Contacts of the helix formed by residues 247 - 257 (chain A) in PDB entry 5VZ7
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 GLY 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A THR* 3.8 7.4 - - - -
246A VAL* 1.3 72.8 - - - +
248A VAL* 1.3 67.1 + - - -
249A LYS 3.3 2.9 - - - -
250A THR 3.3 0.7 + - - -
251A ALA* 2.9 23.4 + - - +
2P G 2.9 25.9 + - - -
3P T 3.9 12.8 - - - -
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLY 3.7 26.5 - - - +
169A PHE* 3.9 17.9 - - + +
171A GLY* 5.2 3.1 - - - +
237A MET* 3.7 14.5 - - + +
241A THR* 3.9 19.0 - - + +
247A GLY* 1.3 72.1 - - - -
249A LYS* 1.3 62.9 + - + +
251A ALA* 3.7 1.0 - - - +
252A ASP* 2.9 31.4 + - + +
2P G 4.7 1.2 + - - -
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Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLY 3.3 0.4 - - - -
248A VAL* 1.3 81.5 - - + +
250A THR* 1.3 62.1 + - - +
252A ASP* 3.5 6.0 + - - +
253A ARG* 3.1 23.1 + - - +
256A ARG* 5.1 1.4 + - - -
1P C 3.6 30.3 - - - +
2P G 4.0 15.0 + - - +
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Residues in contact with THR 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A VAL* 3.9 7.4 - - + -
247A GLY 3.9 2.7 - - - -
249A LYS* 1.3 73.4 - - - +
251A ALA* 1.3 66.3 + - - +
253A ARG* 3.2 22.6 + - - +
254A TRP* 3.0 59.7 + - + -
276A GLN* 3.9 13.8 + - - +
1P C 3.3 10.4 + - - -
2P G 2.7 28.1 + - - -
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A MET* 3.7 14.3 - - - +
240A PHE* 3.7 32.3 - - + -
241A THR* 3.7 16.6 - - + -
246A VAL* 3.8 7.1 - - + +
247A GLY 2.9 17.7 + - - +
248A VAL 3.7 3.6 - - - +
250A THR* 1.3 77.9 - - - +
252A ASP* 1.3 56.9 + - - +
254A TRP* 3.4 4.1 + - - +
255A TYR* 2.9 28.8 + - - +
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Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PHE 5.3 0.2 - - - +
233A ARG* 2.8 39.3 + - - +
237A MET* 3.6 10.3 - - + -
248A VAL* 2.9 21.4 + - + +
249A LYS* 3.8 5.3 - - - +
251A ALA* 1.3 75.8 - - - +
253A ARG* 1.3 58.3 + - - +
255A TYR* 3.2 3.5 + - - +
256A ARG* 2.9 62.9 + - - +
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LYS 3.1 13.4 + - - +
250A THR* 3.2 24.7 + - - +
252A ASP* 1.3 78.6 + - - +
254A TRP* 1.3 90.5 + - - +
256A ARG* 3.2 29.0 + - - +
257A GLU* 3.0 51.7 + - + +
271A LYS* 5.4 6.3 + - - +
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Residues in contact with TRP 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PHE* 3.9 19.7 - + + -
243A ILE* 4.7 1.3 - - + -
246A VAL* 3.7 36.8 - - + -
250A THR* 3.0 32.3 + - + +
251A ALA 3.7 3.6 - - - +
253A ARG* 1.3 103.6 - - - +
255A TYR* 1.3 66.8 + - - +
257A GLU* 3.2 17.8 + - - +
258A GLY 3.3 0.2 + - - -
259A LEU* 3.0 42.6 + - + +
265A LEU* 3.4 35.0 - - + -
271A LYS* 4.5 14.9 + - + +
272A LEU* 3.7 31.2 - - + -
276A GLN* 3.9 10.8 - - + -
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Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLU* 3.8 12.2 + - - +
233A ARG* 3.4 64.9 + - + +
236A THR* 3.7 34.5 - - + -
237A MET* 4.5 3.8 - - + -
240A PHE* 4.4 1.0 - - - -
251A ALA 2.9 18.4 + - - +
252A ASP* 3.4 5.4 - - - +
254A TRP* 1.3 76.6 - - - +
256A ARG* 1.3 61.6 + - + +
258A GLY* 3.0 9.7 + - - -
259A LEU 3.9 3.3 + - - -
260A ARG* 2.9 61.7 + - - +
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Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ARG* 5.0 0.9 - - - +
249A LYS 5.1 1.2 + - - -
252A ASP* 2.9 45.7 + - - +
253A ARG* 3.2 32.8 + - - +
255A TYR* 1.3 82.9 - - + +
257A GLU* 1.3 61.0 + - + +
258A GLY* 3.2 1.4 + - - -
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Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ARG* 3.0 52.1 + - + +
254A TRP* 3.6 19.7 - - - +
255A TYR 3.2 0.4 - - - -
256A ARG* 1.3 78.1 - - + +
258A GLY* 1.3 55.9 + - - +
259A LEU* 3.5 14.4 + - + +
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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
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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