Contacts of the helix formed by residues 247 - 256 (chain A) in PDB entry 4X41
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 MET 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A TRP* 5.7 1.6 - - + -
239A TRP* 3.4 41.0 + - + +
240A GLU 3.6 4.4 + - - -
242A VAL* 3.5 39.9 - - + -
245A PHE* 3.3 9.6 + - + +
246A ASP* 1.3 77.4 + - - +
248A THR* 1.3 61.0 + - - +
249A CYS* 3.0 10.0 + - - +
250A ILE* 3.3 29.7 + - + +
251A ARG 4.0 4.2 + - - -
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Residues in contact with THR 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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236A ILE* 5.9 0.7 - - - -
239A TRP 3.3 11.4 + - - -
240A GLU* 5.2 2.9 - - - -
246A ASP* 3.0 24.4 + - - +
247A MET* 1.3 75.7 - - - +
249A CYS* 1.3 71.1 + - - +
250A ILE 3.1 0.7 + - - -
251A ARG* 2.9 41.1 + - - +
252A ASP* 2.9 23.4 + - - +
349B ARG* 4.6 5.9 + - - +
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Residues in contact with CYS 249 (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 ASP 5.6 4.3 - - - -
247A MET* 3.0 4.2 - - - -
248A THR* 1.3 86.1 - - - +
250A ILE* 1.3 63.2 + - + +
252A ASP* 3.9 10.4 + - - +
253A VAL* 3.4 21.3 + - - +
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Residues in contact with ILE 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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239A TRP* 4.0 32.8 - - + -
247A MET* 3.3 25.6 + - + +
248A THR 3.1 0.4 - - - -
249A CYS* 1.3 80.6 - - + +
251A ARG* 1.3 65.5 + - - +
252A ASP 3.2 1.6 - - - -
253A VAL* 3.0 11.2 + - + +
254A ALA* 2.9 25.5 + - + +
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Residues in contact with ARG 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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235A LYS 4.9 6.5 - - - +
236A ILE* 3.5 31.4 - - + +
239A TRP* 4.2 27.4 - - + -
247A MET 4.0 1.8 + - - -
248A THR* 2.9 29.8 + - - +
250A ILE* 1.3 77.8 - - - +
252A ASP* 1.3 65.1 + - - +
254A ALA* 3.0 7.2 + - - +
255A MET* 2.7 64.3 + - + +
343A GLU* 4.7 12.7 + - - +
347B THR* 5.4 6.9 - - - +
349B ARG* 3.4 25.6 - - - +
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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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248A THR* 2.9 26.3 + - - +
249A CYS* 3.9 11.5 - - - +
250A ILE 3.2 0.4 - - - -
251A ARG* 1.3 101.1 + - - +
253A VAL* 1.3 58.9 + - + +
255A MET* 3.4 13.5 + - + +
256A LYS* 3.1 27.0 + - - +
349B ARG* 4.7 12.3 + - - -
381B GLN* 4.2 27.8 + - - +
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Residues in contact with VAL 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 CYS 3.4 19.1 - - - +
250A ILE* 3.0 10.7 + - + +
252A ASP* 1.3 79.5 - - + +
254A ALA* 1.3 59.1 + - - +
256A LYS* 3.1 35.9 - - + +
257A GLU* 3.7 15.0 + - - +
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Residues in contact with ALA 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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239A TRP* 6.3 3.8 - - + -
250A ILE* 2.9 20.6 + - + +
251A ARG* 3.7 7.2 - - - +
253A VAL* 1.3 76.3 - - - +
255A MET* 1.3 58.5 + - - +
256A LYS 3.4 0.2 - - - -
257A GLU* 3.0 27.6 + - - +
259A LEU* 3.3 24.5 - - + +
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Residues in contact with MET 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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251A ARG* 2.7 50.0 + - + +
252A ASP* 3.7 16.6 - - + +
254A ALA* 1.3 70.8 - - - +
256A LYS* 1.3 59.4 + - - +
257A GLU 3.0 10.4 + - - +
259A LEU* 4.8 3.6 - - - -
305A HIS* 5.4 3.4 - - - -
341A TYR* 3.6 34.2 + - + +
342A LEU 3.9 8.1 - - - +
343A GLU* 3.6 46.4 - - + +
391A TYR* 3.9 12.6 - - - -
381B GLN* 4.5 3.6 - - - +
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Residues in contact with LYS 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 ASP 3.1 13.0 + - - +
253A VAL* 3.1 32.8 - - + +
255A MET* 1.3 76.2 - - - +
257A GLU* 1.3 64.9 + - + +
390A ASP 3.4 4.7 - - - +
391A TYR* 3.0 37.3 - - - +
392A LYS* 3.8 9.7 + - - +
381B GLN* 5.2 6.3 - - - +
382B LEU* 2.5 47.7 - - + +
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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