Contacts of the helix formed by residues 80 - 97 (chain A) in PDB entry 3BJT
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 THR 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLY* 1.3 75.4 - - - -
81A HIS* 1.3 66.1 + - - +
82A GLU* 3.5 11.2 + - - +
83A TYR* 3.2 21.3 + - - +
84A HIS* 3.0 26.2 + - - -
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Residues in contact with HIS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 4.0 15.9 - + - -
79A GLY 5.7 0.4 - - - -
80A THR* 1.3 73.3 - - - +
82A GLU* 1.3 65.3 + - - +
84A HIS* 4.6 2.2 - - - +
85A ALA* 3.0 25.1 + - - +
224A LYS* 5.6 1.1 - - - -
227A GLN* 3.5 31.6 + - + -
228A ASP* 2.8 27.5 + - - -
231A PHE* 3.4 37.8 - + + +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A THR* 3.1 10.8 + - - +
81A HIS* 1.3 78.0 - - - +
83A TYR* 1.3 65.4 + - - +
85A ALA* 3.0 17.1 + - - +
86A GLU* 3.1 20.3 + - - +
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Residues in contact with TYR 83 (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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51A ILE 5.0 2.0 + - - -
52A GLY* 4.1 17.7 - - - -
53A PRO* 4.2 8.3 - - - +
56A ARG* 3.0 74.7 + - - +
78A HIS* 5.7 0.9 - - + -
79A GLY* 4.1 13.7 - - - -
80A THR* 3.2 20.0 + - - +
82A GLU* 1.3 81.0 - - - +
84A HIS* 1.3 87.5 + + - +
86A GLU* 3.1 9.1 + - - -
87A THR* 3.2 8.2 + - - -
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Residues in contact with HIS 84 (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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74A LEU* 4.1 19.0 - - + +
75A ASN 3.5 15.1 + - - -
76A PHE* 3.5 48.7 - + + -
78A HIS 2.8 29.5 + - - -
79A GLY* 3.2 17.6 + - - -
80A THR 3.0 18.8 + - - +
81A HIS 4.1 3.6 - - - +
83A TYR* 1.3 91.4 - + - +
85A ALA* 1.3 60.6 + - - +
86A GLU 3.2 0.2 - - - -
87A THR* 3.4 9.0 + - - -
88A ILE* 3.1 28.7 + - - +
231A PHE* 4.2 5.6 - - + -
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Residues in contact with ALA 85 (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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81A HIS 3.0 17.8 + - - +
82A GLU* 3.0 8.7 + - - +
84A HIS* 1.3 77.1 - - - +
86A GLU* 1.3 63.9 + - - +
88A ILE* 3.5 3.4 + - - +
89A LYS* 3.1 21.1 + - - +
231A PHE* 3.8 16.6 - - + -
235A GLN* 4.3 19.1 - - - +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 3.5 31.9 + - - +
82A GLU* 3.1 18.8 + - - +
83A TYR* 3.1 3.4 + - - +
85A ALA* 1.3 76.7 - - - +
87A THR* 1.3 65.8 + - - +
89A LYS* 3.1 16.1 + - + +
90A ASN* 3.0 38.4 + - - +
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Residues in contact with THR 87 (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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51A ILE* 3.8 28.0 - - + +
56A ARG* 2.8 30.9 + - + +
61A LEU* 5.9 0.7 - - + -
74A LEU* 3.3 28.3 - - + -
83A TYR* 3.2 15.3 + - - -
84A HIS* 3.6 13.4 - - - -
86A GLU* 1.3 76.9 - - - +
88A ILE* 1.3 62.8 + - - +
90A ASN* 3.2 7.8 + - - +
91A VAL* 3.0 28.5 + - + +
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Residues in contact with ILE 88 (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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74A LEU* 3.8 27.8 - - + -
84A HIS 3.1 16.7 + - - +
85A ALA 3.8 4.7 - - - +
86A GLU 3.2 0.2 - - - -
87A THR* 1.3 76.7 - - - +
89A LYS* 1.3 58.5 + - - +
91A VAL* 3.8 5.8 - - - +
92A ARG* 3.0 64.3 + - + +
110A VAL* 4.1 17.0 - - + -
231A PHE* 4.5 6.7 - - + -
235A GLN* 3.8 40.4 - - + +
237A VAL* 4.4 5.8 - - + -
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Residues in contact with LYS 89 (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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85A ALA 3.1 13.7 + - - +
86A GLU* 3.1 18.8 + - + +
88A ILE* 1.3 78.2 - - - +
90A ASN* 1.3 65.5 + - - +
92A ARG* 3.4 7.6 + - - +
93A THR* 2.8 42.7 + - - +
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Residues in contact with ASN 90 (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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56A ARG* 3.2 26.2 + - - +
57A SER* 4.8 1.4 - - - +
58A VAL* 3.5 32.0 - - + +
61A LEU* 3.8 15.2 - - + +
86A GLU* 3.0 35.5 + - - +
87A THR* 3.2 3.7 + - - +
89A LYS* 1.3 83.4 + - - +
91A VAL* 1.3 57.6 + - - +
93A THR* 3.0 2.5 + - - -
94A ALA* 2.6 37.2 + - - +
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Residues in contact with VAL 91 (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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51A ILE* 4.7 1.3 - - + -
61A LEU* 4.2 24.2 - - + +
65A ILE* 5.8 0.7 - - + -
69A MET* 5.6 2.5 - - + -
72A ALA* 4.0 24.9 - - + -
74A LEU* 5.4 1.6 - - + -
87A THR* 3.0 33.7 + - + +
88A ILE* 3.8 7.6 - - - +
90A ASN* 1.3 75.3 - - - +
92A ARG* 1.3 56.8 + - + +
94A ALA* 3.2 2.2 + - - +
95A THR* 2.7 46.2 + - - +
108A VAL* 4.0 21.1 - - + +
110A VAL* 4.5 14.4 - - + -
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Residues in contact with ARG 92 (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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88A ILE* 3.0 42.3 + - + +
89A LYS* 3.8 5.8 - - - +
91A VAL* 1.3 81.5 - - + +
93A THR* 1.3 55.9 + - - +
95A THR* 3.8 5.6 - - - -
96A GLU* 3.0 41.0 + - + +
108A VAL 5.9 0.2 + - - -
110A VAL* 4.2 17.6 - - + +
235A GLN 2.5 31.1 + - - -
236A ASP* 3.7 20.8 + - - +
237A VAL* 5.1 1.0 - - - +
238A ASP* 5.4 0.4 + - - -
461A ARG* 5.0 18.8 - - - +
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Residues in contact with THR 93 (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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58A VAL* 3.5 26.6 - - + +
62A LYS* 5.4 2.0 - - - +
89A LYS* 2.8 34.1 + - - +
90A ASN* 3.0 11.3 + - - -
92A ARG* 1.3 75.0 - - - +
94A ALA* 1.3 66.9 + - - +
96A GLU* 3.3 4.2 + - - +
97A SER* 3.1 22.2 + - - -
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Residues in contact with ALA 94 (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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58A VAL* 4.1 6.0 - - + +
61A LEU* 3.5 29.8 - - + -
62A LYS* 3.8 24.7 - - + +
65A ILE* 4.2 7.6 - - + -
90A ASN 2.6 19.1 + - - +
91A VAL 3.6 4.7 - - - +
93A THR* 1.3 74.0 - - - +
95A THR* 1.3 60.3 + - - +
97A SER* 2.7 24.4 + - - -
98A PHE* 3.5 9.4 - - - -
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Residues in contact with THR 95 (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 ILE* 3.5 13.2 - - - +
91A VAL* 2.7 24.2 + - - +
92A ARG* 3.8 7.6 - - - -
94A ALA* 1.3 77.8 - - - +
96A GLU* 1.3 64.5 + - - +
97A SER 3.4 0.9 + - - -
98A PHE* 3.5 12.1 + - - -
105A TYR* 3.2 37.8 - - - +
106A ARG 3.7 23.7 + - - +
108A VAL* 3.4 31.3 + - + +
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Residues in contact with GLU 96 (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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92A ARG* 3.0 30.2 + - + +
93A THR* 3.3 3.6 + - - +
94A ALA 3.3 0.2 - - - -
95A THR* 1.3 78.5 - - - +
97A SER* 1.3 57.1 + - - +
98A PHE 3.0 6.3 - - - -
99A ALA* 2.8 41.5 + - + +
100A SER* 4.2 1.9 + - - -
105A TYR* 2.7 28.3 + - - -
461A ARG* 5.7 1.9 + - - -
475A LYS* 5.3 3.3 + - - -
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Residues in contact with SER 97 (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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62A LYS* 3.4 32.0 - - - +
93A THR* 3.1 9.9 + - - -
94A ALA 2.7 19.5 + - - -
96A GLU* 1.3 76.8 - - - +
98A PHE* 1.3 71.9 + - - +
99A ALA 3.3 0.7 - - - -
100A SER* 4.5 9.7 + - - -
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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