Contacts of the helix formed by residues 361 - 375 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335H ILE 2.7 17.0 + - - +
337H SER* 4.2 18.1 + - - +
359H GLN 4.0 0.2 + - - -
360H LEU* 1.3 68.8 - - - +
362H GLU* 1.3 65.8 + - - +
363H ASP* 3.1 16.8 - - - +
364H LEU* 2.9 35.4 + - + +
365H VAL* 3.0 14.0 + - - +
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Residues in contact with GLU 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ARG* 2.9 41.2 + - - -
360H LEU* 3.1 12.9 + - + +
361H ALA* 1.3 72.9 - - - +
363H ASP* 1.3 56.5 + - - +
365H VAL* 4.2 7.5 - - - +
366H ALA* 2.9 34.5 + - + +
369H GLU* 4.5 0.2 - - - +
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Residues in contact with ASP 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361H ALA* 3.4 18.9 - - - +
362H GLU* 1.3 75.7 - - - +
364H LEU* 1.3 84.9 + - - +
366H ALA* 3.4 7.2 + - - +
367H GLU* 3.1 28.2 + - - +
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Residues in contact with LEU 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H LEU* 4.6 3.1 - - - +
333H GLU* 3.6 41.3 - - + +
334H ASP 3.3 24.5 - - - +
335H ILE* 4.3 16.3 - - + +
361H ALA* 2.9 21.7 + - + +
363H ASP* 1.3 93.4 + - - +
365H VAL* 1.3 61.0 + - - +
367H GLU* 3.4 22.5 + - + +
368H GLY* 3.0 23.0 + - - -
371H ARG* 4.8 0.9 + - - -
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Residues in contact with VAL 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ARG* 3.4 35.2 - - - +
14H LEU* 3.7 19.2 - - + +
36H LEU* 4.0 9.0 - - + -
335H ILE* 3.9 31.0 - - + -
360H LEU* 4.5 16.6 - - + -
361H ALA 3.0 17.3 + - - +
362H GLU* 3.6 12.1 - - - +
364H LEU* 1.3 72.3 - - - +
366H ALA* 1.3 66.3 + - - +
368H GLY* 3.0 3.5 + - - -
369H GLU* 2.9 21.1 + - - +
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Residues in contact with ALA 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362H GLU* 2.9 25.0 + - + +
363H ASP* 3.5 7.9 - - - +
365H VAL* 1.3 77.3 - - - +
367H GLU* 1.3 62.2 + - + +
369H GLU* 3.1 17.6 + - - +
370H GLY* 2.9 19.6 + - - -
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Residues in contact with GLU 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H GLU* 4.8 5.5 - - - +
363H ASP* 3.1 15.6 + - - +
364H LEU* 3.6 31.4 - - - +
366H ALA* 1.3 78.5 - - - +
368H GLY* 1.3 58.2 + - - +
370H GLY* 3.1 3.9 + - - +
371H ARG* 2.9 57.6 + - - +
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Residues in contact with GLY 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LEU* 3.6 6.0 - - - -
15H VAL 3.2 23.0 + - - -
16H LEU* 3.9 11.0 - - - -
364H LEU 3.0 10.7 + - - -
365H VAL 3.0 8.4 + - - -
367H GLU* 1.3 79.1 - - - +
369H GLU* 1.3 61.0 + - - +
371H ARG* 3.3 14.6 + - - +
372H TYR 3.1 16.3 + - - -
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Residues in contact with GLU 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ARG* 2.8 54.8 + - + +
13H PRO* 3.6 13.5 - - + +
14H LEU* 3.4 20.0 - - + -
365H VAL 2.9 9.1 + - - +
366H ALA* 3.1 19.3 + - - +
368H GLY* 1.3 73.0 - - - +
370H GLY* 1.3 66.9 + - - +
372H TYR* 3.1 6.1 + - - +
373H ALA* 2.9 23.7 + - - +
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Residues in contact with GLY 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366H ALA 2.9 13.6 + - - -
367H GLU* 3.1 5.1 + - - -
369H GLU* 1.3 79.0 - - - +
371H ARG* 1.3 56.1 + - - +
373H ALA* 3.3 7.9 + - - +
374H ALA* 2.9 27.4 + - - +
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Residues in contact with ARG 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H VAL* 3.2 45.2 + - + +
16H LEU* 4.3 4.6 - - - +
17H PRO* 3.4 36.8 - - - +
333H GLU* 4.3 12.9 + - - +
364H LEU* 4.8 1.4 + - - +
367H GLU* 2.9 54.5 + - - +
368H GLY* 3.5 4.7 - - - +
370H GLY* 1.3 75.9 - - - +
372H TYR* 1.3 64.3 + - - +
374H ALA* 3.1 9.9 + - - +
375H SER* 3.0 22.5 + - - -
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Residues in contact with TYR 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H PRO* 3.6 47.3 - - + +
15H VAL* 3.7 13.2 - - + +
57H GLN* 3.4 35.0 - - + -
58H THR* 2.7 40.7 + - - +
61H ALA* 5.4 0.3 - - - +
368H GLY 3.1 9.8 + - - +
369H GLU* 3.1 10.2 + - - +
371H ARG* 1.3 77.2 - - - +
373H ALA* 1.3 69.3 - - + +
375H SER* 2.7 28.1 + - - -
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Residues in contact with ALA 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H GLU 2.9 12.5 + - - +
370H GLY* 3.6 10.5 - - - +
372H TYR* 1.3 85.3 - - + +
374H ALA* 1.3 64.9 + - - +
375H SER 3.4 4.3 + - - -
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Residues in contact with ALA 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370H GLY 2.9 13.6 + - - +
371H ARG* 3.2 14.6 - - - +
373H ALA* 1.3 79.1 - - - +
375H SER* 1.3 62.9 + - - +
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Residues in contact with SER 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H VAL* 4.4 8.4 - - - +
371H ARG 3.0 9.8 + - - -
372H TYR* 2.7 36.9 + - - -
373H ALA 3.9 3.6 - - - -
374H ALA* 1.3 81.3 - - - +
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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