Contacts of the helix formed by residues 34 - 46 (chain B) in PDB entry 1H5Y
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 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B LYS* 5.3 0.7 - - - +
19B VAL* 4.0 0.9 - - - -
33B GLY* 1.3 71.8 - - - -
35B PRO* 1.3 82.8 - - - +
36B VAL* 3.2 9.6 + - - +
37B GLU* 3.0 53.1 + - - +
38B MET* 2.9 25.7 + - - +
71B ARG* 4.3 17.0 + - - -
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Residues in contact with PRO 35 (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 LEU* 3.8 6.3 - - + +
13B ILE* 3.6 31.2 - - + -
18B LYS* 4.4 9.4 - - - -
19B VAL* 3.6 19.5 - - + +
33B GLY 4.0 1.3 - - - +
34B ASP* 1.3 95.2 - - - +
36B VAL* 1.3 53.5 + - + +
38B MET* 3.7 1.2 - - - +
39B ALA* 2.8 37.2 + - - +
52B ILE* 5.9 0.9 - - + -
68B SER* 4.0 22.7 - - - +
71B ARG* 5.8 2.0 - - - +
72B VAL* 4.0 15.5 - - + -
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Residues in contact with VAL 36 (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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34B ASP* 3.2 10.3 + - - +
35B PRO* 1.3 81.5 - - + +
37B GLU* 1.3 67.9 + - + +
39B ALA* 3.2 1.8 + - - +
40B VAL* 3.0 27.5 + - + +
68B SER* 5.1 0.7 - - - +
71B ARG* 3.3 59.9 - - + +
72B VAL* 4.1 9.0 - - + +
75B ALA* 4.2 19.0 - - + +
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Residues in contact with GLU 37 (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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34B ASP* 3.0 35.7 + - + +
36B VAL* 1.3 80.9 - - + +
38B MET* 1.3 58.9 + - + +
40B VAL* 3.9 6.5 - - - +
41B ARG* 3.0 28.9 + - - +
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Residues in contact with MET 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.1 9.6 - - + -
19B VAL* 3.7 28.7 - - - -
32B VAL* 3.9 11.2 - - + +
33B GLY* 3.8 20.0 - - - -
34B ASP 2.9 21.5 + - - +
35B PRO 3.8 2.5 - - - +
37B GLU* 1.3 75.8 - - + +
39B ALA* 1.3 61.1 + - - +
41B ARG* 3.3 7.6 + - - +
42B TYR* 2.9 50.5 + - + +
231B HIS* 3.5 41.1 - - + +
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Residues in contact with ALA 39 (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 LEU* 4.0 13.8 - - + +
35B PRO 2.8 17.4 + - - +
36B VAL* 3.8 3.8 - - - +
38B MET* 1.3 78.1 - - - +
40B VAL* 1.3 54.9 + - - +
42B TYR* 3.4 1.1 + - - -
43B GLU* 3.0 29.3 + - - +
50B ILE* 3.7 20.7 - - + +
72B VAL* 3.6 30.5 - - + -
75B ALA* 6.3 0.2 - - + -
76B VAL* 3.8 10.1 - - + +
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Residues in contact with VAL 40 (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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36B VAL* 3.0 23.3 + - + +
37B GLU* 3.9 7.4 - - - +
39B ALA* 1.3 74.5 - - - +
41B ARG* 1.3 61.1 + - + +
43B GLU* 3.3 8.4 + - - +
44B GLU* 3.0 44.3 + - - +
75B ALA* 3.6 39.7 - - + +
76B VAL* 4.2 6.1 - - + -
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Residues in contact with ARG 41 (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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37B GLU 3.0 18.5 + - - +
38B MET* 3.8 7.2 - - - +
40B VAL* 1.3 78.9 - - - +
42B TYR* 1.3 60.1 + - + +
44B GLU* 3.2 13.7 + - + +
45B GLU* 2.9 50.2 + - - +
233B ARG* 3.3 47.2 - - - +
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Residues in contact with TYR 42 (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 PRO* 3.6 29.2 - - + -
11B LEU* 3.8 13.5 - - + -
38B MET* 2.9 36.7 + - + +
39B ALA* 3.8 5.6 - - - +
41B ARG* 1.3 75.6 - - + +
43B GLU* 1.3 66.6 + - - +
45B GLU* 3.0 14.7 + - - +
46B GLY 2.9 19.1 + - - -
47B ALA* 2.9 12.4 + - + +
50B ILE* 4.1 4.0 - - + -
230B PHE* 3.1 35.5 + + + -
231B HIS* 2.5 45.4 + + - -
233B ARG* 4.1 17.8 + - - -
237B ILE* 4.0 14.2 - - + +
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Residues in contact with GLU 43 (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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39B ALA 3.0 17.8 + - - +
40B VAL* 3.7 8.1 - - - +
41B ARG 3.3 0.2 - - - -
42B TYR* 1.3 77.2 - - - +
44B GLU* 1.3 64.9 + - - +
45B GLU 3.0 0.9 + - - -
46B GLY* 3.0 12.3 + - - -
47B ALA* 4.1 4.4 + - - +
75B ALA 4.0 3.8 - - - +
76B VAL* 3.6 18.7 - - + +
77B SER* 2.6 35.8 + - - -
78B ILE* 3.2 40.1 + - + +
252B ARG* 5.7 0.7 + - - -
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Residues in contact with GLU 44 (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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40B VAL* 3.0 34.4 + - - +
41B ARG* 3.6 14.3 - - + +
43B GLU* 1.3 78.8 - - - +
45B GLU* 1.3 62.8 + - + +
46B GLY 3.5 0.5 + - - -
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Residues in contact with GLU 45 (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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41B ARG* 2.9 40.8 + - + +
42B TYR* 3.4 15.8 - - - +
43B GLU 3.0 1.0 + - - -
44B GLU* 1.3 79.8 - - + +
46B GLY* 1.3 55.4 + - - +
233B ARG* 2.9 44.2 + - - -
236B SER* 5.0 8.4 - - - -
237B ILE* 3.6 14.2 + - + +
238B ALA* 3.6 30.7 + - + +
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Residues in contact with GLY 46 (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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42B TYR 2.9 1.0 + - - -
43B GLU 3.0 8.5 + - - -
44B GLU 3.4 1.2 - - - -
45B GLU* 1.3 81.0 - - - +
47B ALA* 1.3 67.7 + - - +
48B ASP 3.3 0.2 + - - -
237B ILE* 3.6 8.7 - - - -
241B LYS* 2.7 36.3 + - - -
252B ARG* 3.3 6.4 + - - -
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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