Contacts of the helix formed by residues 88 - 107 (chain A) in PDB entry 3BBU
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A THR* 5.7 0.2 - - + -
65A THR* 3.0 35.8 + - + +
67A ILE* 4.0 27.4 - - + -
87A GLU* 1.3 76.4 - - - +
89A ALA* 1.3 60.5 + - - +
90A GLU* 3.7 8.7 + - - +
91A SER* 2.9 28.6 + - - -
92A VAL* 2.9 27.0 + - - +
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Residues in contact with ALA 89 (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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87A GLU 3.7 1.4 + - - -
88A THR* 1.3 72.3 - - - +
90A GLU* 1.3 61.7 + - - +
92A VAL* 2.7 32.4 - - + +
93A GLU* 2.9 18.6 + - + +
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Residues in contact with GLU 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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88A THR* 3.1 7.5 - - - +
89A ALA* 1.3 80.2 - - - +
91A SER* 1.3 61.5 + - - +
93A GLU* 3.5 13.1 + - - +
94A LYS* 2.7 56.1 + - + +
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Residues in contact with SER 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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63A GLU 4.0 2.8 + - - +
64A ARG* 3.3 5.9 - - - -
65A THR* 2.8 39.4 + - - -
87A GLU* 2.8 21.4 + - - +
88A THR* 2.9 25.2 + - - -
90A GLU* 1.3 76.2 - - - +
92A VAL* 1.3 66.2 + - - +
94A LYS* 3.4 6.8 + - - +
95A ARG* 3.1 24.3 + - - +
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Residues in contact with VAL 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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87A GLU* 3.6 31.4 - - + +
88A THR 2.9 18.6 + - - +
89A ALA* 2.7 31.2 - - + +
91A SER* 1.3 74.8 - - - +
93A GLU* 1.3 72.7 + - + +
95A ARG* 3.2 16.3 + - - +
96A GLU* 2.8 36.9 + - + +
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Residues in contact with GLU 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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89A ALA* 2.9 24.9 + - + +
90A GLU* 3.7 14.7 + - - +
92A VAL* 1.3 87.0 - - + +
94A LYS* 1.3 64.7 + - + +
96A GLU* 3.2 8.4 + - - +
97A LYS* 2.8 44.7 + - + +
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Residues in contact with LYS 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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63A GLU* 5.5 8.7 + - - +
90A GLU* 2.7 58.5 + - + +
91A SER* 3.8 6.6 - - - +
92A VAL 3.3 0.2 - - - -
93A GLU* 1.3 77.3 - - + +
95A ARG* 1.3 63.9 + - - +
97A LYS* 3.6 5.9 + - - +
98A MET* 3.1 31.2 + - - +
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Residues in contact with ARG 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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62A ASP* 3.9 24.8 + - + +
63A GLU 3.4 19.7 - - - +
64A ARG* 3.1 38.8 - - - +
87A GLU* 3.0 34.7 + - - -
91A SER 3.1 9.1 + - - +
92A VAL* 3.5 20.8 + - - +
94A LYS* 1.3 76.7 - - - +
96A GLU* 1.3 73.8 + - - +
98A MET* 3.2 8.7 + - - +
99A ALA* 3.0 22.5 + - - +
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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 VAL* 2.8 37.0 + - + +
93A GLU* 3.5 8.3 - - - +
95A ARG* 1.3 85.5 + - - +
97A LYS* 1.3 67.0 + - + +
99A ALA* 2.7 19.3 + - - +
100A LEU* 2.8 29.2 + - + +
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Residues in contact with LYS 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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93A GLU* 2.8 38.4 + - + +
94A LYS* 4.0 5.6 - - - +
96A GLU* 1.3 73.7 - - + +
98A MET* 1.3 62.9 + - + +
100A LEU* 3.3 8.0 + - + +
101A ALA* 2.9 26.4 + - - +
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Residues in contact with MET 98 (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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61A ASN* 5.0 19.3 - - - +
94A LYS* 3.1 21.8 + - - +
95A ARG* 3.6 5.8 - - - +
97A LYS* 1.3 76.9 - - + +
99A ALA* 1.3 57.7 + - - +
101A ALA* 3.8 5.9 - - - +
102A ARG* 3.0 27.9 + - - +
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Residues in contact with ALA 99 (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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95A ARG 3.0 11.4 + - - +
96A GLU* 2.7 20.2 + - - +
98A MET* 1.3 69.7 - - - +
100A LEU* 1.3 69.4 + - + +
102A ARG* 3.1 9.4 - - - +
103A LYS* 3.0 21.5 + - - +
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Residues in contact with LEU 100 (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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96A GLU* 2.8 46.2 + - + +
97A LYS* 3.6 10.1 - - - +
99A ALA* 1.3 72.9 - - + +
101A ALA* 1.3 67.7 + - - +
103A LYS* 2.9 11.1 + - + +
104A LEU* 2.8 25.0 + - - +
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Residues in contact with ALA 101 (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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97A LYS 2.9 17.0 + - - +
98A MET* 3.8 7.2 - - + +
100A LEU* 1.3 75.9 - - - +
102A ARG* 1.3 63.4 + - - +
104A LEU* 3.0 12.2 + - - +
105A ASN* 2.9 25.8 + - - +
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Residues in contact with ARG 102 (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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98A MET 3.0 15.6 + - - +
99A ALA* 3.1 14.1 - - - +
101A ALA* 1.3 77.2 - - - +
103A LYS* 1.3 63.6 + - - +
104A LEU 3.0 1.4 + - - -
105A ASN* 3.3 5.7 + - - +
106A ALA* 3.2 18.8 + - - +
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Residues in contact with LYS 103 (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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99A ALA 3.0 11.1 + - - +
100A LEU* 2.9 13.1 + - + +
102A ARG* 1.3 75.1 - - - +
104A LEU* 1.3 57.2 + - - +
106A ALA* 3.2 21.0 - - - +
107A LEU* 3.3 12.3 + - - +
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Residues in contact with LEU 104 (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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100A LEU 2.8 13.3 + - - +
101A ALA* 3.2 14.8 - - - +
102A ARG 3.0 0.2 - - - -
103A LYS* 1.3 74.4 - - - +
105A ASN* 1.3 57.7 + - - +
106A ALA 2.7 13.6 + - - -
107A LEU* 2.9 22.3 + - + +
108A THR* 3.6 11.1 + - - -
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Residues in contact with ASN 105 (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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101A ALA 2.9 14.2 + - - +
102A ARG* 4.0 5.2 - - - +
104A LEU* 1.3 75.3 - - - +
106A ALA* 1.3 55.8 + - - +
108A THR* 3.2 26.5 - - - +
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Residues in contact with ALA 106 (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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102A ARG 3.2 12.8 + - - +
103A LYS* 3.2 17.9 - - - +
104A LEU 2.7 0.6 + - - -
105A ASN* 1.3 75.6 - - - +
107A LEU* 1.3 52.2 + - - +
108A THR 2.7 23.1 + - - +
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Residues in contact with LEU 107 (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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103A LYS 3.3 10.0 + - - +
104A LEU* 2.9 13.5 + - + +
106A ALA* 1.3 74.9 - - - +
108A THR* 1.3 60.2 + - - +
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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
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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