Contacts of the helix formed by residues 60 - 76 (chain E) in PDB entry 5W97
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 60 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LYS* 5.9 0.9 + - - -
44D GLU* 3.5 3.6 - - - +
48D TRP* 3.7 3.1 - - - -
63D LYS* 3.1 27.8 + - - -
26E ALA* 6.1 1.0 - - - +
29E LEU* 4.7 6.1 - - + +
55E CYS* 2.8 33.8 + - - +
58E LEU* 4.0 13.7 - - + +
59E ASN* 1.3 75.0 - - - +
61E PHE* 1.3 59.8 + - - +
62E ALA* 3.3 5.4 + - - +
63E SER* 2.6 42.4 + - - -
64E ALA 3.8 2.3 + - - -
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Residues in contact with PHE 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLU* 2.7 21.7 + - + +
48D TRP* 3.5 49.1 - + + +
51D LEU* 4.8 0.7 - - + -
56D LYS* 3.4 60.3 - - + -
59D LEU* 4.3 15.3 - - + -
60D TYR* 5.2 0.9 - - + -
60E ASP* 1.3 71.8 - - - +
62E ALA* 1.3 63.1 + - - +
64E ALA* 3.0 23.9 + - - +
65E VAL* 3.3 33.6 + - + +
97E GLY 4.1 2.7 - - - -
98E ILE* 4.1 4.7 - - + -
99E SER 3.9 20.6 - - - -
104E LEU* 4.1 6.7 - - + -
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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
----------------------------------------------------------
44D GLU* 4.0 2.5 + - - +
59D LEU* 3.6 18.2 - - + +
60D TYR* 3.8 15.1 - - - +
63D LYS* 3.6 31.4 - - + -
64D PHE* 3.4 10.1 - - + -
60E ASP* 3.3 5.7 + - - +
61E PHE* 1.3 85.3 - - - +
63E SER* 1.3 62.3 + - - +
65E VAL* 3.2 7.3 + - - +
66E ARG 3.1 17.2 + - - -
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Residues in contact with SER 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 4.0 18.7 - - - +
63D LYS* 3.7 11.1 + - - -
64D PHE* 4.0 11.0 - - - -
29E LEU* 4.4 9.6 - - - +
30E ARG* 6.0 1.4 - - - +
55E CYS* 4.0 14.1 - - - -
60E ASP* 2.6 34.3 + - - -
62E ALA* 1.3 76.2 - - - +
64E ALA* 1.3 55.9 + - - +
66E ARG* 3.6 2.5 - - - +
67E ILE* 2.9 33.3 + - - +
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TRP* 4.5 3.6 - - + -
52E LEU* 3.6 26.3 - - + +
55E CYS* 3.8 19.0 - - + -
60E ASP 3.8 2.4 + - - +
61E PHE* 3.0 18.0 + - + +
63E SER* 1.3 76.2 - - - +
65E VAL* 1.3 62.7 + - - +
67E ILE* 3.4 1.4 + - - -
68E LEU* 3.4 23.9 + - - +
98E ILE* 4.1 25.8 - - + -
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Residues in contact with VAL 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D TYR* 4.0 9.9 - - + -
61E PHE* 3.5 43.7 - - + +
62E ALA 3.2 6.4 + - - +
64E ALA* 1.3 73.0 - - - +
66E ARG* 1.3 63.5 + - - +
68E LEU* 3.1 12.4 + - - +
69E GLU* 3.0 22.2 + - - +
98E ILE* 5.0 0.9 - - + -
99E SER 3.8 12.1 - - - +
101E PRO* 3.9 20.2 - - + -
104E LEU* 3.8 10.1 - - + -
106E LEU* 3.8 28.0 - - + -
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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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16D TYR* 3.9 2.6 + - - -
17D VAL 4.6 3.4 + - - -
18D ASP* 2.9 28.5 + - - +
19D ARG 4.9 0.8 - - - +
22D TYR 5.3 0.2 + - - -
23D PRO* 2.7 39.6 + - + +
24D LEU* 3.7 8.3 - - + -
25D PRO* 4.6 1.0 - - - +
60D TYR* 2.8 27.5 + - - -
64D PHE* 3.5 40.5 - - + -
66D GLU 2.9 19.4 + - - -
67D SER* 4.1 1.4 - - - +
68D PHE* 3.8 14.9 - - + -
71D MET* 3.5 14.7 - - - +
62E ALA 3.1 4.8 + - - -
63E SER 3.6 7.2 - - - +
65E VAL* 1.3 73.4 - - - +
67E ILE* 1.3 67.1 + - - +
69E GLU* 3.2 13.4 + - - +
70E VAL* 3.0 21.7 + - - +
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Residues in contact with ILE 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PRO* 6.4 0.2 - - - -
24D LEU* 4.7 10.5 - - + -
29E LEU* 4.8 2.9 - - + -
33E MET* 3.7 43.5 - - + -
48E ILE* 4.0 31.6 - - + -
51E ALA* 4.3 17.3 - - + +
52E LEU* 4.4 7.0 - - + -
55E CYS* 3.8 22.4 - - - -
63E SER 2.9 22.2 + - - +
64E ALA* 3.7 6.1 - - - +
65E VAL 3.3 0.2 - - - -
66E ARG* 1.3 77.4 - - - +
68E LEU* 1.3 60.7 + - - +
70E VAL* 3.3 9.8 + - - +
71E VAL* 3.2 19.9 + - - +
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Residues in contact with LEU 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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48E ILE* 4.4 11.2 - - + -
52E LEU* 4.4 8.5 - - + -
64E ALA 3.4 13.9 + - - +
65E VAL* 3.1 9.4 + - - +
67E ILE* 1.3 74.2 - - - +
69E GLU* 1.3 63.8 + - - +
71E VAL* 3.4 7.8 + - + +
72E LYS* 3.3 15.9 + - - +
82E TYR* 3.4 18.4 - - + +
85E VAL* 5.7 0.4 - - + -
86E ILE* 4.2 12.1 - - + -
89E LEU* 4.0 27.4 - - + -
93E LEU* 4.3 9.6 - - + -
98E ILE* 4.2 12.8 - - + -
99E SER 4.2 13.9 - - - +
100E THR* 4.2 10.5 - - + -
101E PRO* 3.9 24.9 - - + -
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Residues in contact with GLU 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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60D TYR* 2.5 38.4 + - - -
67D SER* 3.4 9.0 - - - -
68D PHE* 3.0 47.4 + - + +
69D ALA 4.6 0.2 + - - -
65E VAL* 3.0 15.1 + - - +
66E ARG* 3.2 17.1 + - - +
68E LEU* 1.3 76.3 - - - +
70E VAL* 1.3 56.7 + - - +
72E LYS* 3.3 10.3 + - - +
73E ASP* 3.0 27.9 + - - +
101E PRO* 3.6 22.6 - - + +
106E LEU* 4.5 7.5 - - - +
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Residues in contact with VAL 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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20D ARG 4.1 6.7 - - - +
23D PRO* 3.5 33.4 - - + -
68D PHE* 3.7 13.2 - - + -
33E MET* 3.6 27.6 - - + -
37E VAL* 3.7 18.2 - - + -
43E PRO* 6.0 3.4 - - + -
66E ARG 3.0 12.5 + - - +
67E ILE* 3.4 12.3 - - - +
68E LEU 3.3 0.4 - - - -
69E GLU* 1.3 72.5 - - - +
71E VAL* 1.3 66.9 + - + +
73E ASP* 3.7 5.7 - - + +
74E LYS* 2.9 36.0 + - + +
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Residues in contact with VAL 71 (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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42E VAL* 3.7 23.9 - - + +
43E PRO* 5.0 6.1 - - + +
48E ILE* 3.7 37.0 - - + -
67E ILE 3.2 18.0 + - - +
68E LEU* 3.6 11.9 - - + +
69E GLU 3.3 0.2 - - - -
70E VAL* 1.3 80.1 - - + +
72E LYS* 1.3 63.4 + - - +
74E LYS* 3.4 5.0 + - - +
75E ALA* 3.3 18.9 + - - +
81E ILE* 5.4 0.2 - - + -
82E TYR* 4.1 11.7 - - + -
85E VAL* 3.9 29.4 - - + -
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Residues in contact with LYS 72 (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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68E LEU 3.3 3.9 + - - +
69E GLU* 3.3 12.3 + - - +
71E VAL* 1.3 78.6 - - - +
73E ASP* 1.3 63.5 + - - +
75E ALA* 3.2 17.9 - - - +
76E GLY 3.6 5.4 + - - +
79E LYS* 6.0 7.9 - - - +
82E TYR* 3.6 48.4 - - + -
101E PRO* 5.9 1.1 - - - -
102E GLU* 3.0 34.5 + - - +
107E ASP* 5.2 7.8 + - - +
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Residues in contact with ASP 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 4.8 1.6 - - - +
20D ARG* 3.0 49.1 + - - +
68D PHE* 3.7 19.8 - - + -
72D ASN* 3.1 25.8 + - - -
69E GLU 3.0 16.9 + - - +
70E VAL* 3.7 5.7 - - + +
71E VAL 3.2 0.4 - - - -
72E LYS* 1.3 79.8 - - - +
74E LYS* 1.3 65.9 + - - +
76E GLY* 3.1 15.8 + - - -
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Residues in contact with LYS 74 (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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49B LYS 6.0 0.4 - - - -
50B LEU* 3.6 17.4 - - - +
51B THR* 2.8 41.6 + - - +
20D ARG* 5.7 3.1 - - - +
37E VAL* 2.8 47.2 + - + +
39E TYR 3.0 23.6 + - - -
41E LEU 3.6 15.8 - - - +
42E VAL* 3.7 19.8 - - + +
43E PRO* 5.2 4.9 - - + -
70E VAL* 2.9 23.0 + - + +
71E VAL* 3.9 5.6 - - - +
72E LYS 3.4 0.2 - - - -
73E ASP* 1.3 79.6 + - - +
75E ALA* 1.3 60.6 + - - +
76E GLY 3.4 0.3 + - - -
12I LEU* 4.7 1.6 - - - +
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Residues in contact with ALA 75 (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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50B LEU* 3.8 2.0 - - - +
42E VAL* 3.6 10.3 - - + +
71E VAL 3.3 9.2 + - - +
72E LYS* 3.2 17.4 + - + +
73E ASP 3.1 0.4 - - - -
74E LYS* 1.3 79.2 - - - +
76E GLY* 1.3 63.4 + - - +
77E PRO* 3.3 3.6 - - - +
78E HIS* 3.0 42.9 + - - +
79E LYS* 5.9 0.2 - - - -
81E ILE* 4.0 20.1 - - + +
82E TYR* 4.9 4.9 - - + +
12I LEU* 5.0 0.4 - - - -
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Residues in contact with GLY 76 (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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49B LYS* 4.3 17.0 - - - -
50B LEU* 4.1 6.7 - - - -
72E LYS 3.6 4.4 + - - +
73E ASP* 3.1 16.4 + - - -
74E LYS 3.2 0.6 - - - -
75E ALA* 1.3 78.4 - - - +
77E PRO* 1.3 69.2 - - - +
78E HIS 3.3 1.6 + - - -
79E LYS* 3.3 15.9 + - - -
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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
------------------------------------------------------------
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