Contacts of the helix formed by residues 45 - 66 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU* 2.7 44.1 + - + +
44E GLN* 1.3 81.2 - - + +
46E HIS* 1.3 64.3 + - + +
47E HIS 3.5 0.2 - - - -
48E GLN* 3.5 2.3 + - - +
49E GLY* 3.0 25.3 + - - -
188G ASN* 3.5 35.1 - - + +
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Residues in contact with HIS 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E LEU 3.1 12.8 + - - -
42E HIS* 3.5 23.6 - - + +
45E LYS* 1.3 79.6 - - + +
47E HIS* 1.3 67.0 + - - +
49E GLY* 3.1 10.3 + - - -
50E TYR* 3.0 30.4 + - + -
180E HIS* 3.3 47.4 + + + +
179G GLU* 3.9 5.2 - - - -
183G TYR* 2.8 34.8 + + - -
188G ASN* 3.7 21.3 - - + +
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Residues in contact with HIS 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.4 13.2 - - + +
21E PRO* 3.6 25.9 - - + +
42E HIS 2.9 16.6 + - - +
43E HIS* 3.2 15.9 - - - +
45E LYS 3.5 0.2 - - - -
46E HIS* 1.3 73.0 - - - +
48E GLN* 1.3 64.9 + - - +
50E TYR* 3.1 18.8 + - + +
51E VAL* 3.3 7.6 + - + +
86E GLY 4.7 0.2 - - - -
87E HIS* 3.2 35.3 + - - -
90E HIS* 3.2 39.2 - + + +
91E SER 3.7 0.7 - - - -
94E TRP* 2.8 28.7 + - - -
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Residues in contact with GLN 48 (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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20E LEU* 3.5 32.1 - - + +
43E HIS 3.6 4.9 + - - +
44E GLN 3.3 26.6 - - - +
45E LYS 3.5 3.8 + - - +
46E HIS 3.2 0.4 - - - -
47E HIS* 1.3 78.5 - - - +
49E GLY* 1.3 61.8 + - - +
51E VAL* 3.0 26.5 + - - +
52E ASN* 3.0 50.4 + - - +
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Residues in contact with GLY 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LYS 3.0 15.3 + - - -
46E HIS* 3.1 5.7 + - - -
48E GLN* 1.3 76.5 - - - +
50E TYR* 1.3 55.2 + - - +
52E ASN* 3.2 10.5 + - - +
53E GLY* 2.8 32.9 + - - -
83E HIS* 3.8 3.0 - - - -
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Residues in contact with TYR 50 (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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46E HIS* 3.0 34.6 + - + -
47E HIS* 3.1 11.1 + - - +
49E GLY* 1.3 77.5 - - - +
51E VAL* 1.3 58.6 + - - +
54E ALA* 3.0 26.5 + - - +
82E PHE* 3.6 20.2 - + - -
83E HIS* 3.3 42.9 - + - +
86E GLY* 3.9 6.1 - - - -
87E HIS* 3.8 9.8 - - - +
90E HIS* 3.8 22.0 - + - -
161E HIS* 3.0 34.9 - + - -
178E TRP* 3.8 7.6 - - - -
180E HIS* 3.5 21.8 - - - -
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Residues in contact with VAL 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E TYR* 3.4 30.7 - - + +
19E THR* 3.7 13.9 - - - -
20E LEU* 3.9 11.2 - - + +
47E HIS* 3.3 13.2 + - + +
48E GLN* 3.0 20.7 + - - +
50E TYR* 1.3 74.2 - - - +
52E ASN* 1.3 65.4 + - - +
54E ALA* 3.6 4.2 + - - +
55E ASN* 3.0 34.2 + - - +
87E HIS* 3.2 37.9 - - + +
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Residues in contact with ASN 52 (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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48E GLN* 3.0 46.5 + - - +
49E GLY* 3.6 8.2 - - - +
51E VAL* 1.3 76.9 - - - +
53E GLY* 1.3 57.2 + - - +
55E ASN* 3.3 9.6 + - - +
56E ALA* 2.8 36.4 + - - +
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Residues in contact with GLY 53 (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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49E GLY 2.8 11.2 + - - -
51E VAL 3.3 0.2 - - - -
52E ASN* 1.3 77.9 - - - +
54E ALA* 1.3 61.4 + - - +
56E ALA* 3.3 6.4 + - - +
57E ALA* 3.1 23.2 + - - +
79E ASP* 5.6 0.7 - - - +
83E HIS* 3.4 37.0 + - - -
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Residues in contact with ALA 54 (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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18E TYR* 4.0 23.3 - - + -
50E TYR 3.0 18.2 + - - +
51E VAL* 4.0 4.7 - - - +
53E GLY* 1.3 74.0 - - - +
55E ASN* 1.3 62.9 + - - +
57E ALA* 3.4 4.5 + - - +
58E LEU* 3.0 28.5 + - - +
80E LEU* 3.9 10.9 - - + +
83E HIS* 3.2 12.4 - - + +
84E LEU* 4.1 16.6 - - - +
87E HIS* 5.3 1.8 - - + -
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Residues in contact with ASN 55 (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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17E ARG* 3.3 27.6 + - - +
18E TYR* 2.7 48.2 + - - -
51E VAL* 3.0 24.2 + - - +
52E ASN* 3.6 9.1 + - - +
54E ALA* 1.3 74.9 - - - +
56E ALA* 1.3 59.1 + - - +
58E LEU* 3.1 7.3 + - - +
59E GLU* 2.9 31.3 + - - +
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Residues in contact with ALA 56 (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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52E ASN 2.8 21.7 + - - +
53E GLY* 3.3 7.8 + - - +
55E ASN* 1.3 73.3 - - - +
57E ALA* 1.3 60.8 + - - +
59E GLU* 3.3 8.4 + - - +
60E LYS* 3.2 36.4 + - - +
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Residues in contact with ALA 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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53E GLY 3.1 16.2 + - - +
54E ALA 3.8 2.5 - - - +
56E ALA* 1.3 76.5 - - - +
58E LEU* 1.3 61.2 + - - +
60E LYS* 3.6 7.6 + - - +
61E LEU* 3.2 28.4 + - - +
76E VAL* 3.5 17.8 - - + +
79E ASP* 4.3 8.3 - - + -
80E LEU* 3.7 37.5 - - + +
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Residues in contact with LEU 58 (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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15E THR* 4.0 20.4 - - + +
16E LYS 3.1 27.1 - - - +
17E ARG* 3.9 16.8 - - - +
18E TYR* 3.5 26.9 - - + -
54E ALA 3.0 17.0 + - - +
55E ASN 3.1 6.9 + - - +
57E ALA* 1.3 73.6 - - - +
59E GLU* 1.3 55.7 + - - +
61E LEU* 3.2 13.3 + - + +
62E GLU* 2.8 35.2 + - - +
65E ARG* 5.2 0.9 - - - +
80E LEU* 4.0 12.1 - - + -
152H GLN* 3.9 3.6 - - - +
154H LEU* 3.7 28.7 - - + -
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Residues in contact with GLU 59 (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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17E ARG* 2.6 40.2 + - - +
55E ASN 2.9 16.0 + - - +
56E ALA* 3.3 8.9 + - - +
58E LEU* 1.3 76.6 - - - +
60E LYS* 1.3 55.7 + - + +
62E GLU* 3.2 14.3 + - - +
63E LYS* 2.9 79.2 + - - +
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Residues in contact with LYS 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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56E ALA* 3.4 23.7 - - - +
57E ALA* 3.8 10.7 - - - +
58E LEU 3.2 0.6 - - - -
59E GLU* 1.3 73.8 - - + +
61E LEU* 1.3 66.2 + - - +
63E LYS* 3.2 9.3 + - + +
64E PHE* 3.0 23.4 + - - +
69E ALA* 5.3 0.7 - - - +
70E GLN 4.7 2.6 - - - +
71E ILE* 4.4 6.1 - - + +
76E VAL* 4.2 26.5 - - + +
79E ASP* 4.5 13.7 + - - +
72F ASP* 4.6 9.9 + - - -
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Residues in contact with LEU 61 (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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57E ALA 3.2 14.5 + - - +
58E LEU* 3.2 16.0 + - + +
60E LYS* 1.3 78.6 - - - +
62E GLU* 1.3 57.6 + - - +
64E PHE* 3.2 6.3 + - + +
65E ARG* 2.8 58.8 + - - +
71E ILE* 3.6 19.9 - - + +
73E ILE* 4.1 11.0 - - + -
76E VAL* 3.9 8.3 - - + -
77E LEU* 4.2 12.1 - - + -
80E LEU* 3.9 27.4 - - + -
128H GLU* 3.6 28.5 - - - +
155H ILE 5.6 0.7 - - - +
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Residues in contact with GLU 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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13E VAL* 3.9 13.7 - - + -
14E THR* 4.1 0.9 - - - -
15E THR* 2.5 48.0 + - + +
17E ARG* 3.1 9.9 + - - -
58E LEU 2.8 17.1 + - - +
59E GLU* 3.5 20.4 - - - +
61E LEU* 1.3 73.7 - - - +
63E LYS* 1.3 56.1 + - + +
64E PHE 3.0 4.7 - - - -
65E ARG* 3.3 5.4 + - - +
66E LYS* 3.1 67.1 + - + +
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Residues in contact with LYS 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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59E GLU* 2.9 55.7 + - + +
60E LYS* 3.2 8.0 + - + +
62E GLU* 1.3 76.1 - - + +
64E PHE* 1.3 55.7 + - - +
66E LYS* 4.1 9.4 - - + -
68E GLU* 3.2 18.6 + - + +
69E ALA* 2.8 42.0 + - + +
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Residues in contact with PHE 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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60E LYS 3.0 15.2 + - - +
61E LEU* 3.4 8.3 - - + +
63E LYS* 1.3 77.7 - - - +
65E ARG* 1.3 61.2 + - + +
66E LYS 3.1 1.6 - - - -
67E GLY* 3.1 10.9 + - - -
69E ALA 3.1 19.5 - - - +
70E GLN* 3.7 21.3 - - - +
71E ILE* 3.4 33.2 - - + -
73E ILE* 5.0 0.7 - - + -
124H LYS* 2.8 32.2 + - + -
127H GLU* 3.4 35.9 - - + -
128H GLU* 3.6 49.8 - - + -
131H GLN* 4.9 9.6 - - + -
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Residues in contact with ARG 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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13E VAL* 3.7 19.0 - - + +
15E THR* 3.3 23.4 - - - +
58E LEU* 5.2 1.8 - - - +
61E LEU* 2.8 41.0 + - - +
62E GLU* 3.3 0.9 + - - +
64E PHE* 1.3 76.9 - - - +
66E LYS* 1.3 59.1 + - - +
67E GLY 3.2 2.2 + - - -
118H PHE* 3.1 33.4 + - - +
119H PHE* 3.3 37.8 - - + +
120H GLY* 5.6 0.2 - - - -
124H LYS* 3.2 36.6 - - + +
128H GLU* 2.8 43.0 + - - +
152H GLN* 5.5 0.6 + - - -
153H LEU 5.0 2.8 + - - -
154H LEU* 4.5 13.9 - - - +
155H ILE 5.0 3.0 - - - +
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Residues in contact with LYS 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E VAL* 3.5 41.9 + - + +
62E GLU* 3.1 43.6 + - + +
63E LYS* 4.5 2.7 - - + -
64E PHE 3.1 1.2 - - - -
65E ARG* 1.3 75.3 - - - +
67E GLY* 1.3 51.6 - - - +
68E GLU* 2.6 53.2 + - + +
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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
------------------------------------------------------------
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