Contacts of the helix formed by residues 353 - 362 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B TYR* 4.0 22.5 - + - -
344B HIS* 4.3 13.7 - + - -
347B TYR* 3.5 66.0 - + + +
350B MET* 3.1 16.9 + - + +
351B GLU 3.7 5.5 - - - +
352B GLU* 1.3 87.6 - - + +
354B GLU* 1.3 65.9 + - - +
355B ILE* 4.3 9.9 - - + -
356B ALA* 3.1 14.9 + - - +
357B ARG* 4.1 1.2 + - - +
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Residues in contact with GLU 354 (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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262B VAL* 4.1 2.6 - - - +
266B LEU* 3.6 28.3 - - + +
351B GLU 5.4 0.2 - - - -
352B GLU 3.9 3.0 + - - -
353B TYR* 1.3 71.4 - - - +
355B ILE* 1.3 63.1 + - - +
357B ARG* 3.1 31.6 + - - +
358B ARG* 2.8 59.3 + - + +
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Residues in contact with ILE 355 (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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263B MET* 3.6 35.2 - - + +
266B LEU* 4.1 17.9 - - + +
267B THR* 4.5 0.9 - - - +
337B ALA 5.3 1.1 - - - +
340B ALA* 3.5 35.7 - - + +
341B MET* 4.5 3.8 - - - +
344B HIS* 4.0 28.3 - - + +
348B GLY* 3.8 28.3 - - - +
353B TYR* 3.2 9.3 + - + +
354B GLU* 1.3 78.8 - - - +
356B ALA* 1.3 59.4 + - - +
358B ARG* 4.2 2.9 - - + -
359B TYR* 2.8 31.8 + - + +
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Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 3.6 25.4 - - + +
348B GLY 3.7 13.0 - - - +
350B MET 3.3 28.3 - - - +
351B GLU* 4.0 9.2 - - - +
353B TYR 3.1 6.4 + - - +
355B ILE* 1.3 81.6 - - - +
357B ARG* 1.3 60.9 + - - +
359B TYR* 3.4 5.9 + - - +
360B ARG* 3.1 29.1 + - - +
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Residues in contact with ARG 357 (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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33B TYR* 3.5 25.6 - - - +
34B ASN* 4.4 9.1 + - - -
37B GLU* 3.7 25.0 + - - +
84B VAL 2.9 28.1 + - - -
85B GLY* 3.4 12.1 - - - -
86B SER 4.7 0.2 - - - +
351B GLU* 4.2 4.4 + - - +
353B TYR 4.1 0.8 + - - +
354B GLU* 3.1 37.4 + - - +
356B ALA* 1.3 77.3 - - - +
358B ARG* 1.3 86.2 + - - +
360B ARG* 3.2 23.0 + - - +
361B ASP* 3.0 50.4 + - - +
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Residues in contact with ARG 358 (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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30B TYR* 5.6 0.6 - - - -
82B GLU* 2.9 32.1 + - - +
83B LYS 2.8 24.4 + - - -
84B VAL 3.3 9.9 + - - -
85B GLY* 3.9 2.6 - - - -
86B SER* 4.9 1.5 + - - +
259B ALA* 5.5 5.9 - - + +
262B VAL* 3.5 27.7 - - - +
263B MET* 3.7 29.4 - - + +
266B LEU* 4.3 3.6 - - + -
354B GLU* 2.8 47.9 + - + +
355B ILE* 3.7 8.5 - - - +
357B ARG* 1.3 98.3 - - - +
359B TYR* 1.3 63.1 + - - +
361B ASP* 3.2 6.5 + - - +
362B ILE* 3.2 26.5 + - - +
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Residues in contact with TYR 359 (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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208A VAL* 4.8 5.6 - - + -
334A LYS* 5.8 1.2 - - - +
359A TYR* 3.9 39.3 + + - -
360A ARG* 5.8 0.7 - - - -
362A ILE* 5.9 0.3 - - - +
363A PRO* 3.6 25.8 - - + +
263B MET* 4.4 0.8 - - - -
337B ALA* 3.5 39.5 - - + +
338B ALA* 4.1 15.7 - - + +
341B MET* 3.5 40.6 - - + -
348B GLY 5.7 0.2 - - - +
355B ILE* 2.8 19.1 + - + +
356B ALA* 3.4 6.1 - - - +
358B ARG* 1.3 78.2 - - - +
360B ARG* 1.3 71.4 + - + +
362B ILE* 3.5 5.0 - - - +
363B PRO* 3.3 18.0 - - - +
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 4.1 19.5 - - + -
349A TYR* 2.7 29.3 + - - -
359A TYR* 5.9 0.9 - - + -
360A ARG* 4.1 17.0 - - + +
37B GLU* 5.1 4.2 + - - -
208B VAL* 3.0 40.1 + - + +
209B GLY* 3.6 6.9 - - - -
211B HIS* 3.2 30.3 + - - -
351B GLU* 2.8 43.0 + - - -
356B ALA 3.1 11.1 + - - +
357B ARG* 3.2 25.5 + - - +
359B TYR* 1.3 83.6 - - + +
361B ASP* 1.3 57.0 + - - +
363B PRO* 3.3 9.6 - - - +
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Residues in contact with ASP 361 (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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349A TYR* 3.5 3.4 - - - -
33B TYR* 4.1 4.5 + - - -
37B GLU* 4.7 1.7 - - - +
86B SER* 3.6 33.1 + - - +
87B SER 4.7 0.3 + - - -
209B GLY* 3.5 4.7 - - - -
210B LEU* 2.8 37.1 + - + +
211B HIS 4.7 0.7 + - - -
357B ARG* 3.0 42.6 + - - +
358B ARG* 3.2 8.3 + - - +
360B ARG* 1.3 81.6 + - - +
362B ILE* 1.3 62.4 + - - +
364B VAL* 3.4 22.5 - - - +
365B SER* 4.8 0.5 + - - -
368B TYR* 5.4 0.2 + - - -
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Residues in contact with ILE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TYR* 5.9 0.2 - - - +
86B SER* 5.8 1.8 - - - +
256B ALA* 4.4 6.7 - - + -
259B ALA* 4.0 21.3 - - + -
263B MET* 4.2 5.6 - - + -
333B ALA* 3.6 37.5 - - + +
334B LYS* 4.0 12.9 - - + +
337B ALA* 3.5 26.5 - - + -
358B ARG 3.2 10.6 + - - +
359B TYR 3.5 14.6 - - - +
361B ASP* 1.3 76.0 - - - +
363B PRO* 1.4 71.1 - - + +
365B SER* 2.8 45.6 + - - +
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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