCZ 3.9 8.5 - - - -
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Residues in contact with THR 150 (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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146B ALA 3.3 11.8 + - - +
147B GLY 3.3 1.6 + - - -
149B SER* 1.3 78.1 - - - +
151B PRO* 1.4 60.0 - - - +
153B GLY 3.0 8.1 + - - -
154B ILE 3.0 19.7 - - - +
155B PRO* 4.3 1.6 - - + -
156B ASP* 3.6 28.3 - - + +
1393B AR6 2.8 43.5 + - + +
300C GLN* 3.3 0.9 + - - -
1398C EDO 2.7 32.3 + - - -
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Residues in contact with PRO 151 (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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147B GLY 3.5 5.2 - - - +
148B ILE 3.5 12.6 - - - +
149B SER 3.3 4.5 - - - -
150B THR* 1.4 94.4 - - - +
152B SER* 1.3 55.5 + - - +
207B ASN* 3.7 16.9 - - + +
365B ASP* 5.0 2.2 - - - +
366B VAL* 3.8 22.9 - - + -
367B VAL* 3.8 21.5 - - + -
1393B AR6 4.1 9.2 - - - +
300C GLN* 3.3 25.8 + - + +
303C LEU* 3.3 14.0 - - - +
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Residues in contact with SER 152 (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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149B SER 3.0 12.5 + - - -
151B PRO* 1.3 77.1 - - - +
153B GLY* 1.3 56.4 + - - +
154B ILE* 3.5 2.0 - - - -
204B TYR* 4.1 8.2 - - - +
205B LYS 2.7 32.0 + - - -
207B ASN* 2.9 25.3 + - - +
233B LEU* 4.1 13.0 - - - +
303C LEU* 4.0 15.1 - - - +
306C VAL* 3.7 18.9 - - - +
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Residues in contact with GLY 153 (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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150B THR 3.0 5.7 + - - -
151B PRO 3.3 1.6 - - - -
152B SER* 1.3 77.2 - - - +
154B ILE* 1.3 62.0 + - - +
155B PRO 3.8 0.7 - - - -
303C LEU* 3.5 22.1 - - - +
304C LEU* 4.0 8.9 - - - +
306C VAL* 3.8 8.6 - - - +
307C VAL* 3.8 21.3 - - - +
1398C EDO 3.4 20.0 - - - -
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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