Contacts of the helix formed by residues 90 - 108 (chain E) in PDB entry 1BJJ
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 ASN 90 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASN 5.9 1.2 + - - -
61D CYS 4.5 5.5 + - - -
67D ASN* 3.7 48.7 - - - +
69D LYS* 4.7 5.5 - - - +
55E LEU* 5.4 2.3 - - - +
59E ASN* 6.0 0.3 + - - -
61E CYS* 5.1 2.4 - - - -
88E GLY 4.2 0.4 + - - -
89E THR* 1.3 72.9 - - - +
91E CYS* 1.3 63.3 + - - +
93E GLU* 3.8 8.6 + - - -
94E GLN* 2.8 61.6 + - - +
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Residues in contact with CYS 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ASN* 4.2 12.1 - - - -
61E CYS* 2.0 57.2 - - + -
71E ASP* 3.9 14.1 - - - +
89E THR* 3.0 6.5 + - - +
90E ASN* 1.3 80.0 - - - +
92E GLU* 1.3 66.8 + - - +
94E GLN* 4.5 1.6 - - - -
95E ILE* 2.9 32.5 + - + +
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Residues in contact with GLU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASP* 4.3 1.1 - - - -
72A ILE* 2.8 28.6 + - - +
134A CA 2.5 25.6 - - - -
71E ASP* 3.8 11.2 - - - +
72E ILE 2.8 18.6 - - - +
73E TYR* 3.6 20.0 - - + +
74E SER 5.1 1.1 - - - +
86E LYS 6.0 0.2 - - - -
88E GLY* 3.6 7.8 - - - -
89E THR* 2.8 50.7 + - - +
91E CYS* 1.3 78.5 - - - +
93E GLU* 1.3 58.2 + - - +
95E ILE* 3.9 3.3 - - - +
96E CYS* 2.9 32.1 + - - +
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Residues in contact with GLU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LYS* 4.3 3.1 + - - -
84E CYS* 4.9 4.4 - - + +
85E GLY 3.5 20.9 - - - +
86E LYS* 3.0 41.1 + - - +
88E GLY 3.4 21.2 - - - +
89E THR 2.9 20.2 + - - +
90E ASN* 3.9 6.0 + - - +
92E GLU* 1.3 75.1 - - - +
94E GLN* 1.3 73.2 + - - +
96E CYS* 3.8 6.1 + - - +
97E GLU* 3.2 25.6 + - - +
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Residues in contact with GLN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D VAL 4.4 15.6 + - - +
59D ASN* 5.3 8.0 - - - +
55E LEU* 3.9 30.2 - - + +
90E ASN* 2.8 50.0 + - - +
91E CYS* 3.8 3.8 - - - +
93E GLU* 1.3 85.7 + - - +
95E ILE* 1.3 65.4 + - - +
97E GLU* 2.9 23.4 + - - +
98E CYS* 3.1 17.0 + - - -
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Residues in contact with ILE 95 (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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1E ASN 4.4 1.1 - - - +
52E TYR* 3.9 7.4 - - + +
55E LEU* 4.6 5.8 - - + -
61E CYS* 4.0 14.1 - - + -
67E ASN 4.0 5.8 - - - +
68E THR* 3.4 58.3 - - + +
71E ASP* 4.2 13.2 - - + +
73E TYR* 3.7 22.4 - - + -
91E CYS* 2.9 24.3 + - + +
92E GLU* 3.9 3.4 - - - +
94E GLN* 1.3 76.9 - - - +
96E CYS* 1.3 65.1 + - - +
98E CYS* 3.1 10.9 + - - +
99E ASP* 3.0 27.8 + - - +
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Residues in contact with CYS 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E MET* 4.1 4.5 - - - -
73E TYR* 3.8 39.7 - - + -
74E SER 4.1 2.2 - - - +
75E TYR* 3.8 9.0 - - - -
84E CYS* 2.0 53.6 - - + -
85E GLY 5.8 0.2 - - - +
92E GLU 2.9 19.7 + - - +
93E GLU* 3.8 3.8 - - - +
94E GLN 3.2 0.2 - - - -
95E ILE* 1.3 78.2 - - - +
97E GLU* 1.3 55.9 + - - +
99E ASP* 3.2 2.9 + - - +
100E ARG* 2.8 30.5 + - - +
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Residues in contact with GLU 97 (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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56D VAL* 6.6 0.2 - - + -
51E CYS* 5.0 0.2 - - - -
84E CYS* 3.7 14.4 - - + +
93E GLU 3.2 13.5 + - - +
94E GLN* 2.9 20.9 + - - +
96E CYS* 1.3 79.2 - - - +
98E CYS* 1.3 64.0 + - - +
100E ARG* 2.8 43.1 + - - +
101E VAL* 3.0 35.8 + - + +
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Residues in contact with CYS 98 (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 HIS* 3.2 14.7 - - - +
51E CYS* 2.0 63.9 - - + -
52E TYR* 3.5 23.3 - - + -
55E LEU* 3.9 9.0 - - - -
94E GLN* 3.1 17.3 + - - -
95E ILE 3.4 7.2 - - - +
97E GLU* 1.3 75.6 - - - +
99E ASP* 1.3 62.3 + - - +
101E VAL* 3.9 4.5 - - - +
102E ALA* 3.2 17.3 + - - +
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Residues in contact with ASP 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E ASN 4.4 2.3 + - - +
5E PHE* 3.6 24.3 - - + +
8E MET* 3.6 9.9 - - - -
48E HIS* 2.8 17.7 + - - -
52E TYR* 2.6 30.0 + - - -
73E TYR* 2.7 39.5 + - - +
95E ILE* 3.0 7.6 + - - +
96E CYS 3.5 6.3 - - - +
98E CYS* 1.3 74.7 - - - +
100E ARG* 1.3 65.2 + - - +
102E ALA 3.3 0.9 + - - -
103E ALA* 2.9 26.5 + - - +
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Residues in contact with ARG 100 (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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8E MET* 3.7 10.2 - - + -
82E ILE* 2.9 46.6 + - + +
83E THR* 4.6 2.7 - - - +
84E CYS* 4.1 10.3 - - - +
96E CYS 2.8 20.4 + - - +
97E GLU* 2.8 40.1 + - - +
99E ASP* 1.3 74.6 - - - +
101E VAL* 1.3 78.7 + - - +
103E ALA* 3.4 3.3 + - - +
104E GLU* 3.2 55.3 + - - +
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Residues in contact with VAL 101 (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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47E VAL* 5.7 9.2 - - + -
97E GLU* 3.0 24.6 + - + +
98E CYS* 3.9 4.9 - - - +
100E ARG* 1.3 105.5 - - - +
102E ALA* 1.3 58.1 + - - +
104E GLU* 3.5 6.1 + - - +
105E CYS* 3.0 28.5 + - + +
108E ARG* 4.4 10.0 + - - +
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Residues in contact with ALA 102 (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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5E PHE* 3.9 11.2 - - + -
44E CYS* 4.8 7.2 - - + +
48E HIS* 3.5 38.6 - - + -
98E CYS 3.2 4.7 + - - +
99E ASP 3.8 2.9 - - - +
101E VAL* 1.3 77.2 - - - +
103E ALA* 1.3 67.2 + - - +
105E CYS* 3.1 9.4 + - - +
106E PHE* 2.9 35.7 + - + -
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Residues in contact with ALA 103 (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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5E PHE* 4.2 4.4 - - + -
8E MET* 3.7 39.3 - - + +
9E ILE* 4.3 2.5 - - - +
13E GLU* 3.0 21.6 - - + +
14E THR* 4.0 0.9 - - - +
82E ILE* 4.5 3.8 - - + -
99E ASP 2.9 17.0 + - - +
100E ARG 3.4 5.4 + - - +
102E ALA* 1.3 76.1 - - - +
104E GLU* 1.3 60.4 + - - +
106E PHE* 3.3 26.1 - - - +
107E ARG 3.5 1.6 + - - -
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Residues in contact with GLU 104 (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 GLU* 3.3 29.7 - - - +
81E TYR* 5.4 7.6 - - - -
82E ILE* 4.6 12.8 + - + +
100E ARG* 3.2 47.6 + - + +
101E VAL* 3.8 7.9 - - - +
102E ALA 3.2 0.4 - - - -
103E ALA* 1.3 71.4 - - + +
105E CYS* 1.3 62.5 + - - +
106E PHE 3.0 2.0 - - - -
107E ARG* 2.8 30.5 + - - +
108E ARG* 2.9 23.7 + - - +
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Residues in contact with CYS 105 (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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40E GLY 4.7 0.4 - - - -
43E ARG* 6.2 0.2 - - - -
44E CYS* 2.0 51.3 - - + -
101E VAL* 3.0 17.2 + - + +
102E ALA* 3.3 10.5 - - - +
104E GLU* 1.3 75.7 - - - +
106E PHE* 1.3 61.0 + - - +
108E ARG* 3.4 28.0 + - - +
109E ASN* 2.6 38.8 + - - -
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Residues in contact with PHE 106 (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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5E PHE* 4.2 14.4 - + - -
9E ILE* 3.8 37.0 - - + -
14E THR* 3.6 14.8 - - + -
22E TYR* 3.7 39.9 + + + +
41E THR* 4.0 11.3 + - + +
44E CYS* 3.7 23.1 - - + -
45E CYS* 3.6 33.9 - - - -
102E ALA* 2.9 20.4 + - + -
103E ALA* 3.3 11.2 - - - +
104E GLU 3.0 0.2 - - - -
105E CYS* 1.3 77.0 - - - +
107E ARG* 1.3 61.3 + - - +
109E ASN* 3.3 5.0 + - - +
110E LEU* 3.1 25.1 + - - +
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Residues in contact with ARG 107 (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 GLU* 2.9 56.7 + - + +
14E THR* 4.1 5.3 - - - +
103E ALA 3.5 1.4 + - - -
104E GLU* 2.8 26.3 + - - +
106E PHE* 1.3 77.7 - - - +
108E ARG* 1.3 86.4 + - - +
110E LEU* 3.0 34.3 + - + +
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Residues in contact with ARG 108 (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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101E VAL* 4.4 10.5 + - - +
104E GLU* 2.9 17.9 + - - +
105E CYS* 3.7 45.0 - - - +
106E PHE 3.4 0.2 - - - -
107E ARG* 1.3 98.3 - - - +
109E ASN* 1.3 65.0 + - - +
110E LEU 3.7 0.2 + - - -
111E ASP* 3.2 13.7 + - - +
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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