Contacts of the helix formed by residues 10 - 18 (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 ARG 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLU 5.8 0.7 - - - +
9A VAL* 1.3 76.1 - - - +
11A LEU* 1.3 60.2 + - - +
12A ASP* 3.0 34.7 + - - +
13A LYS* 3.2 10.9 + - + +
14A TRP* 2.8 29.5 + - - +
28A ARG* 4.7 4.6 - - - +
45A PRO* 3.5 23.0 - - - +
46A SER* 3.3 36.0 - - - +
47A LYS 3.3 5.6 - - - -
48A ILE* 4.5 7.0 - - + -
49A VAL* 4.0 0.7 - - - -
73A GLU* 4.9 1.0 + - - -
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Residues in contact with LEU 11 (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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10A ARG* 1.3 73.2 - - - +
12A ASP* 1.3 63.9 + - - +
14A TRP* 3.6 1.6 - - + +
15A LEU* 2.9 36.8 + - + +
31A ILE* 3.4 29.2 - - + -
36A VAL* 4.4 9.4 - - + -
38A TYR* 4.3 8.1 - - + -
43A SER* 3.7 28.7 - - - +
44A LYS 3.9 10.8 - - - +
45A PRO 3.4 1.2 + - - -
47A LYS* 2.7 21.0 + - + +
49A VAL* 3.5 20.4 - - + -
55A LEU* 4.2 28.0 - - + -
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Residues in contact with ASP 12 (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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10A ARG* 3.0 40.6 + - - +
11A LEU* 1.3 77.2 - - - +
13A LYS* 1.3 77.6 + - - +
15A LEU 3.4 0.3 + - - -
16A TRP* 3.2 20.4 + - - +
24A ARG* 4.1 26.9 - - - +
27A ALA* 3.6 13.0 - - - +
28A ARG* 3.9 16.8 - - - +
31A ILE* 4.0 17.2 - - + +
45A PRO* 3.2 22.1 + - + +
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Residues in contact with LYS 13 (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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9A VAL* 4.4 8.3 - - + -
10A ARG* 3.2 15.8 + - + +
12A ASP* 1.3 82.6 + - - +
14A TRP* 1.3 61.6 + - - +
16A TRP* 3.2 26.6 + - + +
17A ALA* 2.8 28.3 + - - +
24A ARG* 3.4 35.9 - - - +
73A GLU* 3.7 51.8 + - - +
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Residues in contact with TRP 14 (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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9A VAL* 4.1 10.7 - - + +
10A ARG 2.8 21.2 + - - +
11A LEU* 3.6 4.7 - - + +
13A LYS* 1.3 74.4 - - - +
15A LEU* 1.3 67.5 + - + +
17A ALA* 3.1 6.8 + - + +
18A ALA* 2.8 33.0 + - + -
20A PHE* 3.5 33.0 - + - -
49A VAL* 3.6 28.7 - - + -
55A LEU* 3.4 31.2 - - + -
66A VAL* 4.6 1.1 - - + -
68A VAL* 3.8 19.1 - - + +
70A ALA 2.9 23.1 + - - -
71A ILE* 4.1 13.0 - - + +
72A THR 4.6 3.8 - - - -
84A LEU* 3.5 33.9 - - + +
85A TYR* 4.0 12.3 - - + -
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Residues in contact with LEU 15 (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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11A LEU* 2.9 30.8 + - + +
12A ASP 3.8 3.4 - - - +
14A TRP* 1.3 90.8 - - + +
16A TRP* 1.3 59.3 + - - +
18A ALA 3.6 0.9 + - - -
19A ARG 3.2 2.6 + - - -
20A PHE* 2.9 50.1 + - + +
21A TYR* 3.8 13.5 + - + -
27A ALA* 3.9 15.9 - - + -
31A ILE* 3.6 31.6 - - + -
36A VAL* 4.1 16.2 - - + -
55A LEU* 4.4 6.7 - - + -
57A LEU* 3.9 17.9 - - + -
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Residues in contact with TRP 16 (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 ASP 3.2 13.1 + - - +
13A LYS* 3.2 26.9 + - + +
14A TRP 3.2 0.2 - - - -
15A LEU* 1.3 75.8 - - - +
17A ALA* 1.3 75.4 + - - +
19A ARG 2.9 8.7 + - - -
21A TYR 3.9 6.5 - - - -
22A LYS 3.3 25.2 + - - -
23A THR* 3.5 17.9 - - - +
24A ARG* 3.6 38.7 - - + +
27A ALA* 4.6 1.7 - - - +
73A GLU 3.6 22.0 - - - -
74A GLN* 5.4 0.2 - - - -
75A ARG* 2.8 73.7 + - + +
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Residues in contact with ALA 17 (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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13A LYS 2.8 21.2 + - - +
14A TRP* 3.5 5.6 - - + +
16A TRP* 1.3 78.4 - - + +
18A ALA* 1.3 57.8 + - - +
19A ARG* 3.2 5.5 + - - +
72A THR* 3.9 25.1 - - + +
73A GLU 4.6 2.0 - - - -
74A GLN 3.4 21.7 - - - +
75A ARG* 3.7 18.8 - - - +
81A ALA* 3.4 16.5 - - - +
84A LEU* 3.8 5.4 - - + +
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Residues in contact with ALA 18 (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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14A TRP* 2.8 28.9 + - + +
15A LEU 4.0 0.2 - - - +
17A ALA* 1.3 74.9 - - - +
19A ARG* 1.3 71.1 + - - +
20A PHE* 3.3 31.1 + - + -
81A ALA* 4.1 5.5 - - - +
82A ALA* 4.6 1.0 + - - -
84A LEU* 3.6 18.8 - - + +
85A TYR* 3.8 22.2 + - + -
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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