Contacts of the helix formed by residues 361 - 375 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334B ASP 4.9 0.2 - - - +
335B ILE 2.7 15.6 + - - +
337B SER* 4.1 18.9 + - - +
360B LEU* 1.3 68.0 - - - +
362B GLU* 1.3 70.6 + - - +
363B ASP* 3.2 12.1 - - - +
364B LEU* 2.8 44.2 + - + +
365B VAL* 3.1 12.9 + - - +
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Residues in contact with GLU 362 (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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12B ARG* 5.3 2.1 + - - +
337B SER* 5.1 1.9 + - - -
360B LEU* 2.7 26.5 + - + +
361B ALA* 1.3 74.1 - - - +
363B ASP* 1.3 67.6 + - - +
365B VAL* 3.3 8.6 + - - +
366B ALA* 3.1 23.6 + - - +
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Residues in contact with ASP 363 (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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361B ALA* 3.7 17.0 - - - +
362B GLU* 1.3 82.1 + - - +
364B LEU* 1.3 77.2 + - - +
366B ALA* 3.5 7.4 + - - +
367B GLU* 3.2 29.7 + - + +
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Residues in contact with LEU 364 (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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16B LEU* 4.6 2.8 - - + +
333B GLU* 3.6 46.7 - - + +
334B ASP 3.2 26.2 - - - +
335B ILE* 4.2 15.6 - - + +
361B ALA* 2.8 29.3 + - + +
363B ASP* 1.3 87.3 + - - +
365B VAL* 1.3 60.4 + - - +
367B GLU* 3.3 10.4 + - + +
368B GLY* 2.9 24.1 + - - -
371B ARG* 6.2 0.9 - - - +
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 3.5 31.2 - - - +
14B LEU* 3.5 21.0 - - + +
36B LEU* 3.9 10.8 - - + -
335B ILE* 3.9 30.1 - - + -
360B LEU* 4.3 24.2 - - + -
361B ALA 3.1 13.3 + - - +
362B GLU* 3.6 8.5 - - - +
364B LEU* 1.3 78.3 - - - +
366B ALA* 1.3 56.2 + - - +
368B GLY* 3.0 2.8 + - - -
369B GLU* 2.9 27.3 + - - +
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Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 4.9 2.2 - - - +
362B GLU 3.1 17.2 + - - +
363B ASP* 3.7 8.1 - - - +
365B VAL* 1.3 78.0 - - - +
367B GLU* 1.3 60.8 + - - +
369B GLU* 3.1 19.8 + - - +
370B GLY* 2.9 23.4 + - - -
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ASP* 3.2 16.7 + - + +
364B LEU* 3.6 14.1 - - + +
365B VAL 3.3 0.2 - - - -
366B ALA* 1.3 80.0 - - - +
368B GLY* 1.3 62.0 + - - +
370B GLY* 3.0 4.9 + - - +
371B ARG* 3.0 45.8 + - - +
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Residues in contact with GLY 368 (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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14B LEU* 3.7 5.1 - - - -
15B VAL 3.3 31.9 + - - -
16B LEU* 4.0 12.6 - - - -
364B LEU 2.9 15.2 + - - -
365B VAL 3.0 5.5 + - - -
367B GLU* 1.3 74.5 - - - +
369B GLU* 1.3 63.3 + - - +
371B ARG* 3.2 3.3 + - - +
372B TYR 3.1 17.7 + - - -
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Residues in contact with GLU 369 (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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12B ARG* 3.1 51.7 + - + +
13B PRO* 3.7 14.0 - - + +
14B LEU* 3.5 14.6 - - + +
365B VAL 2.9 12.0 + - - +
366B ALA* 3.3 20.6 - - - +
368B GLY* 1.3 76.3 - - - +
370B GLY* 1.3 62.1 + - - +
372B TYR* 3.4 4.3 + - - +
373B ALA* 3.1 22.9 + - - +
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Residues in contact with GLY 370 (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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366B ALA 2.9 13.2 + - - -
367B GLU* 3.0 7.5 + - - -
369B GLU* 1.3 79.2 - - - +
371B ARG* 1.3 57.2 + - - +
373B ALA* 3.2 8.0 + - - +
374B ALA* 2.9 28.9 + - - +
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Residues in contact with ARG 371 (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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15B VAL* 3.0 41.3 + - + +
16B LEU* 5.3 1.2 - - - +
17B PRO* 3.2 38.3 - - - +
333B GLU* 4.5 13.5 + - - -
364B LEU* 6.2 1.0 - - - +
367B GLU* 3.0 32.3 + - - +
368B GLY* 3.2 2.1 + - - +
370B GLY* 1.3 71.8 - - - +
372B TYR* 1.3 66.3 + - - +
374B ALA* 3.3 8.9 + - - +
375B SER* 3.0 25.0 + - - -
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Residues in contact with TYR 372 (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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13B PRO* 3.4 51.8 - - + +
15B VAL* 3.6 9.5 - - + +
57B GLN* 3.5 40.8 - - + -
58B THR* 2.7 41.0 + - - +
61B ALA* 5.2 0.5 - - - +
368B GLY 3.1 8.5 + - - +
369B GLU* 3.6 6.3 - - - +
370B GLY 3.2 0.2 - - - -
371B ARG* 1.3 76.7 - - - +
373B ALA* 1.3 70.0 + - + +
375B SER* 2.7 30.2 + - - +
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Residues in contact with ALA 373 (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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369B GLU 3.1 11.5 + - - +
370B GLY* 3.5 10.5 - - - +
372B TYR* 1.3 87.8 - - + +
374B ALA* 1.3 60.8 + - - +
375B SER 3.3 4.5 + - - -
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B GLY 2.9 16.6 + - - +
371B ARG* 3.6 9.9 - - - +
372B TYR 3.2 0.2 - - - -
373B ALA* 1.3 76.2 - - - +
375B SER* 1.3 58.0 + - - +
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Residues in contact with SER 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.2 10.8 - - - +
371B ARG 3.0 12.1 + - - -
372B TYR* 2.7 32.2 + - - +
373B ALA 4.3 3.4 - - - -
374B ALA* 1.3 81.0 - - - +
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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