Contacts of the helix formed by residues 361 - 375 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335F ILE 2.9 14.9 + - - +
336F VAL 5.3 0.2 - - - -
337F SER* 4.0 17.6 + - - +
360F LEU* 1.3 69.1 - - - +
362F GLU* 1.3 56.2 + - - +
363F ASP* 3.0 16.6 - - - +
364F LEU* 2.8 46.7 + - + +
365F VAL* 3.1 12.7 + - - +
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Residues in contact with GLU 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ARG* 2.8 41.2 + - - -
360F LEU* 3.3 10.3 + - - +
361F ALA* 1.3 73.2 - - - +
363F ASP* 1.3 55.6 + - - +
365F VAL* 3.7 8.0 - - - +
366F ALA* 2.9 34.3 + - + +
369F GLU* 4.7 0.2 - - - +
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Residues in contact with ASP 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361F ALA* 3.4 19.6 - - - +
362F GLU* 1.3 74.9 + - - +
364F LEU* 1.3 78.2 + - - +
366F ALA* 3.4 7.1 + - - +
367F GLU* 3.0 38.2 + - - +
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Residues in contact with LEU 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU* 4.6 2.9 - - - +
333F GLU* 3.9 42.0 - - + +
334F ASP 3.5 23.6 - - - +
335F ILE* 4.2 16.8 - - + +
361F ALA* 2.8 25.3 + - + +
363F ASP* 1.3 86.4 - - - +
365F VAL* 1.3 60.8 + - - +
367F GLU* 3.4 21.9 + - - +
368F GLY* 3.0 22.7 + - - -
371F ARG* 4.8 0.9 + - - -
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Residues in contact with VAL 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ARG* 3.4 34.3 - - - +
14F LEU* 3.6 19.5 - - + +
36F LEU* 4.0 9.0 - - + -
335F ILE* 4.0 28.9 - - + -
360F LEU* 4.4 20.4 - - + -
361F ALA 3.1 15.4 + - - +
362F GLU* 3.7 11.4 - - - +
363F ASP 3.2 0.2 - - - -
364F LEU* 1.3 75.8 - - - +
366F ALA* 1.3 64.7 + - - +
368F GLY* 2.9 12.3 + - - -
369F GLU* 2.9 13.0 + - + +
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Residues in contact with ALA 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362F GLU* 2.9 27.1 + - + +
363F ASP* 3.7 7.2 - - - +
365F VAL* 1.3 76.4 - - - +
367F GLU* 1.3 61.1 + - + +
369F GLU* 3.3 20.1 + - - +
370F GLY* 3.1 17.5 + - - -
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Residues in contact with GLU 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F GLU* 4.3 6.6 - - - +
363F ASP* 3.0 22.5 + - - +
364F LEU* 3.5 32.5 - - - +
365F VAL 3.1 0.2 - - - -
366F ALA* 1.3 78.2 - - - +
368F GLY* 1.3 62.0 + - - +
370F GLY* 2.9 12.9 + - - -
371F ARG* 3.1 41.9 + - - +
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Residues in contact with GLY 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LEU* 3.6 5.9 - - - -
15F VAL 3.2 28.6 + - - +
16F LEU* 3.8 15.0 - - - -
364F LEU 3.0 7.7 + - - -
365F VAL 2.9 8.2 + - - -
367F GLU* 1.3 76.6 - - - +
369F GLU* 1.3 60.5 + - - +
371F ARG* 3.3 16.5 + - - +
372F TYR 3.2 11.6 + - - -
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Residues in contact with GLU 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ARG* 3.0 54.0 + - + +
13F PRO* 3.6 13.8 - - + +
14F LEU* 3.4 15.9 - - + +
365F VAL 2.9 14.3 + - - +
366F ALA* 3.5 17.9 - - - +
367F GLU 3.2 0.2 - - - -
368F GLY* 1.3 76.1 - - - +
370F GLY* 1.3 57.2 + - - +
372F TYR* 3.3 4.0 + - - +
373F ALA* 2.9 29.2 + - - +
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Residues in contact with GLY 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366F ALA 3.1 9.5 + - - -
367F GLU* 2.9 9.7 + - - -
369F GLU* 1.3 74.9 - - - +
371F ARG* 1.3 58.8 + - - +
373F ALA* 3.3 7.0 + - - +
374F ALA* 2.8 29.0 + - - +
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Residues in contact with ARG 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 3.2 44.9 + - + +
16F LEU* 4.3 4.4 - - - +
17F PRO* 3.3 36.4 - - - +
333F GLU* 4.5 10.5 + - - -
364F LEU 4.8 0.8 + - - -
367F GLU* 3.1 33.7 + - - +
368F GLY* 3.3 21.7 + - - +
370F GLY* 1.3 72.4 - - - +
372F TYR* 1.3 65.9 + - - +
374F ALA* 3.3 8.9 + - - +
375F SER* 3.0 22.7 + - - -
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Residues in contact with TYR 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PRO* 3.5 44.9 - - + +
15F VAL* 3.5 14.1 - - + +
57F GLN* 3.3 40.6 - - + -
58F THR* 2.7 39.1 + - - +
61F ALA* 5.2 0.7 - - - +
368F GLY 3.2 5.6 + - - +
369F GLU 3.5 8.5 - - - +
371F ARG* 1.3 76.6 - - - +
373F ALA* 1.3 70.9 + - + +
375F SER* 2.6 30.3 + - - -
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Residues in contact with ALA 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369F GLU 2.9 17.2 + - - +
370F GLY* 3.6 7.4 - - - +
372F TYR* 1.3 83.8 - - + +
374F ALA* 1.3 62.9 + - - +
375F SER 3.4 4.3 + - - -
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Residues in contact with ALA 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F GLY 2.8 17.3 + - - +
371F ARG* 3.4 10.5 - - - +
372F TYR 3.1 0.2 - - - -
373F ALA* 1.3 79.8 - - - +
375F SER* 1.3 62.1 + - - +
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Residues in contact with SER 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 4.6 6.5 - - - +
371F ARG 3.0 11.1 + - - -
372F TYR* 2.6 38.2 + - - -
373F ALA 4.1 4.0 - - - -
374F ALA* 1.3 81.6 - - - +
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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