Contacts of the helix formed by residues 74 - 102 (chain A) in PDB entry 1BUU
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 ILE 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 1.3 82.7 - - - +
75A GLU* 1.3 76.9 + - + +
76A VAL 3.4 0.3 + - - -
77A LYS* 3.6 8.2 + - - +
78A LEU* 3.5 27.2 + - + +
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA 4.6 0.8 - - - +
74A ILE* 1.3 85.5 - - + +
76A VAL* 1.3 59.9 + - + +
77A LYS 3.3 0.2 - - - -
78A LEU* 3.7 17.4 - - + +
79A ALA* 2.9 33.2 + - + +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 3.3 35.4 - - - +
74A ILE 3.1 0.2 - - - -
75A GLU* 1.3 78.1 - - - +
77A LYS* 1.3 60.3 + - + +
79A ALA* 3.3 5.4 + - - +
80A ASN* 3.0 48.3 + - - +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 3.6 15.9 + - - +
74A ILE* 4.1 5.8 - - - +
76A VAL* 1.3 77.8 - - + +
78A LEU* 1.3 60.1 + - + +
80A ASN* 3.1 7.6 + - - +
81A MET* 2.7 52.9 + - + +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.5 29.3 + - + +
75A GLU* 3.4 19.0 + - + +
76A VAL 3.4 0.4 - - - -
77A LYS* 1.3 77.9 - - + +
79A ALA* 1.3 57.2 + - - +
81A MET* 4.1 12.2 - - + +
82A GLU* 3.0 32.3 + - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 2.9 23.1 + - + +
76A VAL* 3.4 7.4 - - - +
77A LYS 3.1 0.2 - - - -
78A LEU* 1.3 77.4 - - - +
80A ASN* 1.3 64.6 + - - +
82A GLU* 3.3 9.0 + - - +
83A ALA* 3.0 30.0 + - - +
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.0 31.7 + - - +
77A LYS* 3.6 6.9 - - - +
79A ALA* 1.3 81.7 - - - +
81A MET* 1.3 60.1 + - + +
83A ALA* 3.6 5.8 + - - +
84A GLU* 2.9 28.5 + - - +
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Residues in contact with MET 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 2.7 38.5 + - + +
78A LEU* 4.1 11.9 - - + +
80A ASN* 1.3 71.5 - - + +
82A GLU* 1.3 60.5 + - - +
84A GLU* 3.2 9.0 - - + +
85A ILE* 2.8 41.0 + - + +
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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
----------------------------------------------------------
78A LEU 3.0 20.8 + - - +
79A ALA* 3.3 8.7 + - - +
81A MET* 1.3 74.3 - - - +
83A ALA* 1.3 63.1 + - - +
85A ILE* 3.1 14.4 + - + +
86A ASN* 2.8 38.4 + - - +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA 3.0 15.8 + - - +
80A ASN* 3.9 6.3 - - - +
82A GLU* 1.3 76.8 - - - +
84A GLU* 1.3 63.0 + - - +
86A ASN* 3.1 14.3 + - - +
87A THR* 3.0 29.9 + - + +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASN 2.9 20.1 + - - +
81A MET* 3.2 13.0 - - + +
82A GLU 3.1 0.2 - - - -
83A ALA* 1.3 77.6 - - - +
85A ILE* 1.3 62.0 + - + +
87A THR* 2.6 37.3 + - - +
88A LEU* 3.3 19.7 + - + +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 2.8 35.1 + - + +
82A GLU* 3.4 12.8 - - + +
84A GLU* 1.3 77.9 - - + +
86A ASN* 1.3 56.9 + - - +
88A LEU* 3.2 14.2 + - + +
89A LYS* 3.0 48.2 + - + +
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Residues in contact with ASN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 2.8 42.1 + - - +
83A ALA* 3.1 12.6 + - - +
85A ILE* 1.3 77.7 - - - +
87A THR* 1.3 61.2 + - + +
89A LYS* 3.3 23.5 + - - +
90A SER* 3.0 26.6 + - - -
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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
----------------------------------------------------------
83A ALA* 3.0 15.6 + - + +
84A GLU* 2.6 33.9 + - - +
86A ASN* 1.3 77.2 - - + +
88A LEU* 1.3 60.9 + - - +
90A SER* 3.3 7.9 + - - -
91A LYS* 2.9 44.2 + - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 3.3 22.4 + - + +
85A ILE* 3.2 14.0 + - + +
87A THR* 1.3 80.8 + - - +
89A LYS* 1.3 65.2 + - - +
91A LYS* 3.2 24.8 + - + +
92A LEU* 3.0 25.7 + - - +
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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
----------------------------------------------------------
85A ILE* 3.0 38.5 + - + +
86A ASN* 3.3 22.9 + - - +
88A LEU* 1.3 77.4 - - - +
90A SER* 1.3 57.3 + - - +
92A LEU* 3.4 7.2 + - - +
93A GLU* 3.0 40.3 + - - +
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN* 3.0 14.3 + - - +
87A THR* 3.6 10.2 - - - -
88A LEU 3.2 0.2 - - - -
89A LYS* 1.3 75.3 - - - +
91A LYS* 1.3 64.3 - - - +
93A GLU* 3.3 14.3 + - - +
94A LEU* 3.2 21.5 + - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 2.9 30.0 + - - +
88A LEU* 3.2 27.8 + - + +
90A SER* 1.3 75.8 - - - +
92A LEU* 1.3 57.6 + - - +
94A LEU* 3.2 9.2 + - - +
95A THR* 3.0 31.3 + - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU 3.0 17.0 + - - +
89A LYS* 3.8 6.7 - - - +
91A LYS* 1.3 72.7 - - - +
93A GLU* 1.3 66.3 + - + +
95A THR* 3.2 14.2 + - + -
96A ASN* 2.9 44.3 + - - +
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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
----------------------------------------------------------
89A LYS* 3.0 30.8 + - + +
90A SER* 3.6 13.6 + - - +
91A LYS 3.3 0.4 - - - -
92A LEU* 1.3 77.0 - - + +
94A LEU* 1.3 58.0 + - - +
96A ASN* 3.4 7.4 + - - +
97A LYS* 3.0 41.8 + - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 3.2 8.7 + - - +
91A LYS* 3.2 12.2 + - - +
93A GLU* 1.3 77.6 - - - +
95A THR* 1.3 60.0 - - - +
97A LYS* 3.1 16.7 + - + +
98A LEU* 2.8 39.6 + - + +
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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
----------------------------------------------------------
91A LYS* 3.0 15.7 + - - +
92A LEU* 3.2 21.9 + - + +
94A LEU* 1.3 77.1 - - - +
96A ASN* 1.3 62.5 + - - +
98A LEU* 3.4 5.9 + - - +
99A HIS* 2.9 31.8 + - + +
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Residues in contact with ASN 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 LEU* 2.9 38.5 + - - +
93A GLU* 3.7 7.5 - - - +
95A THR* 1.3 82.6 - - - +
97A LYS* 1.3 61.6 + - - +
99A HIS* 3.6 11.2 + - - +
100A ALA* 3.0 24.6 + - - +
103A MET* 5.4 0.2 - - - +
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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* 3.0 27.0 + - - +
94A LEU* 3.5 20.0 - - + +
96A ASN* 1.3 77.3 - - + +
98A LEU* 1.3 62.3 + - - +
100A ALA* 3.3 7.1 + - - +
101A PHE* 3.0 22.8 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 2.8 30.0 + - + +
95A THR* 3.9 6.1 - - - +
97A LYS* 1.3 73.1 - - - +
99A HIS* 1.3 58.9 + - - +
101A PHE* 3.2 22.6 + - + +
102A SER* 2.9 32.2 + - - +
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Residues in contact with HIS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 2.9 21.4 + - + +
96A ASN* 3.6 12.7 + - - +
97A LYS 3.3 0.2 - - - -
98A LEU* 1.3 76.3 - - - +
100A ALA* 1.3 57.6 + - - +
102A SER* 2.5 25.6 + - - -
103A MET* 2.8 51.9 + - + +
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASN 3.0 17.0 + - - +
97A LYS* 3.6 6.7 - - - +
99A HIS* 1.3 76.0 - - - +
101A PHE* 1.3 63.5 + - - +
103A MET* 3.0 23.5 + - + +
104A GLY 3.2 0.2 + - - -
105A LYS* 3.0 48.3 + - + +
111A PHE* 4.1 10.8 - - + -
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Residues in contact with PHE 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 3.0 13.3 + - - +
98A LEU* 3.4 26.5 - - + +
100A ALA* 1.3 76.9 - - - +
102A SER* 1.3 60.2 + - - +
104A GLY* 2.9 21.3 + - - -
105A LYS* 4.0 15.0 + - - +
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 2.9 16.8 + - - -
99A HIS* 2.5 35.3 + - - -
101A PHE* 1.3 81.2 - - - +
103A MET* 1.3 57.8 + - - +
104A GLY 3.1 3.4 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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