Contacts of the helix formed by residues 45 - 66 (chain O) in PDB entry 1P7G
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 LYS 45 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188M ASN* 3.4 39.2 - - + +
41O LEU* 2.7 41.2 + - + +
44O GLN* 1.3 78.1 - - + +
46O HIS* 1.3 63.9 + - + +
48O GLN* 3.5 3.1 + - - +
49O GLY* 2.9 26.5 + - - -
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Residues in contact with HIS 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179M GLU* 3.9 7.2 - - - -
183M TYR* 3.0 30.8 + + - -
188M ASN* 3.4 28.8 - - + +
41O LEU 3.1 14.1 + - - -
42O HIS* 3.3 17.0 - - + +
45O LYS* 1.3 76.5 - - - +
47O HIS* 1.3 67.4 + - - +
49O GLY* 3.2 10.2 + - - -
50O TYR* 3.1 30.7 + - + -
180O HIS* 3.5 49.0 + + + +
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Residues in contact with HIS 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O LEU* 3.4 12.4 - - + +
21O PRO* 3.6 26.3 - - + +
42O HIS* 2.8 15.3 + - - +
43O HIS* 3.3 17.2 + - - +
45O LYS 3.6 0.2 - - - -
46O HIS* 1.3 72.3 - - - +
48O GLN* 1.3 63.9 + - - +
50O TYR* 2.9 20.4 + - + -
51O VAL* 3.1 8.2 + - + +
87O HIS* 2.9 38.6 + - - -
90O HIS* 3.3 29.9 - + + +
91O SER 3.8 9.6 - - - -
94O TRP* 3.0 23.9 + - - -
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Residues in contact with GLN 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O LEU* 3.5 33.0 - - + +
43O HIS 3.5 4.9 + - - +
44O GLN* 3.0 26.6 - - - +
45O LYS 3.5 2.9 + - - +
46O HIS 3.3 0.2 - - - -
47O HIS* 1.3 78.1 - - - +
49O GLY* 1.3 62.3 + - - +
51O VAL* 3.0 18.1 + - - +
52O ASN* 3.0 58.7 + - - +
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Residues in contact with GLY 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O LYS 2.9 15.6 + - - -
46O HIS* 3.2 5.4 + - - -
47O HIS 3.1 0.6 - - - -
48O GLN* 1.3 77.4 - - - +
50O TYR* 1.3 59.3 + - - +
52O ASN* 3.4 11.5 + - - +
53O GLY* 2.9 24.4 + - - -
83O HIS* 3.7 5.3 + - - -
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Residues in contact with TYR 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O HIS* 3.1 32.0 + - + -
47O HIS* 2.9 13.8 + - - +
49O GLY* 1.3 75.7 - - - +
51O VAL* 1.3 61.0 + - - +
54O ALA* 2.9 28.1 + - - +
82O PHE* 3.6 19.7 - + - -
83O HIS* 3.4 44.1 - + - +
86O GLY* 4.0 6.1 - - - -
87O HIS* 3.8 9.6 - - - +
90O HIS* 3.6 22.9 - + - -
161O HIS* 3.0 35.4 - + - -
178O TRP* 3.9 8.5 - - - -
180O HIS* 3.5 21.2 - - - -
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Residues in contact with VAL 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O TYR* 3.4 28.9 - - - +
19O THR* 3.8 7.4 - - - -
20O LEU* 3.8 23.3 - - + +
47O HIS* 3.1 16.7 + - + +
48O GLN* 3.0 22.8 + - - +
50O TYR* 1.3 78.7 - - - +
52O ASN* 1.3 64.0 + - - +
54O ALA* 3.5 4.3 + - - +
55O ASN* 3.1 34.4 + - - +
87O HIS* 3.6 30.5 - - + +
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Residues in contact with ASN 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O GLN* 3.0 46.4 + - - +
49O GLY* 3.7 9.7 - - - +
51O VAL* 1.3 79.5 - - - +
53O GLY* 1.3 57.9 + - - +
55O ASN* 3.7 7.3 + - - +
56O ALA* 2.8 32.0 + - - +
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Residues in contact with GLY 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O GLY 2.9 11.4 + - - -
51O VAL 3.2 0.2 - - - -
52O ASN* 1.3 75.3 - - - +
54O ALA* 1.3 64.5 + - - +
56O ALA* 3.2 7.3 + - - +
57O ALA* 3.0 23.9 + - - +
79O ASP* 5.7 0.3 - - - +
83O HIS* 3.4 35.7 + - - -
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Residues in contact with ALA 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18O TYR* 4.2 20.4 - - + -
50O TYR 2.9 17.0 + - - +
51O VAL* 3.9 5.4 - - - +
53O GLY* 1.3 74.6 - - - +
55O ASN* 1.3 59.1 + - - +
57O ALA* 3.4 3.8 + - - +
58O LEU* 3.0 34.2 + - - +
80O LEU* 4.0 12.6 - - + +
83O HIS* 3.3 6.5 - - - +
84O LEU* 4.1 23.6 - - + +
87O HIS* 5.3 2.0 - - + -
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Residues in contact with ASN 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O ARG* 3.4 32.5 + - - +
18O TYR* 2.8 51.3 + - - -
51O VAL* 3.1 26.0 + - - +
52O ASN* 3.7 7.5 + - - +
54O ALA* 1.3 74.4 - - - +
56O ALA* 1.3 63.5 + - - +
58O LEU* 3.3 2.9 + - - +
59O GLU* 3.0 24.3 + - - +
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Residues in contact with ALA 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O ASN 2.8 22.1 + - - +
53O GLY* 3.2 8.0 + - - +
55O ASN* 1.3 73.5 - - - +
57O ALA* 1.3 60.6 + - - +
59O GLU* 3.5 7.9 + - - +
60O LYS* 3.5 32.0 + - - +
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Residues in contact with ALA 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O GLY 3.0 15.8 + - - +
54O ALA 3.8 3.8 - - - +
56O ALA* 1.3 75.4 - - - +
58O LEU* 1.3 65.2 + - - +
59O GLU 3.1 0.4 - - - -
60O LYS* 3.2 13.1 + - - +
61O LEU* 3.1 26.2 + - - +
76O VAL* 3.8 12.1 - - + +
79O ASP* 4.4 8.3 - - + -
80O LEU* 3.9 36.8 - - + +
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Residues in contact with LEU 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152N GLN* 3.8 4.3 - - - +
154N LEU* 3.6 29.6 - - + -
15O THR* 4.0 17.4 - - + +
16O LYS 2.9 30.3 - - - +
17O ARG* 3.8 19.1 - - - +
18O TYR* 3.7 21.5 - - + -
54O ALA 3.0 17.7 + - - +
55O ASN 3.3 4.9 + - - +
57O ALA* 1.3 76.4 - - - +
59O GLU* 1.3 53.1 + - - +
61O LEU* 3.3 16.7 + - + +
62O GLU* 2.7 35.3 + - - +
65O ARG* 5.3 0.9 - - - +
80O LEU* 4.3 10.1 - - + -
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Residues in contact with GLU 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O ARG* 2.5 40.1 + - - +
55O ASN 3.0 15.9 + - - +
56O ALA* 3.6 10.3 - - - +
57O ALA 3.1 0.4 - - - -
58O LEU* 1.3 75.1 - - - +
60O LYS* 1.3 63.1 + - + +
62O GLU* 3.3 12.2 + - - +
63O LYS* 3.0 37.0 + - + +
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Residues in contact with LYS 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O ALA* 3.6 20.6 - - - +
57O ALA* 3.2 10.5 + - - +
59O GLU* 1.3 77.6 - - + +
61O LEU* 1.3 58.7 + - - +
63O LYS* 3.5 5.7 + - - +
64O PHE* 3.0 28.4 + - - +
69O ALA* 5.8 0.5 - - - +
70O GLN 4.8 1.4 - - - +
71O ILE* 3.7 15.8 - - + +
76O VAL* 3.8 20.0 - - + +
79O ASP* 4.2 16.0 + - - -
72P ASP* 4.4 11.9 + - - -
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Residues in contact with LEU 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N GLU* 3.7 26.9 - - - +
154N LEU* 5.4 0.2 - - + -
155N ILE 5.7 0.2 - - - +
15O THR* 5.4 0.2 - - + -
57O ALA 3.1 15.4 + - - +
58O LEU* 3.5 18.4 - - + +
59O GLU 3.2 0.2 - - - -
60O LYS* 1.3 78.4 - - - +
62O GLU* 1.3 59.6 + - - +
64O PHE* 3.3 3.3 + - + +
65O ARG* 2.9 54.3 + - - +
71O ILE* 3.7 19.1 - - + -
73O ILE* 4.1 12.6 - - + -
76O VAL* 3.6 15.7 - - + -
77O LEU* 4.4 5.8 - - + -
80O LEU* 3.7 29.8 - - + -
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Residues in contact with GLU 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O VAL* 3.6 14.7 - - + +
14O THR* 4.4 0.8 - - - -
15O THR* 2.5 46.1 + - + +
17O ARG* 3.1 14.3 + - - +
58O LEU 2.7 20.5 + - - +
59O GLU* 3.3 12.6 + - - +
61O LEU* 1.3 74.3 - - - +
63O LYS* 1.3 56.4 + - - +
65O ARG* 3.3 7.0 + - - +
66O LYS* 2.9 68.6 + - + +
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Residues in contact with LYS 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O GLU* 3.0 29.2 + - + +
60O LYS* 4.0 5.4 - - - +
62O GLU* 1.3 73.4 - - - +
64O PHE* 1.3 65.8 + - - +
66O LYS* 3.2 7.8 + - + -
67O GLY 3.2 2.9 + - - -
68O GLU* 3.0 71.1 + - + +
69O ALA* 3.5 18.0 + - + -
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Residues in contact with PHE 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124N LYS* 3.0 36.8 + - + -
127N GLU* 3.2 41.5 - - + -
128N GLU* 3.5 48.7 - - + -
131N GLN* 5.1 5.6 - - + -
60O LYS 3.0 19.0 + - - +
61O LEU* 3.5 4.5 - - + +
63O LYS* 1.3 75.0 - - - +
65O ARG* 1.3 59.1 + - - +
67O GLY* 3.1 12.3 + - - -
69O ALA 2.9 24.9 + - - +
70O GLN* 3.6 20.4 + - - +
71O ILE* 3.6 34.3 - - + -
73O ILE* 5.3 0.2 - - + -
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Residues in contact with ARG 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N PHE* 2.8 35.1 + - - +
119N PHE* 3.4 27.1 - - + +
124N LYS* 3.5 35.6 - - + +
128N GLU* 2.9 42.3 + - - +
152N GLN* 5.7 1.4 + - - -
153N LEU 4.8 3.4 + - - -
154N LEU* 4.7 14.1 - - - +
155N ILE 4.9 3.0 - - - +
13O VAL* 3.6 27.0 - - + +
15O THR* 3.5 19.8 - - - +
58O LEU* 5.3 0.8 - - - +
61O LEU* 2.9 43.4 + - - +
62O GLU* 3.5 4.9 - - - +
63O LYS 3.2 0.2 - - - -
64O PHE* 1.3 76.5 - - + +
66O LYS* 1.3 59.4 + - - +
67O GLY 3.2 1.1 + - - -
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Residues in contact with LYS 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O SER* 5.2 7.4 - - - -
13O VAL* 3.0 42.7 + - + +
62O GLU* 2.9 44.5 + - - +
63O LYS* 3.6 8.3 - - + +
64O PHE 3.2 0.6 - - - -
65O ARG* 1.3 75.8 - - - +
67O GLY* 1.3 57.1 + - - +
68O GLU* 3.1 38.0 + - + +
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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