Contacts of the helix formed by residues 90 - 108 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU* 5.6 1.9 - - - +
89C THR* 1.3 71.8 - - - +
91C CYS* 1.3 56.1 + - - +
93C GLU* 3.4 10.6 + - - +
94C GLN* 2.7 61.8 + - - +
56E VAL* 3.0 32.9 - - - +
59E ASN* 3.4 42.2 - - - +
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Residues in contact with CYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASN* 4.1 10.3 - - - -
61C CYS* 2.0 57.2 - - + -
71C ASP* 4.2 9.6 - - - +
89C THR* 3.0 8.2 - - - +
90C ASN* 1.3 80.2 - - - +
92C GLU* 1.3 57.2 + - - +
94C GLN* 3.9 1.9 - - - +
95C ILE* 2.8 44.3 + - + +
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ASP* 3.5 10.2 + - - +
72C ILE 3.5 17.9 - - - +
73C TYR* 3.6 20.5 - - + +
74C SER 5.2 0.6 + - - +
88C GLY* 3.2 12.7 - - - -
89C THR* 3.0 39.6 + - - +
91C CYS* 1.3 77.8 - - - +
93C GLU* 1.3 59.7 - - + +
95C ILE* 4.5 5.2 - - - -
96C CYS* 2.9 32.3 + - - +
134C CA 2.5 22.0 - - - -
71D ASP* 3.0 12.6 - - - +
72D ILE* 3.1 22.4 + - - +
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Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C CYS* 4.9 3.2 - - + +
85C GLY 3.6 19.5 - - - +
86C LYS* 3.2 25.7 + - - +
88C GLY* 2.6 39.4 + - - +
89C THR 2.8 14.7 + - - +
90C ASN* 3.9 8.2 + - - +
92C GLU* 1.3 78.6 - - + +
94C GLN* 1.3 68.2 + - - +
96C CYS* 3.9 5.5 - - - +
97C GLU* 3.1 28.8 + - - +
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Residues in contact with GLN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C CYS* 6.0 1.2 - - - -
55C LEU* 3.7 35.5 - - + +
90C ASN* 2.7 49.1 + - - +
91C CYS* 3.9 1.8 - - - +
93C GLU* 1.3 76.8 - - - +
95C ILE* 1.3 66.2 + - - +
97C GLU* 3.2 15.4 + - - +
98C CYS* 3.1 25.5 + - - -
56E VAL* 6.0 0.4 - - + -
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Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ASN 4.4 3.1 - - - +
52C TYR* 4.0 11.9 - - + +
55C LEU* 4.3 8.7 - - + -
61C CYS* 3.8 19.3 - - + -
68C THR* 3.8 46.2 - - + +
71C ASP* 4.0 22.4 - - + +
73C TYR* 3.5 22.0 - - + -
91C CYS* 2.8 35.3 + - + +
92C GLU* 3.9 3.6 - - - +
94C GLN* 1.3 72.7 - - - +
96C CYS* 1.3 64.7 + - - +
98C CYS* 3.1 7.5 + - - +
99C ASP* 3.0 21.2 + - - +
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Residues in contact with CYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 4.1 4.0 - - - +
73C TYR* 3.7 38.6 - - + -
74C SER 4.3 2.2 - - - +
75C TYR* 3.8 9.2 - - - -
84C CYS* 2.0 51.8 - - + -
85C GLY 6.0 0.2 - - - +
92C GLU 2.9 20.6 + - - +
93C GLU* 3.9 2.7 - - - +
95C ILE* 1.3 78.1 - - - +
97C GLU* 1.3 50.5 + - - +
99C ASP* 3.2 2.8 + - - +
100C ARG* 2.8 35.5 + - - +
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Residues in contact with GLU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C CYS* 4.9 1.8 - - - -
84C CYS* 3.8 14.6 + - + +
93C GLU* 3.1 18.7 + - + +
94C GLN* 3.2 21.3 + - - +
96C CYS* 1.3 74.3 - - - +
98C CYS* 1.3 65.1 + - - +
100C ARG* 2.5 43.1 + - - -
101C VAL* 3.0 36.1 + - + +
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Residues in contact with CYS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C HIS* 3.3 14.3 - - + -
51C CYS* 2.0 63.9 - - + -
52C TYR* 3.4 24.5 - - + -
55C LEU* 3.8 9.0 - - - -
94C GLN* 3.1 18.6 + - - -
95C ILE 3.3 7.9 - - - +
97C GLU* 1.3 76.3 - - - +
99C ASP* 1.3 62.0 + - - +
101C VAL* 4.2 3.4 - - - +
102C ALA* 3.3 17.2 + - - +
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Residues in contact with ASP 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ASN 4.4 3.1 + - - -
5C PHE* 3.7 25.4 - - + +
8C MET* 3.8 9.9 - - - -
48C HIS* 3.0 13.8 + - - -
52C TYR* 2.6 28.7 + - - -
73C TYR* 2.5 38.7 + - - +
95C ILE* 3.0 9.1 + - - +
96C CYS 3.4 7.9 - - - +
98C CYS* 1.3 74.9 - - - +
100C ARG* 1.3 66.5 + - - +
102C ALA* 3.2 3.1 + - - +
103C ALA* 3.0 23.9 + - - +
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 3.7 10.4 - - - -
82C ILE* 3.3 46.8 + - + +
83C THR* 4.9 1.6 - - - +
84C CYS* 4.3 8.3 - - - +
96C CYS 2.8 20.0 + - - +
97C GLU* 2.5 47.2 + - - +
99C ASP* 1.3 75.6 - - - +
101C VAL* 1.3 85.9 + - - +
103C ALA* 3.3 2.6 + - - +
104C GLU* 3.1 49.5 + - - +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 6.2 4.5 - - + -
97C GLU* 3.0 22.3 + - + +
98C CYS* 4.2 3.4 - - - +
100C ARG* 1.3 100.3 - - - +
102C ALA* 1.3 58.9 + - - +
104C GLU* 3.4 7.6 + - - +
105C CYS* 2.9 28.8 + - + +
108C ARG* 4.9 9.4 + - - +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.9 12.3 - - + -
44C CYS 4.5 7.6 - - - +
48C HIS* 3.7 27.1 - - + -
98C CYS 3.3 16.3 + - - +
99C ASP 3.2 4.9 + - - +
101C VAL* 1.3 78.3 - - - +
103C ALA* 1.3 61.8 + - - +
105C CYS* 3.1 9.3 - - - +
106C PHE* 3.1 34.4 + - + -
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 4.3 3.1 - - + -
8C MET* 3.7 40.2 - - + +
9C ILE* 4.1 2.9 - - - +
13C GLU* 3.5 19.2 - - + +
14C THR* 4.1 0.3 - - - +
82C ILE* 4.4 1.6 - - + -
99C ASP 3.0 16.3 + - - +
100C ARG 3.7 4.3 - - - +
102C ALA* 1.3 76.4 - - - +
104C GLU* 1.3 62.3 + - - +
106C PHE* 3.4 17.1 - - - +
107C ARG 3.3 14.2 + - - -
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLU* 3.8 24.1 - - + +
81C TYR* 5.2 11.3 - - - -
82C ILE* 4.3 14.6 + - + +
100C ARG* 3.1 53.2 + - + +
101C VAL* 3.8 5.6 - - - +
103C ALA* 1.3 74.5 - - - +
105C CYS* 1.3 64.5 + - - +
107C ARG* 3.2 20.8 + - - +
108C ARG* 3.0 40.4 + - - +
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Residues in contact with CYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLY 4.8 0.7 - - - -
44C CYS* 2.0 50.7 - - + -
101C VAL* 2.9 17.1 + - + +
102C ALA* 3.1 13.0 - - - +
104C GLU* 1.3 74.3 - - - +
106C PHE* 1.3 64.9 + - - +
108C ARG* 3.4 21.9 + - - +
109C ASN* 2.7 36.7 + - - +
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Residues in contact with PHE 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 4.2 10.3 - + - -
9C ILE* 3.9 33.4 - - + -
14C THR* 3.5 14.6 - - + -
22C TYR* 3.4 40.2 + + + +
41C THR* 4.0 11.7 + - + -
44C CYS* 3.7 26.2 - - + -
45C CYS* 3.8 28.5 - - - -
102C ALA* 3.1 23.5 + - + -
103C ALA* 3.4 15.7 - - - +
105C CYS* 1.3 78.9 - - - +
107C ARG* 1.3 63.3 + - - +
109C ASN* 3.4 4.2 + - - +
110C LEU* 3.2 25.5 + - - +
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Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLU* 2.8 51.9 + - - +
14C THR* 4.0 1.7 - - - +
81C TYR* 6.2 1.6 - - - -
103C ALA 3.3 8.1 + - - +
104C GLU* 3.2 32.8 + - - +
106C PHE* 1.3 81.4 - - - +
108C ARG* 1.3 90.5 + - - +
110C LEU* 3.0 37.6 + - + +
111C ASP* 4.6 1.2 - - - +
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C VAL* 4.9 8.9 + - - +
104C GLU* 3.0 32.6 + - - +
105C CYS* 3.4 29.2 + - - +
107C ARG* 1.3 95.3 - - - +
109C ASN* 1.3 63.6 + - - +
110C LEU 3.3 0.2 - - - -
111C ASP* 3.3 19.2 - - - +
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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