Contacts of the helix formed by residues 90 - 108 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 5.3 3.5 - - - +
89D THR* 1.3 72.0 - - - +
91D CYS* 1.3 63.7 + - - +
93D GLU* 3.9 6.0 + - - +
94D GLN* 2.9 52.4 + - - +
56F VAL* 3.2 44.1 - - + +
59F ASN* 3.4 29.5 - - - +
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Residues in contact with CYS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASN* 4.3 5.6 - - - -
61D CYS* 2.0 59.2 - - + -
71D ASP* 4.0 14.6 - - - +
89D THR* 3.1 6.1 + - - +
90D ASN* 1.3 81.3 - - - +
92D GLU* 1.3 60.5 + - - +
94D GLN* 3.7 1.7 - - - +
95D ILE* 2.8 38.8 + - + +
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C SER 3.8 3.8 - - - +
71C ASP* 3.2 0.6 - - - +
72C ILE* 2.6 32.0 + - - +
134C CA 2.4 32.1 - - - -
71D ASP* 3.7 10.5 - - - +
72D ILE 3.2 7.3 - - - +
73D TYR* 3.6 20.9 - - + +
74D SER 5.3 0.6 + - - +
85D GLY 5.7 0.7 - - - -
86D LYS 6.0 0.2 - - - -
88D GLY* 3.1 14.4 - - - -
89D THR* 2.8 44.2 + - - +
91D CYS* 1.3 76.2 - - - +
93D GLU* 1.3 58.0 - - + +
95D ILE* 4.8 4.9 - - - -
96D CYS* 3.0 30.1 + - - +
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Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D CYS* 4.8 3.0 - - + +
85D GLY 3.7 20.4 - - - +
86D LYS* 2.7 36.1 + - - -
88D GLY 2.9 23.5 + - - +
89D THR 2.9 16.3 + - - +
90D ASN* 3.9 7.0 + - - +
92D GLU* 1.3 77.4 - - - +
94D GLN* 1.3 65.9 + - - +
96D CYS* 3.5 6.5 + - - +
97D GLU* 3.1 27.5 + - - +
59F ASN* 4.6 7.4 + - - +
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Residues in contact with GLN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 3.1 38.8 - - + -
90D ASN* 2.9 38.9 + - - +
91D CYS 3.7 2.5 - - - +
93D GLU* 1.3 78.1 - - - +
95D ILE* 1.3 66.2 + - - +
97D GLU* 3.1 24.9 + - - +
98D CYS* 3.1 18.9 + - - -
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Residues in contact with ILE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ASN 4.4 2.0 - - - +
52D TYR* 4.1 7.6 - - + +
55D LEU* 3.8 20.0 - - + -
61D CYS* 4.1 9.2 - - + -
67D ASN 4.0 1.1 - - - -
68D THR* 3.5 45.5 - - + +
71D ASP* 3.7 25.8 - - + +
73D TYR* 3.7 20.6 - - + -
91D CYS 2.8 27.6 + - - +
92D GLU* 4.0 3.1 - - - +
94D GLN* 1.3 73.5 - - - +
96D CYS* 1.3 63.2 + - - +
98D CYS* 3.2 6.0 + - - +
99D ASP* 3.1 27.8 + - - +
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Residues in contact with CYS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D MET* 4.1 4.7 - - - -
73D TYR* 3.8 36.1 - - + -
74D SER 4.3 2.2 - - - +
75D TYR* 3.9 9.4 - - - -
84D CYS* 2.0 52.0 - - + -
85D GLY 5.8 0.2 - - - +
92D GLU 3.0 20.3 + - - +
93D GLU* 3.6 5.4 - - - +
95D ILE* 1.3 78.2 - - - +
97D GLU* 1.3 55.2 + - - +
99D ASP* 3.2 2.4 + - - +
100D ARG* 2.8 27.9 + - - +
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D CYS* 3.7 17.0 + - + +
93D GLU 3.1 16.9 + - - +
94D GLN* 3.1 22.8 + - - +
96D CYS* 1.3 72.8 - - - +
98D CYS* 1.3 67.7 + - - +
100D ARG* 2.6 42.0 + - - +
101D VAL* 3.0 35.0 + - + +
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Residues in contact with CYS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D HIS* 3.2 18.6 - - + -
51D CYS* 2.0 66.4 - - + -
52D TYR* 3.7 21.5 - - + -
55D LEU* 4.3 7.4 - - - -
94D GLN* 3.1 17.1 + - - -
95D ILE 3.5 6.3 - - - +
97D GLU* 1.3 77.8 - - - +
99D ASP* 1.3 62.6 + - - +
101D VAL* 4.2 3.2 - - - +
102D ALA* 3.2 14.2 + - - +
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ASN 4.4 3.1 + - - -
5D PHE* 3.5 24.8 - - + +
8D MET* 3.8 9.4 - - - -
48D HIS* 3.1 13.3 + - - -
52D TYR* 2.7 28.2 + - - -
73D TYR* 2.6 38.5 + - - +
95D ILE* 3.1 12.4 + - - +
96D CYS 3.4 7.6 - - - +
98D CYS* 1.3 75.3 - - - +
100D ARG* 1.3 65.9 + - - +
102D ALA* 3.2 4.0 + - - +
103D ALA* 3.0 21.7 + - - +
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D MET* 3.6 11.5 - - - -
82D ILE* 3.0 47.3 - - + +
83D THR* 4.9 1.3 - - - +
84D CYS* 4.3 8.1 - - - +
96D CYS 2.8 19.5 + - - +
97D GLU* 2.6 41.4 + - - +
99D ASP* 1.3 73.5 - - - +
101D VAL* 1.3 81.0 + - - +
103D ALA* 3.2 2.8 + - - +
104D GLU* 3.1 51.3 + - - +
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 6.2 4.0 - - + -
97D GLU* 3.0 21.1 + - - +
98D CYS* 4.2 3.8 - - - +
100D ARG* 1.3 101.7 - - - +
102D ALA* 1.3 57.5 + - - +
104D GLU* 3.6 8.1 + - - +
105D CYS* 2.9 29.6 + - + +
108D ARG* 4.5 6.8 + - - +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 3.8 11.2 - - + -
44D CYS* 4.8 7.0 - - - +
48D HIS* 3.5 27.1 - - + -
98D CYS 3.2 17.0 + - - +
99D ASP 3.2 5.2 + - - +
101D VAL* 1.3 77.6 - - - +
103D ALA* 1.3 66.8 + - - +
105D CYS* 3.0 8.8 + - - +
106D PHE* 3.0 35.6 + - + -
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 4.2 4.8 - - + -
8D MET* 3.8 39.5 - - + +
9D ILE* 4.1 4.3 - - - +
13D GLU* 3.6 17.8 - - + +
14D THR* 4.0 1.0 - - - +
82D ILE* 4.4 2.2 - - + -
99D ASP 3.0 11.9 + - - +
100D ARG 3.5 7.9 - - - +
102D ALA* 1.3 77.8 - - - +
104D GLU* 1.3 62.8 + - - +
106D PHE* 3.3 21.3 + - - +
107D ARG 3.3 7.8 + - - -
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLU* 4.1 25.9 - - + +
81D TYR* 5.1 10.1 - - - -
82D ILE* 4.4 14.2 + - + +
100D ARG* 3.1 51.6 + - + +
101D VAL* 4.0 5.7 - - - +
103D ALA* 1.3 72.0 - - + +
105D CYS* 1.3 59.8 + - - +
107D ARG* 3.1 21.7 + - - +
108D ARG* 2.9 42.5 + - - +
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Residues in contact with CYS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLY 4.6 0.7 - - - -
44D CYS* 2.0 51.7 - - + -
47D VAL* 6.4 0.7 - - - -
101D VAL* 2.9 18.2 + - + +
102D ALA* 3.2 11.2 - - - +
104D GLU* 1.3 76.4 - - - +
106D PHE* 1.3 60.4 + - - +
108D ARG* 3.6 24.8 + - - +
109D ASN* 2.9 38.4 + - - -
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Residues in contact with PHE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 4.5 8.5 - + - -
9D ILE* 4.0 35.4 - - + -
14D THR* 3.6 13.2 - - + -
22D TYR* 3.9 36.4 + + + +
41D THR* 3.7 13.6 + - + -
44D CYS* 3.3 31.4 - - + -
45D CYS* 3.7 26.2 - - - -
48D HIS* 6.3 0.4 - - + -
102D ALA* 3.0 25.6 + - + -
103D ALA* 3.4 13.9 - - - +
105D CYS* 1.3 73.6 - - - +
107D ARG* 1.3 67.4 + - - +
109D ASN* 3.2 5.0 + - - +
110D LEU* 3.1 25.3 + - - +
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Residues in contact with ARG 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLU* 2.7 52.8 + - - +
14D THR* 4.0 2.0 - - - +
81D TYR* 6.4 0.2 - - - -
103D ALA 3.3 6.3 + - - +
104D GLU* 3.1 31.7 + - - +
106D PHE* 1.3 80.0 - - - +
108D ARG* 1.3 90.8 + - - +
109D ASN 3.1 0.9 + - - -
110D LEU* 3.1 33.8 + - + +
111D ASP* 5.7 0.3 - - - -
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Residues in contact with ARG 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL* 4.5 7.1 + - - +
104D GLU* 2.9 26.1 + - - +
105D CYS* 3.6 43.1 + - - +
107D ARG* 1.3 95.4 - - - +
109D ASN* 1.3 64.7 + - - +
110D LEU 3.4 0.2 - - - -
111D ASP* 2.9 19.1 - - - +
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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