Contacts of the helix formed by residues 247 - 259 (chain A) in PDB entry 5V2C
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 ASN 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A SER* 3.0 13.4 + - - -
224A ILE* 4.1 11.6 - - + +
246A TYR* 1.3 74.0 - - - +
248A ILE* 1.3 57.0 + - - +
249A VAL* 3.0 16.2 + - - +
250A ALA* 3.0 27.3 + - - +
251A ALA 3.0 21.1 + - - -
482B ILE* 3.7 22.8 - - + +
483B ASP 5.2 1.2 + - - -
486B LEU* 4.1 28.5 + - - +
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Residues in contact with ILE 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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244A GLU* 6.3 1.1 - - + -
246A TYR* 3.6 35.2 + - + +
247A ASN* 1.3 69.5 + - - +
249A VAL* 1.3 73.1 + - + +
251A ALA* 4.1 4.9 - - + -
252A HIS* 2.8 30.5 + - + +
265A PHE 5.0 8.1 - - - +
266A ASN* 4.0 20.2 - - - +
267A ASN 4.6 0.2 - - - -
268A SER* 3.9 38.1 - - - +
271A LEU* 5.5 7.4 - - + -
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 3.0 11.5 + - - +
248A ILE* 1.3 87.4 - - + +
250A ALA* 1.3 57.0 + - - +
252A HIS* 3.8 7.2 - - + +
253A GLY* 2.8 25.8 + - - -
488B PRO* 4.4 16.8 - - + -
491B VAL* 3.2 27.9 - - + +
492B GLU* 4.1 14.1 - - - +
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Residues in contact with ALA 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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222A SER* 4.5 3.8 - - - -
247A ASN* 3.0 29.2 + - - +
249A VAL* 1.3 74.1 - - - +
251A ALA* 1.3 59.3 + - - +
253A GLY* 3.1 1.6 + - - -
254A TYR* 2.8 30.0 + - - +
482B ILE* 3.9 18.8 - - + -
486B LEU* 4.5 13.2 - - + -
491B VAL* 4.2 14.6 - - + +
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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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218A LEU* 4.1 22.5 - - + +
219A VAL* 6.2 0.2 - - + -
221A SER* 4.8 3.1 - - - -
222A SER* 3.6 25.2 - - - +
246A TYR* 4.6 5.6 - - + -
247A ASN 3.0 9.3 + - - +
248A ILE* 3.7 13.7 - - + +
250A ALA* 1.3 74.1 - - - +
252A HIS* 1.3 58.5 + - - +
254A TYR* 3.2 9.3 + - - +
255A PHE* 2.9 30.8 + - - +
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Residues in contact with HIS 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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248A ILE* 2.8 22.4 + - + +
249A VAL* 3.8 6.3 - - + +
251A ALA* 1.3 71.3 - - - +
253A GLY* 1.3 58.1 + - - +
255A PHE* 4.8 0.2 - - - -
256A GLY* 2.7 32.4 + - - -
261A GLN* 3.5 27.7 + - - +
264A SER* 2.7 41.8 + - - -
265A PHE 3.4 14.7 + - - +
266A ASN* 3.7 33.6 + - + +
493B TRP* 3.4 35.5 - + - -
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Residues in contact with GLY 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 VAL 2.8 19.9 + - - -
250A ALA 3.1 5.1 + - - -
252A HIS* 1.3 73.2 - - - +
254A TYR* 1.3 59.7 + - - +
257A ARG* 2.9 48.9 + - - +
491B VAL* 3.9 15.9 - - - -
493B TRP* 3.9 4.0 - - - -
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Residues in contact with TYR 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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214A MET* 5.2 1.3 - - + -
218A LEU* 3.3 30.1 - - + -
221A SER* 5.6 6.7 - - - +
250A ALA 2.8 12.9 + - - +
251A ALA* 3.4 9.9 - - - +
252A HIS 3.1 0.2 - - - -
253A GLY* 1.3 76.6 - - - +
255A PHE* 1.3 63.9 + - - +
257A ARG* 3.0 5.9 + - - +
258A LEU* 2.9 62.5 + - + +
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Residues in contact with PHE 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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214A MET* 3.2 38.4 - - + -
218A LEU* 4.1 20.6 - - + -
251A ALA 2.9 18.8 + - - +
252A HIS* 4.8 0.2 - - - -
254A TYR* 1.3 79.4 - - + +
256A GLY* 1.3 63.0 + - - +
258A LEU* 3.1 23.4 + - + -
259A ILE* 3.1 39.0 + - + +
263A ALA 3.6 21.8 - - - -
264A SER* 3.4 27.4 - - - +
265A PHE* 5.0 4.5 - + - -
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Residues in contact with GLY 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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252A HIS 2.7 23.6 + - - -
255A PHE* 1.3 74.9 - - - +
257A ARG* 1.3 55.4 + - - +
260A PHE* 2.8 37.3 + - - -
261A GLN* 3.1 3.9 + - - -
264A SER* 3.6 16.9 - - - -
493B TRP* 3.6 17.7 + - - -
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Residues in contact with ARG 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 GLY* 2.9 40.6 + - - +
254A TYR* 3.0 6.1 + - - +
256A GLY* 1.3 74.2 - - - +
258A LEU* 1.3 67.8 + - - +
259A ILE 3.2 8.5 - - - +
490B GLN 4.7 3.2 + - - -
491B VAL* 3.2 28.5 + - - +
492B GLU 3.2 33.1 + - - -
493B TRP* 3.5 33.5 - - - +
494B GLY 4.9 0.6 - - - +
499B VAL* 3.8 41.9 - - - +
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Residues in contact with LEU 258 (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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214A MET* 4.2 8.7 - - + -
254A TYR* 2.9 44.0 + - + +
255A PHE* 3.1 33.4 + - + +
257A ARG* 1.3 79.8 - - - +
259A ILE* 1.3 72.1 + - + +
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Residues in contact with ILE 259 (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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255A PHE* 3.1 38.4 + - + +
256A GLY 3.7 1.3 - - - -
257A ARG 3.6 5.4 - - - +
258A LEU* 1.3 99.2 - - + +
260A PHE* 1.3 80.2 + - + +
263A ALA* 3.8 23.1 - - + -
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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