Contacts of the helix formed by residues 90 - 108 (chain A) in PDB entry 1BBC
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 SER 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLN* 3.9 12.3 + - - +
89A ASP* 1.3 74.1 + - - +
91A CYS* 1.3 67.6 + - - +
93A SER* 3.6 2.8 - - - -
94A GLN* 3.2 43.6 + - - +
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Residues in contact with CYS 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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55A LEU* 4.7 2.3 - - - +
59A GLY 4.4 0.9 - - - -
61A CYS* 2.1 66.4 - - - -
67A GLY 4.9 0.8 - - - +
71A LEU* 4.0 14.1 - - + -
89A ASP* 2.9 13.1 + - - +
90A SER* 1.3 78.2 - - - +
92A ARG* 1.3 57.8 + - + +
94A GLN* 3.2 3.1 + - - +
95A LEU* 2.9 30.1 + - - +
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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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71A LEU* 3.1 39.5 - - + +
72A SER* 3.1 27.6 + - - +
73A TYR* 3.6 23.6 - - + +
74A LYS* 5.9 4.0 - - - +
86A LYS* 4.4 14.2 - - - +
88A GLN 5.9 0.2 - - - -
89A ASP* 3.1 30.4 + - + +
91A CYS* 1.3 73.2 - - + +
93A SER* 1.3 59.2 + - - +
95A LEU* 3.9 2.0 - - - -
96A CYS* 3.1 29.1 + - - +
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Residues in contact with SER 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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84A CYS* 4.8 8.0 - - - +
85A ALA 4.7 2.8 + - - -
86A LYS 4.6 1.6 + - - -
88A GLN* 2.1 38.6 + - - -
89A ASP 2.8 12.0 + - - -
90A SER* 3.6 5.8 - - - -
91A CYS 3.2 0.2 - - - -
92A ARG* 1.3 78.8 - - - +
94A GLN* 1.3 59.0 + - - +
96A CYS* 3.5 5.2 + - - +
97A GLU* 3.1 24.4 + - - +
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Residues in contact with GLN 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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54A ARG* 2.6 31.9 - - - +
55A LEU* 3.8 12.8 - - + +
61A CYS* 4.5 12.1 - - - -
90A SER* 3.2 32.6 + - - +
91A CYS 3.6 3.6 - - - +
93A SER* 1.3 77.4 - - - +
95A LEU* 1.3 59.1 - - - +
97A GLU* 2.3 43.9 - - - +
98A CYS* 2.9 10.1 + - - -
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Residues in contact with LEU 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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1A ASN 4.5 0.4 - - - +
52A TYR* 3.6 36.1 - - + +
55A LEU* 4.3 6.2 - - + +
67A GLY 3.9 3.8 - - - +
68A THR* 3.3 39.5 - - + +
71A LEU* 3.4 40.4 - - + +
73A TYR* 3.8 15.9 - - + -
91A CYS 2.9 17.3 + - - +
92A ARG* 4.2 4.3 - - - +
94A GLN* 1.3 72.9 - - - +
96A CYS* 1.3 66.4 + - - +
97A GLU 3.0 2.1 + - - -
98A CYS* 3.1 15.4 + - - +
99A ASP* 3.2 15.8 + - - +
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Residues in contact with CYS 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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8A MET* 3.9 4.5 - - - +
73A TYR* 3.5 39.2 - - + -
74A LYS 4.2 2.0 - - - +
75A PHE* 3.7 11.0 - - - -
84A CYS* 2.1 57.2 - - + -
92A ARG 3.1 20.5 + - - +
93A SER* 3.9 1.3 - - - +
94A GLN 3.4 0.2 - - - -
95A LEU* 1.3 74.3 - - - +
97A GLU* 1.3 56.6 + - - +
99A ASP* 3.6 1.2 + - - +
100A LYS* 3.0 32.6 + - - +
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Residues in contact with GLU 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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51A CYS* 3.2 9.5 - - - -
54A ARG* 2.8 32.9 + - - -
84A CYS* 4.0 4.9 - - - -
93A SER 3.1 14.6 + - - +
94A GLN* 2.3 42.5 + - - +
96A CYS* 1.3 80.0 - - - +
98A CYS* 1.3 64.4 + - - +
100A LYS* 3.8 3.8 - - - +
101A ALA* 3.3 22.7 + - + +
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Residues in contact with CYS 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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48A HIS* 3.5 9.8 - - + -
51A CYS* 2.2 65.4 - - + +
52A TYR* 3.9 19.1 - - + -
54A ARG* 4.4 0.4 - - - -
55A LEU* 4.3 7.6 - - - -
94A GLN 2.9 21.2 + - - -
95A LEU* 3.1 6.9 + - - +
97A GLU* 1.3 74.5 - - - +
99A ASP* 1.3 69.2 - - - +
101A ALA* 3.3 5.7 + - - +
102A ALA* 3.0 18.2 + - - +
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Residues in contact with ASP 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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1A ASN 4.2 2.8 + - - +
5A PHE* 3.5 34.0 + - + +
8A MET* 3.9 5.4 - - - -
48A HIS* 3.0 11.8 + - - -
52A TYR* 2.8 32.7 + - - -
73A TYR* 2.9 35.8 + - - +
95A LEU* 3.2 13.0 + - - +
96A CYS 4.0 1.3 - - - +
98A CYS* 1.3 77.0 - - - +
100A LYS* 1.3 51.3 + - - +
102A ALA 3.2 1.2 + - - -
103A ALA* 2.8 35.5 + - - +
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Residues in contact with LYS 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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8A MET* 3.6 12.5 - - + -
80A SER 5.1 0.6 + - - -
81A ARG* 2.8 55.5 - - - +
82A ILE* 3.0 43.1 + - + +
83A THR* 5.7 0.2 - - - -
84A CYS* 4.7 9.2 - - - -
96A CYS 3.0 20.1 + - - +
97A GLU* 3.8 6.3 - - - +
99A ASP* 1.3 72.8 - - - +
101A ALA* 1.3 67.8 + - - +
103A ALA* 3.2 1.9 + - - +
104A THR* 3.0 30.2 + - + +
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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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47A THR* 6.2 3.6 - - + -
51A CYS* 6.1 1.6 - - - -
81A ARG* 4.8 3.6 - - - +
97A GLU* 3.3 12.3 + - + +
98A CYS* 3.5 9.9 - - - +
99A ASP 3.2 0.4 - - - -
100A LYS* 1.3 80.8 - - - +
102A ALA* 1.4 65.4 + - - +
104A THR* 3.2 7.7 + - - -
105A CYS* 2.9 26.1 + - - +
108A ARG* 5.0 0.9 + - - -
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Residues in contact with ALA 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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5A PHE* 4.0 10.1 - - + -
44A CYS* 3.8 9.6 - - - +
48A HIS* 3.4 44.4 - - + -
98A CYS 3.0 6.2 + - - +
99A ASP 3.6 4.7 - - - +
101A ALA* 1.4 78.0 - - - +
103A ALA* 1.3 56.3 + - - +
105A CYS* 3.4 6.8 + - - +
106A PHE* 3.0 38.6 + - + -
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Residues in contact with ALA 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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5A PHE* 4.3 7.6 - - + -
8A MET* 4.3 10.5 - - + -
9A ILE* 4.1 21.8 - - - +
12A THR* 2.5 39.6 + - + +
99A ASP 2.8 19.4 + - - +
100A LYS 3.2 4.0 + - - +
102A ALA* 1.3 71.5 - - - +
104A THR* 1.3 64.4 + - - +
106A PHE* 3.9 9.9 - - - +
107A ALA 3.4 10.0 + - - -
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Residues in contact with THR 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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12A THR* 4.4 11.9 - - + -
81A ARG* 3.1 61.9 + - + +
100A LYS* 3.0 13.1 + - + +
101A ALA* 3.2 9.7 + - - -
103A ALA* 1.3 77.4 - - - +
105A CYS* 1.3 62.5 + - - +
106A PHE 3.2 0.2 - - - -
107A ALA* 3.2 7.9 + - - +
108A ARG* 2.9 45.2 + - - +
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Residues in contact with CYS 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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40A ALA 4.5 0.7 - - - -
43A ARG* 6.0 1.8 - - - -
44A CYS* 2.2 52.5 - - + -
47A THR* 6.2 0.4 - - - -
101A ALA 2.9 19.9 + - - +
102A ALA* 3.5 5.4 - - - +
104A THR* 1.3 76.1 + - - +
106A PHE* 1.3 65.6 + - - +
108A ARG* 3.0 32.4 + - - +
109A ASN* 2.8 28.7 + - - -
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Residues in contact with PHE 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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5A PHE* 3.6 31.0 - + - -
9A ILE* 4.1 20.2 - - + -
13A THR* 3.8 14.4 - - + -
22A TYR* 3.7 41.2 + + + -
29A CYS* 5.3 0.2 - - + -
41A THR* 3.5 20.8 + - + -
44A CYS* 3.8 14.6 - - + -
45A CYS* 3.5 33.9 - - - -
48A HIS* 5.8 0.7 - - - -
102A ALA* 3.0 24.6 + - + +
103A ALA* 3.9 8.1 - - - +
105A CYS* 1.3 76.8 - - - +
107A ALA* 1.3 60.9 + - - +
109A ASN* 3.1 15.1 + - - +
110A LYS* 3.2 15.1 + - - +
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Residues in contact with ALA 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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12A THR* 3.6 32.1 - - - +
13A THR* 3.5 9.8 - - + +
103A ALA 3.4 15.1 + - - +
104A THR* 3.2 7.5 + - - +
106A PHE* 1.3 76.8 - - - +
108A ARG* 1.4 65.0 + - - +
110A LYS* 3.8 18.7 + - - +
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Residues in contact with ARG 108 (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 ARG* 5.3 4.8 - - - +
101A ALA 5.0 0.8 + - - -
104A THR* 2.9 30.1 + - - +
105A CYS* 3.0 36.2 + - - +
107A ALA* 1.4 80.4 - - - +
109A ASN* 1.3 66.8 + - - +
110A LYS* 3.3 4.4 + - - +
111A THR* 4.1 11.6 + - - +
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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