Contacts of the helix formed by residues 11 - 22 (chain A) in PDB entry 1EJI
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ARG* 1.3 88.2 + - - +
12A ALA* 1.3 65.0 + - - +
13A THR* 2.7 6.3 + - - -
14A LEU* 2.9 17.2 + - + +
15A TRP* 3.4 17.9 + - + -
326B ILE* 3.9 29.4 - - + +
330B GLN* 5.8 0.2 - - - +
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Residues in contact with ALA 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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7A MET 5.4 0.4 - - - +
8A ALA* 3.5 43.5 - - + +
9A ASP 4.2 4.1 + - - -
10A ARG* 2.7 15.0 + - - +
11A ASP* 1.3 70.6 - - - +
13A THR* 1.3 67.8 + - - +
15A TRP* 3.4 5.4 + - - +
16A ALA* 3.1 21.4 + - - +
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Residues in contact with THR 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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11A ASP 2.7 5.3 + - - -
12A ALA* 1.3 79.0 - - - +
14A LEU* 1.3 79.4 + - + +
16A ALA* 3.1 16.9 + - - +
17A SER* 3.3 10.8 + - - +
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Residues in contact with LEU 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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11A ASP* 2.9 12.9 + - + +
13A THR* 1.3 87.6 - - + +
15A TRP* 1.3 54.7 + - - +
16A ALA 2.9 4.3 - - - -
17A SER* 2.7 29.2 + - - +
18A HIS* 2.8 16.2 + - - +
322B THR* 3.5 33.2 - - + -
323B GLU* 4.2 11.3 - - + +
326B ILE* 3.7 34.8 - - + -
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Residues in contact with TRP 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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10A ARG* 4.2 22.2 - - - +
11A ASP* 3.4 22.6 + - + +
12A ALA* 4.0 8.3 - - - +
14A LEU* 1.3 76.1 - - - +
16A ALA* 1.3 56.3 + - - +
18A HIS* 3.6 34.5 - + + -
19A GLU* 3.1 29.7 + - + +
326B ILE* 3.9 25.7 - - + +
327B TYR* 4.9 7.0 - + - -
330B GLN* 3.6 35.2 + - + +
409B THR* 3.5 25.8 - - + -
410B SER 5.3 0.2 - - - -
412B GLY* 4.0 24.9 - - - -
414B LEU* 4.1 11.9 - - + +
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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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12A ALA 3.1 11.1 + - - +
13A THR* 3.1 14.7 + - - +
14A LEU 2.9 0.6 - - - -
15A TRP* 1.3 75.9 - - - +
17A SER* 1.3 62.2 + - - +
19A GLU* 2.9 24.3 - - - +
20A LYS* 3.1 10.4 + - - +
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Residues in contact with SER 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 THR* 3.3 12.2 + - - +
14A LEU* 2.7 18.4 + - - +
16A ALA* 1.3 69.8 - - - +
18A HIS* 1.3 64.9 + - - -
19A GLU 2.8 3.8 - - - -
20A LYS* 2.7 20.3 + - - +
21A MSE 2.8 14.0 + - - +
323B GLU* 3.2 30.2 + - - -
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Residues in contact with HIS 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 LEU 2.8 16.9 + - - +
15A TRP* 3.6 36.5 - + + +
17A SER* 1.3 73.6 - - - +
19A GLU* 1.3 63.9 + - - +
21A MSE 3.7 17.1 + - + +
22A LEU* 3.4 41.8 + - + +
260B ARG* 2.9 26.9 + - - -
323B GLU* 3.5 26.9 - - + +
326B ILE* 5.2 2.2 - - + -
327B TYR* 3.4 32.6 - + + +
410B SER* 4.1 10.1 - - - -
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Residues in contact with GLU 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 TRP* 3.1 20.1 + - + +
16A ALA* 2.9 17.9 + - - +
17A SER 2.8 0.6 + - - -
18A HIS* 1.3 84.7 + - - +
20A LYS* 1.3 60.8 + - + +
22A LEU* 3.5 12.4 + - - +
23A SER* 3.5 12.6 + - - +
411B ARG 6.0 0.3 - - - -
412B GLY* 6.0 1.6 - - - -
477B SER* 3.8 30.0 + - - -
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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 6.4 + - - +
17A SER* 2.7 15.5 + - - +
19A GLU* 1.3 75.0 - - + +
21A MSE 1.3 53.4 + - - +
22A LEU 3.0 2.5 - - - -
23A SER* 2.7 15.5 + - - +
24A GLN* 2.6 59.1 + - + +
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Residues in contact with MSE 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 SER 2.8 19.5 + - - +
18A HIS* 3.8 20.6 - - + +
20A LYS* 1.3 73.9 - - - +
22A LEU* 1.3 62.9 + - + +
23A SER 3.3 0.9 + - - -
24A GLN* 3.9 27.5 + - - +
29A SER* 4.5 2.2 + - - +
58B SER* 4.0 9.7 - - - -
260B ARG* 3.6 27.4 - - - +
318B GLN* 4.1 38.7 + - + +
321B THR* 3.7 29.2 - - - +
323B GLU* 4.2 19.1 - - + +
324B PHE* 4.5 3.4 - - - +
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Residues in contact with LEU 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 HIS* 3.4 35.7 - - + +
19A GLU* 3.5 8.7 + - - +
20A LYS 2.9 1.0 + - - -
21A MSE 1.3 80.5 - - + +
23A SER* 1.3 58.3 + - - +
24A GLN 3.8 0.2 - - - -
58B SER* 3.8 23.5 - - - +
59B ARG 3.3 18.8 + - - -
260B ARG* 3.7 37.5 - - - +
318B GLN* 4.3 4.3 - - - +
410B SER* 3.7 9.9 - - - +
479B PRO* 3.5 33.6 - - + +
480B GLY 3.6 15.1 + - - -
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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