Contacts of the helix formed by residues 353 - 362 (chain A) in PDB entry 2PG0
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 TYR 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A TYR* 4.0 21.2 + + - -
344A HIS* 4.4 13.5 - + - -
347A TYR* 3.4 67.0 - + + +
350A MET* 2.9 18.3 + - + +
351A GLU 3.7 5.3 - - - +
352A GLU* 1.3 86.9 - - + +
354A GLU* 1.3 66.2 + - - +
355A ILE* 3.2 9.6 - - + -
356A ALA* 3.1 14.7 + - - +
357A ARG* 4.2 1.4 + - - +
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Residues in contact with GLU 354 (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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262A VAL* 4.1 2.9 - - - +
266A LEU* 3.7 28.7 - - + +
351A GLU 5.5 0.2 - - - -
352A GLU 3.9 2.2 + - - -
353A TYR* 1.3 72.1 - - - +
355A ILE* 1.3 63.1 + - - +
357A ARG* 3.1 36.4 + - - +
358A ARG* 2.8 51.7 + - + +
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Residues in contact with ILE 355 (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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263A MET* 3.6 34.1 - - + +
266A LEU* 4.1 16.8 - - + +
337A ALA* 5.1 2.0 - - - +
340A ALA* 3.5 37.7 - - + -
341A MET* 4.2 4.5 - - - +
344A HIS* 3.9 29.2 - - + +
348A GLY* 3.7 29.4 - - - +
353A TYR* 4.4 6.7 - - + +
354A GLU* 1.3 78.8 - - - +
356A ALA* 1.3 58.5 + - - +
358A ARG* 3.3 3.3 + - + -
359A TYR* 2.9 32.0 + - + +
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Residues in contact with ALA 356 (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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348A GLY 3.7 12.3 - - - +
350A MET 3.4 25.8 - - - +
351A GLU* 3.9 10.3 - - - +
353A TYR 3.1 6.2 + - - +
355A ILE* 1.3 80.5 - - - +
357A ARG* 1.3 58.5 + - - +
359A TYR* 3.3 6.2 + - - +
360A ARG* 3.1 33.7 + - - +
208B VAL* 3.5 26.6 - - + +
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Residues in contact with ARG 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 3.5 24.5 - - - -
34A ASN* 4.4 9.2 + - - -
37A GLU* 3.4 36.3 - - - +
84A VAL 2.8 25.5 + - - -
85A GLY* 3.4 7.7 - - - -
86A SER 4.8 0.4 - - - +
351A GLU* 4.2 4.4 + - - +
353A TYR 4.2 0.9 + - - +
354A GLU* 3.1 29.2 + - - +
356A ALA* 1.3 76.6 - - - +
358A ARG* 1.3 96.4 + - - +
360A ARG* 3.2 24.1 + - - +
361A ASP* 2.9 41.3 + - - +
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Residues in contact with ARG 358 (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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30A TYR* 5.5 1.0 - - - -
82A GLU* 2.9 31.7 + - - +
83A LYS 2.8 24.2 + - - -
84A VAL 3.3 8.3 + - - -
85A GLY* 3.8 3.0 - - - -
86A SER* 4.9 1.5 + - - +
259A ALA* 5.5 6.5 - - - +
262A VAL* 3.5 26.3 - - - +
263A MET* 3.6 26.5 - - + +
266A LEU* 4.2 11.0 - - + -
354A GLU* 2.8 45.9 + - + +
355A ILE* 3.7 6.1 - - + +
357A ARG* 1.3 99.1 - - - +
359A TYR* 1.3 62.3 + - - +
361A ASP* 3.3 8.5 + - - +
362A ILE* 3.2 26.0 + - - +
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Residues in contact with TYR 359 (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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263A MET* 4.4 0.6 - - - -
334A LYS 5.7 0.4 - - - -
337A ALA* 3.6 35.4 - - + +
338A ALA* 4.1 20.7 - - + +
341A MET* 3.5 39.5 - - + -
355A ILE* 2.9 19.8 + - + +
356A ALA 3.4 5.6 - - - +
357A ARG 3.2 0.2 - - - -
358A ARG* 1.3 78.7 - - - +
360A ARG* 1.3 70.5 + - + +
362A ILE* 3.4 5.7 - - - +
363A PRO* 3.3 18.2 - - - +
208B VAL* 4.9 5.6 - - + -
334B LYS* 5.8 1.9 - - - +
359B TYR* 3.9 38.5 + + - -
360B ARG* 5.9 0.7 - - + -
362B ILE* 5.9 0.5 - - - +
363B PRO* 3.6 25.2 - - + +
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Residues in contact with ARG 360 (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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37A GLU* 4.9 4.4 + - - -
208A VAL* 3.0 41.7 + - + +
209A GLY* 3.6 7.7 - - - -
211A HIS* 3.3 28.8 + - - -
351A GLU* 2.8 41.7 + - - -
356A ALA 3.1 14.9 + - - +
357A ARG* 3.2 25.4 + - - +
359A TYR* 1.3 81.1 - - + +
361A ASP* 1.3 58.4 + - - +
363A PRO* 3.3 10.3 - - - +
208B VAL* 4.1 17.9 - - + -
349B TYR* 2.7 28.8 + - - -
359B TYR* 5.8 0.7 - - + -
360B ARG* 4.1 17.3 - - + +
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Residues in contact with ASP 361 (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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33A TYR* 4.0 8.7 + - - -
37A GLU* 4.6 2.3 - - - +
86A SER* 3.7 28.6 + - - +
209A GLY* 3.5 5.2 - - - -
210A LEU* 2.8 38.5 + - + +
211A HIS 4.7 0.5 + - - -
357A ARG* 2.9 43.1 + - - +
358A ARG* 3.7 7.8 - - - +
359A TYR 3.2 0.4 - - - -
360A ARG* 1.3 81.7 + - - +
362A ILE* 1.3 63.4 + - - +
363A PRO* 3.4 0.2 - - - -
364A VAL* 3.4 21.7 - - - +
365A SER* 4.8 0.5 + - - -
368A TYR* 5.4 0.5 + - - -
349B TYR* 3.5 3.6 - - - -
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Residues in contact with ILE 362 (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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82A GLU* 5.9 0.2 - - - +
86A SER* 5.7 0.2 - - - -
256A ALA* 4.5 7.4 - - - -
259A ALA* 3.9 23.6 - - + -
263A MET* 4.3 5.2 - - + -
333A ALA* 3.7 38.6 - - + +
334A LYS* 4.0 12.2 - - + +
337A ALA* 3.5 26.9 - - + -
358A ARG 3.2 10.1 + - - +
359A TYR 3.4 16.4 - - - +
361A ASP* 1.3 78.7 - - - +
363A PRO* 1.4 69.2 - - + +
365A SER* 2.8 44.9 + - - +
359B TYR* 5.9 0.4 - - - +
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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