Contacts of the helix formed by residues 78 - 91 (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 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74E HIS* 5.5 1.2 - - - +
75E SER* 3.0 27.5 + - - +
77E HIS* 1.3 80.8 - - - +
79E VAL* 1.3 65.3 + - - +
80E ALA 3.3 2.9 - - - -
81E PRO* 3.0 10.4 - - + +
82E LEU* 3.0 36.6 + - + +
126G HIS* 5.6 0.3 - - - -
127G GLN* 3.1 28.2 + - - +
130G GLY 3.5 5.8 - - - -
131G GLY* 3.8 8.2 - - - -
132G ALA 4.4 3.3 + - - -
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Residues in contact with VAL 79 (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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76E PRO 3.6 4.2 + - - +
78E ASP* 1.3 77.5 - - - +
80E ALA* 1.3 65.4 + - - +
82E LEU* 4.3 2.0 - - - -
83E ILE* 2.9 45.7 + - + +
110E ASP* 3.3 23.1 - - - +
113E MSE 3.7 39.6 - - + +
114E TRP* 3.9 21.8 - - + +
117E GLN* 3.7 21.3 - - - +
279E GLN* 4.2 2.7 - - - +
130G GLY* 3.9 7.2 - - - +
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Residues in contact with ALA 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E VAL* 1.3 82.0 - - - +
81E PRO* 1.3 70.4 - - + +
83E ILE* 3.5 4.1 + - - +
84E ALA* 3.1 21.5 + - - +
279E GLN* 3.6 28.5 - - - +
129G LEU 5.2 0.2 - - - +
130G GLY* 3.0 15.0 + - - +
133G HIS* 3.7 21.5 + - + +
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Residues in contact with PRO 81 (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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78E ASP* 3.0 33.2 - - + +
80E ALA* 1.3 83.3 - - + +
82E LEU* 1.3 59.6 + - + +
84E ALA* 3.3 4.0 + - + +
85E ARG* 2.9 30.0 + - - +
130G GLY 3.2 12.6 - - - +
131G GLY* 4.0 9.0 - - - -
132G ALA 3.3 26.9 - - - +
133G HIS* 3.8 23.8 - - + +
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Residues in contact with LEU 82 (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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6E ILE* 5.5 0.2 - - + -
70E HIS 5.2 0.4 - - - +
71E LEU* 4.0 20.6 - - + -
74E HIS* 3.8 41.5 - - + +
75E SER 3.5 23.8 - - - +
78E ASP* 3.0 35.5 + - + +
79E VAL* 3.8 3.1 - - - +
81E PRO* 1.3 78.1 - - + +
83E ILE* 1.3 57.4 + - - +
85E ARG* 3.3 19.0 + - - +
86E ILE* 3.0 35.9 + - + +
113E MSE 3.8 13.9 - - + -
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Residues in contact with ILE 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E LEU* 5.5 2.0 - - + -
79E VAL* 2.9 40.1 + - + +
80E ALA* 3.9 4.3 - - - +
82E LEU* 1.3 74.6 - - + +
84E ALA* 1.3 66.9 + - - +
86E ILE* 3.3 3.7 + - + -
87E PHE* 2.9 23.4 + - + +
106E PHE* 3.5 48.4 - - + +
109E ILE* 4.2 20.0 - - + -
110E ASP* 4.1 20.9 - - + +
276E GLY 5.2 2.0 - - - +
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Residues in contact with ALA 84 (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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80E ALA 3.1 17.8 + - - +
81E PRO* 3.3 9.2 + - + +
83E ILE* 1.3 78.6 - - - +
85E ARG* 1.3 57.0 + - - +
87E PHE* 3.5 8.6 + - - +
88E HIS* 3.0 28.4 + - - +
133G HIS* 4.9 9.9 - - + +
318G PRO* 6.3 0.7 - - + -
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Residues in contact with ARG 85 (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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26D TYR* 3.3 31.8 + - + +
70E HIS* 3.1 51.1 + - - +
74E HIS* 4.0 18.2 + - - -
81E PRO 2.9 16.6 + - - +
82E LEU* 3.7 17.2 + - - +
83E ILE 3.2 0.2 - - - -
84E ALA* 1.3 76.3 - - - +
86E ILE* 1.3 68.1 + - - +
88E HIS* 3.3 1.8 + - - +
89E GLN* 2.8 58.0 + - - +
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Residues in contact with ILE 86 (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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67E LEU* 3.5 44.2 - - + +
70E HIS* 3.5 41.3 - - + -
71E LEU* 3.8 22.4 - - + -
82E LEU* 3.0 19.4 + - + +
83E ILE* 3.8 7.6 - - + +
85E ARG* 1.3 85.2 - - - +
87E PHE* 1.3 58.3 + - - +
89E GLN* 4.4 4.3 - - - -
90E GLU* 2.8 32.4 + - + +
106E PHE* 3.8 11.2 - - + -
109E ILE* 5.8 2.0 - - + -
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Residues in contact with PHE 87 (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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228D TRP* 3.7 31.0 - + - -
83E ILE* 2.9 18.8 + - + +
84E ALA* 3.6 8.5 - - - +
86E ILE* 1.3 75.4 - - - +
88E HIS* 1.3 56.8 + - - +
91E TYR* 2.9 55.9 + + + +
92E LEU* 3.2 37.3 + - + -
98E ILE 4.4 3.1 - - - -
99E MSE 3.9 29.6 - - + -
102E ALA* 3.5 27.4 - - + -
106E PHE* 3.7 15.0 - + + -
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Residues in contact with HIS 88 (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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25D SER* 3.5 28.3 + - - -
26D TYR* 3.5 22.8 + + + +
84E ALA 3.0 16.8 + - - +
85E ARG* 3.7 3.8 - - - +
87E PHE* 1.3 77.2 - - - +
89E GLN* 1.3 58.9 + - - +
92E LEU* 3.7 30.5 - - + -
93E GLY* 2.8 34.3 + - - -
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Residues in contact with GLN 89 (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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24D TRP* 3.4 12.9 - - + -
26D TYR* 3.5 38.7 - - + -
70E HIS* 3.2 28.6 + - - -
85E ARG* 2.8 51.4 + - - +
86E ILE* 3.9 3.4 - - - +
88E HIS* 1.3 74.3 - - - +
90E GLU* 1.3 65.1 + - + +
91E TYR 3.5 0.2 - - - -
94E HIS* 3.1 22.5 + - - -
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Residues in contact with GLU 90 (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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54D ALA* 3.7 2.4 - - - +
55D PRO* 3.6 24.6 - - + +
66E ARG* 2.9 51.7 + - - +
67E LEU* 4.0 22.4 - - + -
70E HIS* 2.8 33.6 + - - +
86E ILE* 2.8 25.0 + - + +
89E GLN* 1.3 82.9 - - + +
91E TYR* 1.3 62.2 + - + +
94E HIS* 3.3 17.8 + - - -
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Residues in contact with TYR 91 (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* 3.5 40.8 - - + +
63E ILE* 3.9 6.9 - - - +
67E LEU* 3.7 33.8 - - + +
87E PHE* 2.9 38.5 + + + +
90E GLU* 1.3 83.2 - - + +
92E LEU* 1.3 65.9 + - - +
93E GLY 3.3 1.1 - - - -
94E HIS* 3.1 14.7 + - - +
96E ALA* 3.1 32.8 + - + +
98E ILE* 3.6 32.5 - - + -
101E ALA* 4.6 1.6 + - + -
102E ALA* 3.7 29.0 - - + -
105E ILE* 4.0 5.2 - - - +
106E PHE* 4.1 4.7 - + - -
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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