Contacts of the helix formed by residues 15 - 22 (chain A) in PDB entry 1BV1
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 ALA 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PRO* 1.3 70.9 - - - +
16A ALA* 1.3 58.4 + - - +
18A LEU* 3.4 1.7 + - - +
19A PHE* 2.9 32.4 + - - +
79A PHE* 3.7 20.4 - - + -
104A ILE* 3.7 19.6 - - + +
106A ALA* 4.1 25.6 - - + +
111A GLY 4.2 1.4 + - - -
112A SER* 2.7 20.1 + - - +
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Residues in contact with ALA 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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14A PRO* 3.3 3.4 + - + +
15A ALA* 1.3 77.4 - - - +
17A ARG* 1.3 60.0 + - - +
19A PHE* 3.4 2.4 + - - +
20A LYS* 3.1 37.4 + - + +
79A PHE* 3.6 24.0 - - + -
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Residues in contact with ARG 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 ILE* 4.0 23.0 - - + +
14A PRO* 3.3 21.5 + - + +
16A ALA* 1.3 75.9 - - - +
18A LEU* 1.3 65.5 + - - +
20A LYS* 3.5 7.8 + - - +
21A ALA* 3.2 22.9 + - - +
151A LEU* 3.0 49.6 + - + +
152A LEU* 5.4 2.6 - - - +
154A HIS 3.1 11.3 + - - -
155A SER* 3.7 14.6 + - - +
157A ALA 3.0 26.8 + - - -
158A TYR* 3.4 25.4 + - + +
159A ASN* 4.0 16.6 + - - +
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Residues in contact with LEU 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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11A SER* 3.5 29.6 - - - +
13A ILE* 3.7 21.0 - - + +
14A PRO 3.1 17.7 + - - +
15A ALA* 3.8 4.7 - - - +
17A ARG* 1.3 73.1 - - - +
19A PHE* 1.3 62.2 + - - +
22A PHE* 2.8 51.2 + - + +
104A ILE* 4.2 12.8 - - + -
112A SER* 4.3 10.3 - - - -
114A LEU* 3.8 20.9 - - + -
144A LEU* 4.0 15.7 - - + +
147A VAL* 4.6 5.6 - - + -
148A GLU* 5.7 1.8 - - - +
151A LEU* 4.6 9.9 - - + -
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Residues in contact with PHE 19 (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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15A ALA 2.9 18.1 + - - +
16A ALA 3.7 4.5 - - - +
17A ARG 3.3 0.2 - - - -
18A LEU* 1.3 77.0 - - - +
20A LYS* 1.3 61.9 + - + +
23A ILE* 3.1 43.5 + - + +
24A LEU* 3.0 52.5 + - + -
74A VAL* 4.3 8.3 - - + -
75A ASP 3.9 16.2 - - - -
76A HIS* 3.9 17.9 - - + -
79A PHE* 3.5 53.4 - + + -
80A LYS 3.9 10.5 - - - -
104A ILE* 3.8 13.8 - - + +
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Residues in contact with LYS 20 (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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16A ALA* 3.1 26.6 + - + +
17A ARG* 3.8 8.5 - - - +
18A LEU 3.3 0.4 - - - -
19A PHE* 1.3 79.5 - - + +
21A ALA* 1.3 55.9 + - - +
24A LEU* 3.3 24.5 - - + +
25A ASP* 3.0 28.8 + - - +
79A PHE* 6.4 0.2 - - + -
158A TYR* 4.1 35.6 + - + +
159A ASN* 5.7 1.6 + - - +
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Residues in contact with ALA 21 (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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17A ARG 3.2 13.7 + - - +
18A LEU 4.2 0.4 - - - +
20A LYS* 1.3 78.7 - - - +
22A PHE* 1.3 60.1 + - - +
25A ASP* 3.2 6.5 - - - -
26A GLY* 3.2 20.4 + - - -
29A LEU* 3.4 18.4 - - + +
147A VAL* 4.1 2.0 - - + -
151A LEU* 4.0 20.0 - - + -
158A TYR* 3.6 37.0 - - + -
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Residues in contact with PHE 22 (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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18A LEU* 2.8 32.5 + - + +
21A ALA* 1.3 74.7 - - - +
23A ILE* 1.3 76.1 + - + +
26A GLY* 3.1 22.0 - - - -
30A PHE* 3.6 36.3 - + - -
102A ILE* 4.7 11.9 - - + -
104A ILE* 5.0 2.7 - - + -
114A LEU* 3.7 29.6 - - + -
140A GLY* 4.3 9.4 - - - -
143A LEU* 3.8 4.0 - - + -
144A LEU* 3.6 42.4 - - + -
147A VAL* 3.9 15.9 - - + +
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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