Contacts of the helix formed by residues 361 - 376 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334C ASP 5.0 0.2 - - - +
335C ILE 2.9 15.5 + - - +
337C SER* 4.0 18.9 + - - +
360C LEU* 1.3 68.3 - - - +
362C GLU* 1.3 66.3 + - - +
363C ASP* 3.2 10.3 - - - +
364C LEU* 3.0 42.8 + - + +
365C VAL* 3.1 14.2 + - - +
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Residues in contact with GLU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG* 4.4 19.2 + - - -
360C LEU* 3.1 27.7 + - - +
361C ALA* 1.3 71.9 - - - +
363C ASP* 1.3 59.0 + - - +
365C VAL* 3.3 9.2 + - - +
366C ALA* 2.9 28.5 + - - +
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Residues in contact with ASP 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ALA* 3.7 15.4 - - - +
362C GLU* 1.3 76.4 + - - +
364C LEU* 1.3 68.4 + - - +
366C ALA* 3.4 7.8 + - - +
367C GLU* 3.0 43.2 + - - +
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Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 4.5 3.6 - - - +
333C GLU* 3.8 43.3 - - + +
334C ASP 3.3 25.6 - - - +
335C ILE* 4.4 14.7 - - + +
361C ALA* 3.0 27.4 + - + +
363C ASP* 1.3 83.6 - - - +
365C VAL* 1.3 60.0 + - - +
367C GLU* 3.3 21.7 + - - +
368C GLY* 2.9 23.6 + - - -
371C ARG* 4.7 1.4 + - - +
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Residues in contact with VAL 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG* 3.3 33.2 - - - +
14C LEU* 3.5 10.9 - - + +
36C LEU* 3.8 18.6 - - + -
335C ILE* 3.9 28.3 - - + -
360C LEU* 4.3 20.4 - - + -
361C ALA 3.1 16.7 + - - +
362C GLU* 3.5 10.1 - - - +
363C ASP 3.3 0.2 - - - -
364C LEU* 1.3 75.8 - - - +
366C ALA* 1.3 58.8 + - - +
368C GLY* 2.9 3.9 + - - -
369C GLU* 2.8 27.0 + - - +
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Residues in contact with ALA 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 4.6 1.8 - - - +
362C GLU 2.9 17.5 + - - +
363C ASP* 3.5 9.6 - - - +
365C VAL* 1.3 78.4 - - - +
367C GLU* 1.3 57.3 + - + +
369C GLU* 3.1 19.6 + - - +
370C GLY* 2.8 24.3 + - - -
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Residues in contact with GLU 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C GLU* 4.6 6.9 - - - +
363C ASP* 3.0 28.2 + - - +
364C LEU* 3.6 25.3 - - - +
366C ALA* 1.3 74.3 - - + +
368C GLY* 1.3 61.8 + - - +
370C GLY* 3.1 3.3 + - - +
371C ARG* 2.9 56.5 + - - +
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Residues in contact with GLY 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 3.6 5.5 - - - -
15C VAL 3.2 22.1 + - - -
16C LEU* 3.8 11.0 - - - -
364C LEU 2.9 13.5 + - - -
365C VAL 2.9 5.8 + - - -
367C GLU* 1.3 78.8 - - - +
369C GLU* 1.3 60.1 + - - +
371C ARG* 3.3 16.0 + - - +
372C TYR 3.1 17.5 + - - -
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Residues in contact with GLU 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG* 2.9 53.9 + - + +
13C PRO 3.7 13.7 - - - +
14C LEU* 3.5 14.6 - - + -
365C VAL 2.8 11.8 + - - +
366C ALA* 3.1 19.7 + - - +
368C GLY* 1.3 75.9 - - - +
370C GLY* 1.3 62.4 + - - +
372C TYR* 3.3 5.2 + - - +
373C ALA* 3.0 22.5 + - - +
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Residues in contact with GLY 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C ALA 2.8 14.3 + - - -
367C GLU* 3.1 6.2 + - - -
369C GLU* 1.3 75.7 - - - +
371C ARG* 1.3 64.2 + - - +
373C ALA* 3.2 8.8 + - - +
374C ALA* 3.0 21.5 + - - +
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Residues in contact with ARG 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.1 47.7 + - + +
16C LEU* 4.1 5.1 - - - +
17C PRO* 3.5 33.9 - - - +
31C SER* 6.4 0.2 - - - -
333C GLU* 4.5 9.9 + - - -
364C LEU* 4.7 1.2 + - - +
367C GLU* 2.9 46.4 + - - +
368C GLY* 3.3 9.2 + - - +
370C GLY* 1.3 72.2 - - - +
372C TYR* 1.3 67.6 + - - +
374C ALA* 3.1 9.8 + - - +
375C SER* 2.9 22.2 + - - -
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Residues in contact with TYR 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PRO* 3.4 47.5 - - + +
15C VAL* 3.7 10.0 - - + +
57C GLN* 3.4 41.7 - - + -
58C THR* 2.7 38.8 + - - +
61C ALA* 5.3 0.3 - - - +
368C GLY 3.1 9.1 + - - +
369C GLU 3.5 6.5 - - - +
370C GLY 3.2 0.2 - - - -
371C ARG* 1.3 75.8 - - - +
373C ALA* 1.3 64.8 + - + +
375C SER* 2.6 28.5 + - - -
376C ARG* 3.2 35.2 + - + +
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Residues in contact with ALA 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C GLU 3.0 12.6 + - - +
370C GLY* 3.5 11.7 - - - +
372C TYR* 1.3 82.1 - - + +
374C ALA* 1.3 63.4 + - - +
376C ARG* 3.1 19.7 + - - +
377C GLU* 3.5 5.5 + - - +
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Residues in contact with ALA 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C GLY 3.0 12.4 + - - +
371C ARG* 3.2 13.2 - - - +
373C ALA* 1.3 72.4 - - - +
375C SER* 1.3 59.2 + - - +
376C ARG 2.9 9.8 + - - -
377C GLU* 2.9 33.1 + - - +
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Residues in contact with SER 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 4.5 9.4 - - - +
57C GLN* 5.4 0.2 + - - -
371C ARG 2.9 12.2 + - - -
372C TYR* 2.6 28.9 + - - -
374C ALA* 1.3 75.5 - - - +
376C ARG* 1.3 73.5 + - - +
377C GLU* 3.4 0.8 + - - -
378C GLY* 4.4 4.9 + - - -
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Residues in contact with ARG 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ASP* 4.7 10.5 + - - -
58C THR* 3.0 37.5 + - - +
372C TYR* 3.2 37.1 + - + +
373C ALA* 3.5 10.8 - - - +
374C ALA 2.9 1.4 + - - -
375C SER* 1.3 92.0 + - - +
377C GLU* 1.3 63.1 + - - +
378C GLY* 3.2 8.1 + - - -
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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