Contacts of the helix formed by residues 56 - 70 (chain E) 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 ASP 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D ALA* 4.1 16.1 - - - +
63D ILE* 4.1 20.4 - - + -
66D ARG* 2.8 38.4 + - - +
53E VAL 3.1 5.1 + - - -
55E PRO* 1.3 83.3 - - - +
57E GLN* 1.3 63.5 + - - +
58E THR* 3.5 12.0 + - - -
59E GLY* 3.0 23.0 + - - -
60E THR* 2.8 31.5 + - - +
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Residues in contact with GLN 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ARG* 4.3 4.0 - - - +
13E PRO* 3.7 1.1 - - + +
14E LEU 2.8 30.9 + - - +
15E VAL* 3.7 7.3 - - - +
33E ALA* 3.5 19.8 - - + +
34E VAL 3.2 10.3 + - - +
35E ASN* 3.1 24.8 + - - +
53E VAL* 3.4 26.1 + - + +
56E ASP* 1.3 72.5 + - - +
58E THR* 1.3 59.3 + - - +
60E THR* 3.7 0.2 - - - -
61E ALA* 2.9 33.4 + - - +
372E TYR* 3.3 32.1 - - + -
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Residues in contact with THR 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ALA* 5.4 6.5 - - + -
56E ASP* 3.3 12.2 + - - -
57E GLN* 1.3 78.2 - - - +
59E GLY* 1.3 64.2 + - - +
61E ALA* 3.6 4.3 - - - +
62E ALA* 3.1 23.5 + - + +
372E TYR* 2.9 30.1 + - - +
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Residues in contact with GLY 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLY* 3.9 26.7 - - - -
62D ALA* 4.5 4.2 - - - +
63D ILE* 4.8 2.0 - - - -
56E ASP* 3.0 20.6 + - - -
58E THR* 1.3 79.1 - - - +
60E THR* 1.3 56.4 + - - +
62E ALA* 3.4 4.1 + - - +
63E ILE* 3.1 35.1 + - - +
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Residues in contact with THR 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE* 4.7 6.7 - - + -
35E ASN* 3.3 15.3 + - - -
52E THR 4.3 2.0 + - - -
53E VAL* 3.0 33.8 + - - +
54E ALA 3.5 17.5 - - - +
55E PRO* 4.1 8.1 - - + -
56E ASP 2.8 17.6 + - - +
57E GLN 3.3 0.9 + - - -
59E GLY* 1.3 71.4 - - - -
61E ALA* 1.3 62.5 + - - +
62E ALA 3.3 0.2 - - - -
63E ILE* 3.4 12.1 + - + +
64E LEU* 2.9 27.7 + - - +
104E GLN* 4.5 2.7 - - - +
105E ILE* 4.1 17.7 - - + +
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E VAL* 3.9 9.6 - - + +
13E PRO* 3.9 18.4 - - + -
35E ASN* 3.3 23.6 - - - +
57E GLN 2.9 20.0 + - - +
58E THR* 3.6 6.1 - - - +
60E THR* 1.3 76.9 + - - +
62E ALA* 1.3 60.7 + - - +
64E LEU* 3.2 5.8 + - - +
65E TYR* 2.9 29.5 + - - +
372E TYR* 5.5 0.4 - - - +
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Residues in contact with ALA 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ASP* 4.3 17.2 - - - +
58D THR* 5.6 5.6 - - + -
59D GLY* 4.7 4.9 - - - +
58E THR* 3.1 16.9 + - + +
59E GLY* 3.7 7.2 - - - +
61E ALA* 1.3 77.6 - - - +
63E ILE* 1.3 62.1 + - - +
65E TYR* 3.6 7.2 + - - +
66E ARG* 3.1 23.7 + - - +
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Residues in contact with ILE 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D PRO* 3.6 35.9 - - + -
56D ASP* 4.0 19.7 - - + -
59D GLY* 4.6 4.3 - - - -
60D THR* 4.7 8.3 - - + -
63D ILE* 4.5 16.8 - - + -
59E GLY 3.1 22.5 + - - +
60E THR* 3.6 11.7 - - + +
61E ALA 3.2 0.2 - - - -
62E ALA* 1.3 75.8 - - - +
64E LEU* 1.3 65.3 + - - +
66E ARG* 3.3 7.2 + - - +
67E LEU* 3.1 25.8 + - + +
91E TYR* 3.9 11.4 - - - +
105E ILE* 4.1 16.8 - - + -
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Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 3.8 11.0 - - + -
35E ASN* 3.6 37.7 - - + +
36E LEU 4.0 11.0 - - - +
37E ILE* 4.0 15.5 - - + -
51E CYS* 3.8 20.2 - - + -
60E THR 2.9 18.0 + - - +
61E ALA 3.2 5.1 + - - +
63E ILE* 1.3 77.4 - - - +
65E TYR* 1.3 62.9 + - - +
67E LEU* 3.4 1.0 + - - +
68E ALA* 3.0 25.3 + - - +
105E ILE* 3.6 28.5 - - + +
109E ILE* 3.9 20.9 - - + -
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Residues in contact with TYR 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.9 26.9 + - + -
10E ARG* 4.7 2.0 - - - -
11E VAL* 3.5 28.6 - - + +
61E ALA 2.9 16.5 + - - +
62E ALA* 3.9 7.9 - - - +
64E LEU* 1.3 76.6 - - - +
66E ARG* 1.3 64.8 + - - +
68E ALA* 3.2 3.0 + - - +
69E LYS* 3.0 70.6 + - + +
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Residues in contact with ARG 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D PRO 3.2 24.2 + - - -
56D ASP* 3.0 36.0 + - - +
57D GLN 4.4 2.8 - - - +
62E ALA 3.1 16.3 + - - +
63E ILE* 3.3 5.4 + - - +
65E TYR* 1.3 81.3 - - + +
67E LEU* 1.3 64.2 + - + +
69E LYS* 3.6 17.8 + - - +
70E HIS* 3.4 13.9 + - - +
90E GLU* 2.9 37.2 + - - +
94E HIS* 5.5 4.8 + - - -
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Residues in contact with LEU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D PRO* 4.6 8.3 - - + -
63E ILE* 3.1 18.8 + - + +
64E LEU 3.9 3.1 - - - +
66E ARG* 1.3 82.5 - - + +
68E ALA* 1.3 64.5 + - - +
70E HIS* 3.2 24.8 + - - +
86E ILE* 3.5 25.4 - - + +
90E GLU* 4.0 29.6 - - + -
91E TYR* 3.7 25.6 - - + +
105E ILE* 3.7 23.3 - - + -
106E PHE* 3.8 22.4 - - + -
109E ILE* 4.0 11.4 - - + -
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Residues in contact with ALA 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.7 19.9 - - + +
11E VAL* 5.3 0.2 - - + -
37E ILE* 3.7 29.8 - - + -
64E LEU 3.0 18.2 + - - +
65E TYR* 3.2 6.0 + - - +
67E LEU* 1.3 75.8 - - - +
69E LYS* 1.3 65.2 + - - +
71E LEU* 2.9 34.3 + - + +
109E ILE* 4.2 7.5 - - + +
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Residues in contact with LYS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.9 10.5 - - + +
65E TYR* 3.0 69.2 + - + +
66E ARG* 3.9 10.5 - - - +
67E LEU 3.3 0.6 - - - -
68E ALA* 1.3 75.9 - - - +
70E HIS* 1.3 61.9 + - + +
71E LEU 3.0 1.6 + - - -
72E VAL* 3.1 24.7 + - + +
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Residues in contact with HIS 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ARG* 3.4 22.7 + - - +
67E LEU* 3.2 17.0 + - - +
68E ALA 3.1 1.0 - - - -
69E LYS* 1.3 77.8 - - + +
71E LEU* 1.3 58.3 + - - +
72E VAL 4.0 0.7 - - - +
74E HIS* 3.2 26.7 + - - -
82E LEU* 5.2 0.3 - - - +
85E ARG* 3.1 25.3 + - - +
86E ILE* 3.5 26.7 - - + -
89E GLN* 3.2 29.4 - - - -
90E GLU* 2.8 27.5 + - - +
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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