Contacts of the helix formed by residues 361 - 375 (chain G) in PDB entry 2PGW
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 ALA 361 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334G ASP 4.7 0.2 - - - +
335G ILE 2.7 18.3 + - - +
337G SER* 4.1 16.5 - - - +
359G GLN 4.1 0.2 + - - -
360G LEU* 1.3 67.9 - - - +
362G GLU* 1.3 66.4 + - - +
363G ASP* 3.2 10.3 - - - +
364G LEU* 2.9 41.5 + - + -
365G VAL* 3.0 14.2 + - - +
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Residues in contact with GLU 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ARG* 3.7 23.0 + - - -
360G LEU* 3.1 23.9 + - - +
361G ALA* 1.3 72.1 - - - +
363G ASP* 1.3 59.7 + - - +
365G VAL* 3.3 6.5 + - - +
366G ALA* 2.9 29.6 + - - +
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Residues in contact with ASP 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361G ALA* 3.7 14.5 - - - +
362G GLU* 1.3 76.3 + - - +
364G LEU* 1.3 71.2 + - - +
366G ALA* 3.4 7.2 + - - +
367G GLU* 3.0 36.7 + - + +
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Residues in contact with LEU 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU* 4.5 1.7 - - + +
333G GLU* 3.7 42.0 - - + +
334G ASP 3.2 26.5 - - - +
335G ILE* 4.3 13.3 - - + +
361G ALA* 2.9 24.7 + - + +
363G ASP* 1.3 85.1 - - - +
365G VAL* 1.3 59.9 + - - +
367G GLU* 3.2 23.8 + - - +
368G GLY* 2.9 23.9 + - - -
371G ARG* 4.3 5.1 + - - +
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Residues in contact with VAL 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G ARG* 3.6 33.4 - - - +
14G LEU* 3.6 11.8 - - + +
36G LEU* 3.8 17.9 - - + -
335G ILE* 3.8 28.5 - - + -
360G LEU* 4.3 20.0 - - + -
361G ALA 3.0 23.3 + - - +
362G GLU* 3.6 10.3 - - - +
364G LEU* 1.3 75.6 - - - +
366G ALA* 1.3 64.9 + - - +
368G GLY* 3.0 11.7 + - - +
369G GLU* 3.0 13.0 + - - +
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Residues in contact with ALA 366 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G ARG* 4.9 2.0 - - - +
362G GLU 2.9 17.0 + - - +
363G ASP* 3.5 9.0 - - - +
365G VAL* 1.3 77.4 - - - +
367G GLU* 1.3 57.5 + - + +
369G GLU* 3.2 19.7 + - - +
370G GLY* 3.0 23.4 + - - -
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Residues in contact with GLU 367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G GLU* 4.6 5.5 - - - +
363G ASP* 3.0 19.2 + - - +
364G LEU* 3.2 36.0 - - - +
365G VAL 3.2 0.2 - - - -
366G ALA* 1.3 74.1 - - + +
368G GLY* 1.3 65.5 + - - +
370G GLY* 3.3 2.6 + - - +
371G ARG* 3.1 45.5 + - - +
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Residues in contact with GLY 368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 3.6 5.4 - - - -
15G VAL 3.1 33.3 + - - -
16G LEU* 3.9 10.1 - - - -
364G LEU 2.9 12.6 + - - -
365G VAL 3.0 5.3 + - - -
367G GLU* 1.3 78.7 - - - +
369G GLU* 1.3 60.2 + - - +
371G ARG* 3.3 8.0 + - - +
372G TYR 3.1 17.2 + - - -
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Residues in contact with GLU 369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ARG* 2.8 55.0 + - + +
13G PRO* 3.6 13.4 - - + +
14G LEU* 3.3 20.2 - - + -
365G VAL 3.0 8.3 + - - +
366G ALA* 3.2 21.7 + - - +
368G GLY* 1.3 75.0 - - - +
370G GLY* 1.3 60.1 + - - +
372G TYR* 3.2 4.0 + - - +
373G ALA* 2.9 29.5 + - - +
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Residues in contact with GLY 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366G ALA 3.0 13.4 + - - -
367G GLU* 3.3 4.9 + - - -
368G GLY 3.2 0.4 - - - -
369G GLU* 1.3 79.1 - - - +
371G ARG* 1.3 55.9 + - - +
373G ALA* 3.3 7.2 + - - +
374G ALA* 2.8 29.9 + - - +
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Residues in contact with ARG 371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G VAL* 2.7 42.1 + - + +
16G LEU* 3.8 9.5 - - - +
17G PRO* 3.2 36.0 - - - +
333G GLU* 5.3 8.9 + - - +
364G LEU* 4.3 3.0 + - - +
367G GLU* 3.1 31.2 + - - +
368G GLY* 3.7 22.8 - - - +
369G GLU 3.3 0.2 - - - -
370G GLY* 1.3 76.3 - - - +
372G TYR* 1.3 60.6 + - - +
374G ALA* 3.4 10.3 - - + +
375G SER* 2.9 23.4 + - - -
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Residues in contact with TYR 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G PRO* 3.6 45.0 - - + +
15G VAL* 3.5 16.1 - - + +
57G GLN* 3.5 38.8 - - + -
58G THR* 2.9 39.1 + - - +
61G ALA* 5.2 0.9 - - - +
368G GLY 3.1 8.0 + - - +
369G GLU* 3.5 9.0 - - + +
370G GLY 3.2 0.2 - - - -
371G ARG* 1.3 75.0 - - - +
373G ALA* 1.3 64.9 + - + +
375G SER* 2.8 34.2 + - - -
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Residues in contact with ALA 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369G GLU 2.9 16.8 + - - +
370G GLY* 3.6 7.4 - - - +
372G TYR* 1.3 83.8 - - + +
374G ALA* 1.3 63.4 + - - +
375G SER 3.1 6.1 + - - -
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Residues in contact with ALA 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370G GLY 2.8 18.4 + - - +
371G ARG* 3.4 12.3 - - - +
373G ALA* 1.3 77.1 - - - +
375G SER* 1.3 62.2 + - - +
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Residues in contact with SER 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G VAL* 4.3 8.5 - - - +
371G ARG 2.9 15.2 + - - -
372G TYR* 2.8 27.3 + - - -
373G ALA 3.9 5.2 - - - -
374G ALA* 1.3 82.9 - - - +
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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