Contacts of the helix formed by residues 65 - 81 (chain A) in PDB entry 1CEC
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 GLU 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TYR 3.5 8.8 + - - +
64A LYS* 1.3 69.8 - - - +
66A ASP* 1.3 62.0 + - - +
68A LEU* 3.7 9.1 - - - +
69A SER* 2.8 30.8 + - - -
121A PHE* 4.6 4.0 - - - -
125A ARG* 3.0 41.1 + - - -
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 5.9 1.9 - - - -
64A LYS* 3.2 26.2 - - - +
65A GLU* 1.3 79.6 - - - +
67A GLY* 1.3 73.9 + - - +
69A SER* 2.6 24.0 + - - -
70A TYR* 3.3 15.6 - - + -
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 6.3 1.1 - - - -
53A ILE* 3.0 42.1 - - - +
54A ILE* 4.8 0.2 - - - -
64A LYS 3.2 2.6 + - - -
65A GLU 3.2 0.4 - - - -
66A ASP* 1.3 84.5 + - - +
68A LEU* 1.3 64.9 + - - +
70A TYR* 3.0 28.4 + - - +
71A ILE* 4.0 1.9 + - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE 4.3 0.2 + - - -
54A ILE* 3.6 30.9 - - + +
63A TYR* 4.1 9.0 - - + -
64A LYS 2.9 28.4 + - - +
65A GLU* 3.7 17.5 - - - +
67A GLY* 1.3 77.2 - - - +
69A SER* 1.3 56.4 + - - +
71A ILE* 3.0 12.2 + - + +
72A ASP* 2.8 32.4 + - - +
121A PHE* 3.6 39.7 - - + -
122A LEU* 4.0 12.6 - - + -
125A ARG* 3.9 22.4 - - - +
126A TYR* 4.7 1.8 - - - +
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU 2.8 15.1 + - - -
66A ASP* 2.6 25.2 + - - -
67A GLY 3.1 0.2 + - - -
68A LEU* 1.3 77.0 - - - +
70A TYR* 1.3 57.1 + - - +
72A ASP* 3.7 11.9 + - - +
73A ARG* 2.8 52.5 + - - +
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP* 3.4 25.0 - + + -
14A ILE* 4.1 27.8 - - + -
22A LYS* 3.9 10.7 + - - +
25A PHE* 3.1 56.4 - + + +
26A ASP* 3.0 24.9 + - - -
53A ILE* 5.1 1.3 - - + -
66A ASP* 3.3 28.9 - - + -
67A GLY* 3.0 15.8 + - - +
69A SER* 1.3 76.5 + - - +
71A ILE* 1.3 59.2 + - - +
73A ARG* 3.1 39.4 + - - +
74A CYS* 3.1 21.7 + - - +
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.9 24.2 - - + -
47A LEU* 4.6 5.8 - - + -
49A PHE* 4.5 5.4 - - + -
53A ILE* 5.0 1.3 - - + -
54A ILE* 3.6 33.0 - - + -
67A GLY 4.6 2.9 - - - +
68A LEU* 3.0 12.3 + - + +
70A TYR* 1.3 74.3 - - - +
72A ASP* 1.3 58.1 + - - +
74A CYS* 3.2 6.8 + - - +
75A LEU* 2.9 28.5 + - + +
85A LEU* 4.7 3.4 - - + +
87A LEU* 3.9 41.7 - - + -
122A LEU* 5.0 1.6 - - + -
126A TYR* 3.3 24.2 - - + +
133A ILE* 5.3 5.6 - - + -
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Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU 2.8 20.2 + - - +
69A SER* 3.7 8.3 - - - +
71A ILE* 1.3 76.2 - - - +
73A ARG* 1.3 58.1 + - - +
75A LEU* 3.2 8.6 + - - +
76A GLU* 2.9 33.2 + - + +
125A ARG* 2.7 35.1 + - - -
126A TYR* 2.4 36.4 + - - -
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP* 4.6 0.7 - - - -
22A LYS* 5.9 1.2 - - - +
25A PHE 4.7 0.8 + - - -
26A ASP* 2.9 31.7 + - - +
29A ILE 5.7 0.6 + - - -
69A SER* 2.8 41.7 + - - +
70A TYR* 3.1 46.6 + - - +
72A ASP* 1.3 70.8 - - - +
74A CYS* 1.3 64.6 + - - +
76A GLU* 3.0 9.4 + - - +
77A TRP* 2.9 66.8 + - + +
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Residues in contact with CYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.1 18.6 - - - -
13A TRP* 3.8 25.6 - - + -
34A ILE* 4.4 9.6 - - - -
45A VAL* 4.6 1.8 - - - -
47A LEU* 4.1 11.4 - - + -
70A TYR 3.1 19.8 + - - +
71A ILE 3.6 4.3 - - - +
73A ARG* 1.3 75.8 - - - +
75A LEU* 1.3 62.6 + - - +
77A TRP* 3.1 13.8 + - - +
78A CYS* 2.9 36.2 + - - -
85A LEU* 3.9 14.6 - - + -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 2.9 14.7 + - + +
72A ASP* 3.5 9.2 - - - +
74A CYS* 1.3 79.1 - - - +
76A GLU* 1.3 66.9 + - - +
78A CYS* 3.3 2.5 + - + +
79A LYS* 3.0 43.8 + - + +
85A LEU* 3.7 15.2 - - + +
126A TYR* 3.4 36.1 - - + -
129A GLU* 4.0 31.9 - - + -
132A HIS* 4.1 20.0 - - + +
133A ILE* 4.4 12.1 - - + -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASP* 2.9 21.1 + - + +
73A ARG* 3.0 11.0 + - - +
75A LEU* 1.3 82.0 - - - +
77A TRP* 1.3 66.8 + - + +
79A LYS* 2.9 39.8 + - - +
80A LYS* 3.1 22.2 + - - +
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Residues in contact with TRP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP* 3.9 13.7 - + - -
29A ILE* 3.7 38.4 - - + -
30A THR* 3.9 7.0 - - - -
31A GLU* 3.7 45.7 + - + +
34A ILE* 3.8 32.3 - - + -
73A ARG* 2.9 50.6 + - + +
74A CYS* 3.6 17.0 - - + +
76A GLU* 1.3 79.7 - - + +
78A CYS* 1.3 63.4 + - - +
80A LYS* 3.3 7.2 + - + +
81A TYR* 3.2 30.5 + - - -
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Residues in contact with CYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 4.3 12.1 - - - -
45A VAL* 3.9 28.7 - - - -
74A CYS* 2.9 24.6 + - - +
75A LEU* 3.7 7.6 - - + +
77A TRP* 1.3 74.5 - - - +
79A LYS* 1.3 58.8 + - - +
81A TYR 3.1 1.2 + - - -
82A ASN 2.8 10.7 + - - -
83A LEU* 2.8 53.2 + - + +
84A GLY 4.0 8.7 - - - +
85A LEU* 4.1 13.9 - - + -
132A HIS* 5.3 0.4 - - + +
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.0 33.6 + - + +
76A GLU* 2.9 41.0 + - - +
78A CYS* 1.3 74.5 - - - +
80A LYS* 1.3 62.4 + - - +
81A TYR 3.2 1.2 + - - -
82A ASN* 3.3 11.3 + - - -
129A GLU* 3.6 20.4 + - - +
132A HIS* 3.9 37.6 + - + +
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 2.7 37.5 + - - +
76A GLU 3.1 13.0 + - - +
77A TRP* 3.5 10.5 - - + +
78A CYS 3.2 0.2 - - - -
79A LYS* 1.3 78.0 - - - +
81A TYR* 1.3 81.3 + - + +
82A ASN 3.5 0.2 - - - -
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 2.8 40.1 + - + -
34A ILE* 3.7 12.3 - - + -
35A GLU* 3.5 42.3 + - + +
38A ALA* 3.6 30.0 - - + +
77A TRP 3.2 22.5 + - - +
78A CYS 3.1 3.2 + - - -
80A LYS* 1.3 102.0 + - + +
82A ASN* 1.3 70.3 + - - +
83A LEU* 3.3 15.3 + - + +
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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