Contacts of the helix formed by residues 17 - 28 (chain B) in PDB entry 2H1H
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 THR 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ILE* 4.5 6.1 - - + -
7B LYS* 3.0 32.8 - - + +
13B ASP 3.1 7.3 + - - -
14B VAL 3.0 9.5 + - - -
16B HIS* 1.3 77.2 - - - +
18B LEU* 1.3 66.2 + - - +
19B PRO 3.3 1.1 - - - -
20B ALA* 3.0 16.5 + - - +
21B LEU* 3.2 21.1 - - + +
35B TRP* 3.7 14.4 - - + -
93B ALA* 4.7 2.0 - - + -
144B THR* 3.7 23.7 + - + +
148B PHE* 4.0 11.7 - - + -
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Residues in contact with LEU 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 VAL 4.1 2.7 - - - +
15B LEU* 3.2 34.1 - - + +
17B THR* 1.3 76.9 - - - +
19B PRO* 1.3 65.6 - - + +
21B LEU* 3.1 19.3 + - + +
22B THR* 3.2 14.9 + - - -
35B TRP* 3.9 24.5 - - + -
44B ILE* 4.3 7.2 - - + +
45B PRO* 4.7 9.2 - - + -
48B HIS* 3.6 26.1 + - + -
163B TYR* 3.7 18.4 - - + +
165B ILE* 3.5 35.7 - - + -
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Residues in contact with PRO 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 LEU 3.7 5.4 - - - +
16B HIS 3.5 10.1 - - - +
17B THR 3.4 4.0 - - - -
18B LEU* 1.3 92.8 - - + +
20B ALA* 1.3 64.1 + - - +
22B THR* 3.1 3.5 + - - -
23B ASP* 3.0 26.0 + - - +
141B VAL* 3.8 28.5 - - + -
145B ARG* 4.2 5.2 - - - -
161B GLY* 4.0 6.5 - - - -
162B ASP 3.5 25.1 + - - +
163B TYR* 3.7 31.0 - - + +
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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 HIS 5.1 0.8 + - - -
17B THR 3.0 12.7 + - - +
19B PRO* 1.3 77.0 - - - +
21B LEU* 1.3 62.7 - - - +
23B ASP* 3.0 8.2 + - - +
24B ALA* 3.0 18.9 + - - +
144B THR* 3.6 24.9 - - + +
145B ARG* 3.8 17.7 - - - +
148B PHE* 3.4 30.3 - - + -
154B TYR* 3.6 4.9 + - - -
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Residues in contact with LEU 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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5B ILE* 3.5 28.5 - - + -
17B THR* 3.2 31.6 - - + +
18B LEU* 3.1 8.4 + - + +
20B ALA* 1.3 78.3 - - - +
22B THR* 1.3 57.7 + - - +
24B ALA* 3.2 3.9 + - - +
25B GLN* 2.8 29.6 + - - +
33B PHE* 3.8 30.9 - - + -
35B TRP* 3.8 19.1 - - + -
48B HIS* 3.8 21.4 - - + +
50B ALA* 4.8 0.2 - - + -
51B VAL* 3.5 31.6 - - + -
148B PHE* 3.9 4.3 - - + -
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Residues in contact with THR 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 LEU 3.2 3.5 + - - -
19B PRO 3.1 5.9 + - - -
21B LEU* 1.3 74.3 - - - +
23B ASP* 1.3 69.8 + - - +
25B GLN* 3.3 9.1 + - - +
26B GLN* 3.1 47.2 + - + +
48B HIS* 2.8 27.0 + - - -
162B ASP* 2.8 42.0 + - + +
164B ALA* 3.5 13.4 - - + +
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Residues in contact with ASP 23 (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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19B PRO 3.0 11.6 + - - +
20B ALA* 3.3 6.7 - - - +
22B THR* 1.3 78.8 - - - +
24B ALA* 1.3 64.1 + - - +
26B GLN* 3.2 12.4 + - - +
27B ALA* 3.1 23.9 + - - +
145B ARG* 2.5 63.9 + - - +
154B TYR* 3.5 20.9 - - + +
156B LYS* 4.3 0.5 - - - +
157B PRO* 3.5 21.8 - - + +
159B THR* 5.2 0.7 + - - -
161B GLY* 5.5 0.7 - - - -
162B ASP 5.7 1.2 + - - -
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Residues in contact with ALA 24 (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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20B ALA 3.0 9.1 + - - +
21B LEU 3.4 8.3 - - - +
23B ASP* 1.3 76.7 - - - +
25B GLN* 1.3 56.9 + - - +
28B ILE* 2.8 35.2 + - - +
31B ILE* 3.7 4.4 - - + +
33B PHE* 3.5 27.4 - - + -
148B PHE* 4.5 0.9 - - + -
152B LEU* 4.0 8.3 - - + -
154B TYR* 3.2 28.2 + - + +
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Residues in contact with GLN 25 (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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21B LEU 2.8 18.8 + - - +
22B THR* 3.7 11.1 + - - +
23B ASP 3.3 0.2 - - - -
24B ALA* 1.3 73.9 - - - +
26B GLN* 1.3 64.1 + - + +
28B ILE 3.5 0.4 - - - +
29B PRO* 3.5 22.7 - - + +
30B GLY 5.4 5.6 - - - +
31B ILE* 3.8 14.5 - - + +
32B LYS* 4.8 5.2 + - - -
48B HIS* 4.0 15.6 - - - -
49B ALA* 3.9 15.5 - - - +
50B ALA* 3.8 31.7 + - + +
164B ALA* 5.9 1.8 - - - +
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Residues in contact with GLN 26 (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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22B THR* 3.1 34.1 + - + +
23B ASP* 3.7 16.1 - - - +
25B GLN* 1.3 79.9 - - + +
27B ALA* 1.3 64.3 + - - +
29B PRO* 4.4 9.0 - - - +
157B PRO* 4.7 9.5 - - - +
159B THR* 5.5 1.9 + - - -
162B ASP* 5.6 3.8 + - - +
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Residues in contact with ALA 27 (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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23B ASP 3.1 14.2 + - - +
24B ALA 4.0 0.9 - - - +
26B GLN* 1.3 80.3 - - - +
28B ILE* 1.3 61.0 + - + +
29B PRO* 3.5 8.3 - - - +
154B TYR* 3.6 42.4 - - + -
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Residues in contact with ILE 28 (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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1B MET* 3.6 37.5 - - + +
24B ALA 2.8 10.9 + - - +
25B GLN 3.5 4.1 - - - +
27B ALA* 1.3 87.0 - - + +
29B PRO* 1.3 74.6 - - + +
31B ILE* 3.0 41.4 + - + +
152B LEU* 3.9 34.3 - - + +
154B TYR* 4.0 11.7 - - + -
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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