Contacts of the helix formed by residues 45 - 67 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40J GLN* 4.9 1.4 - - - +
41J LEU* 2.9 39.2 + - + +
44J GLN* 1.3 92.4 + - + +
46J HIS* 1.3 61.3 + - - +
47J HIS 3.6 0.2 - - - -
48J GLN* 3.5 2.8 + - - +
49J GLY* 3.0 25.3 + - - -
188L ASN* 3.6 36.6 - - + +
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Residues in contact with HIS 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J LEU 3.0 20.3 + - - -
42J HIS* 3.5 23.1 - - + +
45J LYS* 1.3 74.0 - - - +
47J HIS* 1.3 65.6 + - - +
49J GLY* 3.0 11.3 + - - -
50J TYR* 3.1 28.2 + - + -
180J HIS* 3.3 45.7 + + + +
179L GLU* 3.8 9.9 - - - -
183L TYR* 2.7 31.2 + + - -
188L ASN* 3.8 24.4 - - + +
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Residues in contact with HIS 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 3.2 11.9 - - + +
21J PRO* 3.5 27.4 - - + -
42J HIS 2.9 17.0 + - - +
43J HIS* 3.3 15.6 + - - +
45J LYS 3.6 0.2 - - - -
46J HIS* 1.3 72.5 - - - +
48J GLN* 1.3 63.5 + - - +
50J TYR* 3.0 19.4 + + - +
51J VAL* 3.1 7.6 + - + +
86J GLY 4.4 0.4 - - - -
87J HIS* 3.1 40.6 + - - -
90J HIS* 3.6 26.6 - + + +
91J SER* 3.8 6.3 - - - -
94J TRP* 2.9 30.2 + - + -
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Residues in contact with GLN 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J LEU* 3.4 33.1 - - + +
43J HIS 3.4 5.3 + - - +
44J GLN 3.1 28.2 - - - +
45J LYS 3.7 1.8 - - - +
46J HIS 3.3 0.4 - - - -
47J HIS* 1.3 78.2 - - - +
49J GLY* 1.3 58.0 + - - +
51J VAL* 3.1 17.2 + - - +
52J ASN* 2.9 66.1 + - - +
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Residues in contact with GLY 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J LYS 3.0 15.2 + - - -
46J HIS* 3.0 6.4 + - - -
48J GLN* 1.3 78.0 - - - +
50J TYR* 1.3 59.4 + - - +
52J ASN* 3.4 9.7 + - - +
53J GLY* 2.8 25.3 + - - -
83J HIS* 3.9 4.8 + - - -
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Residues in contact with TYR 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J HIS* 3.1 30.1 + - + +
47J HIS* 3.0 13.7 + - - +
49J GLY* 1.3 75.5 - - - +
51J VAL* 1.3 61.3 + - - +
54J ALA* 2.9 30.3 + - - +
82J PHE* 3.6 18.6 - + - -
83J HIS* 3.4 41.3 - + - +
86J GLY* 4.1 6.3 - - - -
87J HIS* 3.9 9.4 - - - +
90J HIS* 3.6 25.8 - + - -
161J HIS* 3.1 31.4 - + - -
178J TRP* 4.0 6.9 - - - -
180J HIS* 3.3 25.0 - + - -
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Residues in contact with VAL 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J TYR* 3.2 35.5 - - + +
19J THR* 3.8 5.8 - - - -
20J LEU* 3.9 25.8 - - + +
47J HIS 3.1 13.8 + - - +
48J GLN* 3.1 19.0 + - - +
50J TYR* 1.3 78.8 - - - +
52J ASN* 1.3 64.3 + - - +
54J ALA* 3.4 3.0 + - - +
55J ASN* 3.1 30.5 + - - +
87J HIS* 3.6 32.8 - - + +
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Residues in contact with ASN 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J GLN* 2.9 48.7 + - - +
49J GLY* 3.7 7.1 - - - +
51J VAL* 1.3 77.6 - - - +
53J GLY* 1.3 52.3 - - - +
55J ASN* 3.1 10.4 + - - +
56J ALA* 2.7 37.4 + - - +
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Residues in contact with GLY 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J GLY 2.8 14.8 + - - -
50J TYR 3.5 0.2 + - - -
52J ASN* 1.3 76.3 - - - +
54J ALA* 1.3 60.5 + - - +
56J ALA* 3.2 9.0 + - - +
57J ALA* 3.1 23.4 + - - +
79J ASP* 5.6 0.5 - - - +
83J HIS* 3.4 34.9 + - - -
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Residues in contact with ALA 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J TYR* 4.3 20.2 - - + -
50J TYR 2.9 18.8 + - - +
51J VAL* 3.8 4.5 - - - +
53J GLY* 1.3 74.3 - - - +
55J ASN* 1.3 62.6 + - - +
57J ALA* 3.3 6.1 + - - +
58J LEU* 3.0 27.3 + - - +
80J LEU* 3.9 12.1 - - + +
83J HIS* 3.2 15.0 - - + +
84J LEU* 4.0 17.0 - - + +
87J HIS* 5.2 1.1 - - + -
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Residues in contact with ASN 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J ARG* 3.2 25.8 + - - +
18J TYR* 2.7 51.4 + - - -
51J VAL* 3.1 18.6 + - - +
52J ASN* 3.1 10.0 + - - +
54J ALA* 1.3 73.3 - - - +
56J ALA* 1.3 62.3 + - - +
58J LEU* 3.0 8.3 + - - +
59J GLU* 2.9 29.9 + - - +
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Residues in contact with ALA 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J ASN 2.7 21.6 + - - +
53J GLY* 3.5 9.6 - - - +
55J ASN* 1.3 73.6 - - - +
57J ALA* 1.3 60.6 + - - +
59J GLU* 3.5 7.4 + - - +
60J LYS* 3.4 38.5 + - - +
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Residues in contact with ALA 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J GLY 3.1 11.9 + - - +
54J ALA 3.6 7.9 - - - +
55J ASN 3.1 0.2 - - - -
56J ALA* 1.3 74.9 - - - +
58J LEU* 1.3 66.0 + - - +
60J LYS* 3.3 10.3 + - - +
61J LEU* 3.1 28.2 + - - +
76J VAL* 3.7 14.8 - - + +
79J ASP* 4.6 7.2 - - + -
80J LEU* 3.9 35.2 - - + +
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Residues in contact with LEU 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J THR* 4.5 9.4 + - + +
16J LYS 2.9 29.4 - - - +
17J ARG* 3.6 16.5 + - - +
18J TYR* 3.3 28.0 - - + -
54J ALA 3.0 15.3 + - - +
55J ASN* 3.0 13.4 + - - +
57J ALA* 1.3 77.8 - - - +
59J GLU* 1.3 57.1 + - - +
61J LEU* 3.7 11.3 - - + +
62J GLU* 2.8 31.4 + - - +
65J ARG* 5.7 0.9 - - - +
80J LEU* 4.3 11.9 - - + -
152K GLN* 3.7 7.4 - - - +
154K LEU* 3.9 27.6 - - + -
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Residues in contact with GLU 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J ARG* 3.1 24.4 + - - +
55J ASN 2.9 15.2 + - - +
56J ALA* 3.7 8.7 - - - +
57J ALA 3.2 0.4 - - - -
58J LEU* 1.3 79.1 - - - +
60J LYS* 1.3 61.0 + - + +
62J GLU* 3.4 17.1 + - - +
63J LYS* 3.2 46.7 + - + +
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Residues in contact with LYS 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ASP* 4.8 8.5 + - - -
56J ALA* 3.4 26.4 + - - +
57J ALA* 3.3 11.1 + - - +
58J LEU 3.2 0.2 - - - -
59J GLU* 1.3 76.1 - - + +
61J LEU* 1.3 65.0 + - - +
63J LYS* 3.6 6.0 + - - +
64J PHE* 3.2 21.8 + - - +
69J ALA* 5.8 0.7 - - - +
70J GLN 5.0 2.1 - - - +
71J ILE* 4.0 6.5 - - + +
76J VAL* 4.4 25.5 - - + +
79J ASP* 4.4 15.5 + - - +
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Residues in contact with LEU 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J THR* 5.9 0.4 - - + -
57J ALA 3.1 22.6 + - - +
58J LEU* 3.7 12.6 - - + +
60J LYS* 1.3 73.1 - - - +
62J GLU* 1.3 67.6 + - - +
64J PHE* 3.1 3.7 + - + +
65J ARG* 2.8 50.6 + - - +
71J ILE* 3.5 22.2 - - + -
73J ILE* 4.2 4.9 - - + -
76J VAL* 3.8 9.4 - - + -
77J LEU* 4.1 19.5 - - + -
80J LEU* 4.0 26.2 - - + -
128K GLU* 3.7 26.7 - - - +
154K LEU* 5.3 0.7 - - + -
155K ILE 5.7 0.2 - - - +
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Residues in contact with GLU 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J VAL* 4.3 7.5 - - + +
15J THR* 2.9 21.8 + - - +
17J ARG* 2.9 25.3 + - - +
58J LEU 2.8 20.6 + - - +
59J GLU* 3.4 23.1 - - - +
60J LYS 3.3 0.2 - - - -
61J LEU* 1.3 72.4 - - - +
63J LYS* 1.3 65.1 + - + +
65J ARG* 3.0 21.6 + - - +
66J LYS* 3.0 52.2 + - + +
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Residues in contact with LYS 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J GLU* 3.2 36.5 + - + +
60J LYS* 4.1 5.6 - - - +
62J GLU* 1.3 80.6 - - + +
64J PHE* 1.3 64.0 + - - +
66J LYS* 3.1 1.9 + - - +
67J GLY 2.9 18.9 + - - -
68J GLU* 2.9 55.2 + - + +
69J ALA* 3.2 30.4 - - + +
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Residues in contact with PHE 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J LYS 3.2 11.7 + - - +
61J LEU* 3.1 9.0 + - + +
63J LYS* 1.3 77.1 - - - +
65J ARG* 1.3 63.5 + - - +
67J GLY* 3.2 9.0 + - - -
69J ALA* 3.5 25.0 - - - +
70J GLN* 3.8 17.3 - - - +
71J ILE* 3.4 46.7 - - + -
73J ILE* 5.7 0.7 - - + -
124K LYS* 2.8 40.0 + - + -
127K GLU* 3.4 36.3 - - + -
128K GLU* 4.3 33.0 - - + -
131K GLN* 5.3 6.5 - - + -
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Residues in contact with ARG 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J VAL* 3.6 24.6 - - + +
15J THR* 3.2 22.4 - - - +
58J LEU* 5.7 1.0 - - - +
61J LEU* 2.8 43.5 + - - +
62J GLU* 3.4 7.0 - - - +
64J PHE* 1.3 80.1 - - + +
66J LYS* 1.3 58.8 + - - +
118K PHE* 2.9 33.0 + - - +
119K PHE* 3.6 26.2 - - - +
120K GLY* 5.4 0.2 - - - -
124K LYS* 3.4 32.0 - - + +
128K GLU* 2.8 40.8 + - - +
152K GLN* 5.5 0.4 + - - -
153K LEU 4.5 9.3 + - - -
154K LEU* 4.5 11.1 - - - +
155K ILE 4.9 0.6 - - - +
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Residues in contact with LYS 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J VAL* 3.6 38.8 + - + +
62J GLU* 3.0 49.3 + - + +
63J LYS* 3.1 4.9 + - - +
65J ARG* 1.3 77.5 - - - +
67J GLY* 1.3 59.5 + - - +
68J GLU* 3.1 31.6 + - + +
124K LYS* 5.4 0.9 - - - -
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Residues in contact with GLY 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J LYS 2.9 3.2 + - - -
64J PHE 3.2 12.1 + - - -
66J LYS* 1.3 80.2 - - - +
68J GLU* 1.3 62.6 + - - +
69J ALA* 3.2 8.0 + - - +
124K LYS* 4.8 4.9 - - - +
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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