Contacts of the helix formed by residues 9 - 22 (chain B) in PDB entry 2B9R
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 ASP 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B VAL 2.7 9.4 + - - +
8B LYS* 1.3 78.9 - - - +
10B ILE* 1.3 70.8 + - - +
11B TYR 3.4 1.8 - - - -
12B ALA* 3.8 9.6 - - - +
13B TYR* 2.9 40.5 + - + +
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Residues in contact with ILE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 3.6 23.3 + - - +
9B ASP* 1.3 80.9 - - - +
11B TYR* 1.3 61.8 + - + +
13B TYR* 5.0 0.2 - - - +
14B LEU* 3.6 19.6 + - - +
144B ARG* 5.7 3.8 - - - +
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Residues in contact with TYR 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 1.3 79.3 - - + +
12B ALA* 1.3 61.4 + - + +
13B TYR 3.5 0.2 - - - -
14B LEU* 3.1 15.1 - - + +
15B ARG* 2.6 42.7 + - + +
141B PHE* 3.4 38.9 - + + -
144B ARG* 3.3 48.9 - - + +
178B SER* 4.4 8.4 + - - -
204B TYR 4.2 8.5 - - - -
205B LEU* 3.6 41.8 + - + +
207B TYR* 4.4 9.7 - - - -
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS 5.5 0.9 - - - -
9B ASP* 3.1 13.6 + - - +
11B TYR* 1.3 84.6 - - + +
13B TYR* 1.3 54.2 + - - +
15B ARG* 2.7 11.5 + - - +
16B GLN* 2.6 32.9 + - - +
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Residues in contact with TYR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASP* 2.9 30.9 + - + +
10B ILE 5.0 0.2 - - - +
12B ALA* 1.3 69.1 - - - +
14B LEU* 1.3 67.4 + - - +
16B GLN* 2.9 12.2 + - + +
17B LEU* 2.9 24.1 + - - +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE 3.6 18.1 + - - +
11B TYR* 3.1 20.8 - - + +
13B TYR* 1.3 77.3 - - - +
15B ARG* 1.3 60.5 + - - +
16B GLN 3.3 0.3 + - - -
17B LEU* 3.3 10.6 + - - -
18B GLU* 3.3 10.2 + - - +
136B PRO* 3.2 54.1 - - + +
140B HIS* 4.9 21.5 - - + +
141B PHE* 4.1 15.7 - - + -
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 2.6 35.6 + - + +
12B ALA* 2.7 18.8 + - - +
14B LEU* 1.3 72.1 - - - +
16B GLN* 1.3 60.7 + - - +
18B GLU* 3.1 26.2 - - + +
19B ALA* 3.6 6.2 + - - +
141B PHE* 4.3 5.8 - - + -
178B SER* 4.8 3.6 - - - +
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Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA 2.6 15.7 + - - +
13B TYR* 2.9 14.8 + - + +
15B ARG* 1.3 72.5 - - - +
17B LEU* 1.3 53.9 + - - +
19B ALA* 2.7 35.1 + - - +
20B ALA* 3.8 3.1 + - - +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR 2.9 14.6 + - - +
14B LEU* 3.3 2.0 + - - -
16B GLN* 1.3 75.0 - - - +
18B GLU* 1.3 57.4 + - - +
19B ALA 3.4 0.2 - - - -
20B ALA* 3.9 16.7 + - + +
21B GLN 4.1 2.8 + - - -
134B GLY 4.1 12.6 - - - +
135B ARG* 3.8 15.3 - - + +
136B PRO* 3.6 30.7 - - + -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 3.3 9.3 + - - +
15B ARG* 3.1 26.3 - - - +
16B GLN 2.9 1.6 + - - -
17B LEU* 1.3 75.5 - - - +
19B ALA* 1.3 61.2 + - + +
20B ALA 3.0 6.7 + - - -
21B GLN* 3.5 21.0 + - - +
22B ALA 4.1 2.8 + - - -
135B ARG* 4.6 2.7 - - - +
136B PRO* 4.3 17.0 - - + +
141B PHE* 4.2 1.6 - - + -
176B PRO* 3.6 20.4 - - - +
177B PRO* 2.4 63.4 - - + +
178B SER* 3.0 18.1 + - - +
207B TYR* 3.9 4.5 + - - -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG 4.0 7.2 - - - +
16B GLN* 2.7 15.1 + - - +
18B GLU* 1.3 82.7 - - + +
20B ALA* 1.3 57.2 + - - +
22B ALA* 4.4 6.4 + - - +
176B PRO* 6.2 0.7 - - - -
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLN 3.8 3.4 + - - +
17B LEU* 4.1 16.8 - - + +
18B GLU 3.0 0.6 - - - -
19B ALA* 1.3 78.2 - - - +
21B GLN* 1.3 65.9 + - - +
22B ALA* 2.8 12.4 + - - +
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU 4.1 2.6 + - - -
18B GLU* 3.5 14.1 + - - +
20B ALA* 1.3 77.0 - - - +
22B ALA* 1.3 69.9 + - - +
23B VAL* 3.1 11.1 + - + +
68B ARG* 4.6 17.3 + - - +
71B GLN* 4.1 5.5 + - - -
135B ARG* 2.9 50.9 - - - +
177B PRO* 5.6 1.8 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU 4.1 4.1 + - - +
19B ALA 4.4 5.7 + - - +
20B ALA* 2.8 12.5 + - - +
21B GLN* 1.3 82.8 - - - +
23B VAL* 1.3 78.9 + - - +
24B ARG* 5.3 1.6 - - + +
71B GLN* 4.5 5.4 - - - +
173B VAL 5.0 0.5 - - - +
174B HIS 4.5 7.6 - - - +
175B PHE 5.8 0.2 - - - +
176B PRO* 5.8 3.3 - - - +
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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