Contacts of the helix formed by residues 29 - 41 (chain A) in PDB entry 2HI3
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASN* 4.2 18.3 + - - +
27A HIS* 3.2 9.2 + - - +
28A PRO* 1.3 76.5 - - - +
30A PRO* 1.3 78.3 - - - +
31A THR* 3.9 8.5 + - - -
32A THR* 2.9 32.2 + - - +
33A LEU* 3.0 36.0 + - - +
51A PHE* 5.5 0.2 - - - -
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Residues in contact with PRO 30 (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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28A PRO 4.7 0.7 - - - +
29A ASP* 1.3 99.3 - - - +
31A THR* 1.3 71.3 + - - +
33A LEU* 3.4 8.3 + - + +
34A CYS* 3.0 25.7 + - - -
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Residues in contact with THR 31 (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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29A ASP* 3.9 9.5 + - - -
30A PRO* 1.3 81.3 - - - +
32A THR* 1.3 64.1 + - - +
34A CYS* 3.7 5.0 + - - +
35A LEU* 3.4 32.4 + - + +
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Residues in contact with THR 32 (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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24A VAL* 3.5 36.8 - - + -
25A ASN* 4.5 4.1 + - - +
29A ASP* 2.9 33.9 + - + +
30A PRO 3.2 0.2 - - - -
31A THR* 1.3 76.3 - - - +
33A LEU* 1.3 66.2 + - + +
35A LEU* 3.2 4.5 + - - -
36A ILE* 2.8 41.0 + - + +
51A PHE* 5.7 0.9 - - + -
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Residues in contact with LEU 33 (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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28A PRO* 4.4 4.3 - - + -
29A ASP* 3.0 35.1 + - + +
30A PRO* 3.4 6.9 + - + +
32A THR* 1.3 74.7 - - - +
34A CYS* 1.3 59.7 + - - +
36A ILE* 3.4 4.7 - - - +
37A ALA* 2.9 35.2 + - - +
44A GLU* 3.6 32.1 - - + +
47A THR* 4.1 12.8 - - + -
48A GLN* 3.6 28.7 - - + +
51A PHE* 3.6 33.7 - - + -
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Residues in contact with CYS 34 (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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30A PRO 3.0 20.9 - - - -
31A THR* 4.1 5.6 - - - +
32A THR 3.4 0.2 - - - -
33A LEU* 1.3 78.2 - - - +
35A LEU* 1.3 64.0 + - + +
37A ALA* 3.8 1.8 - - - +
38A ALA* 3.4 20.4 + - - +
44A GLU* 3.9 30.3 - - + +
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Residues in contact with LEU 35 (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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31A THR* 3.4 23.6 + - + +
32A THR* 3.2 5.0 + - - +
34A CYS* 1.3 83.7 - - + +
36A ILE* 1.3 64.3 + - + +
38A ALA* 3.5 6.1 + - + +
39A GLU* 3.4 23.6 + - - +
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Residues in contact with ILE 36 (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 LEU* 5.6 0.9 - - + -
20A ASN* 3.4 28.9 + - - +
23A LYS* 6.5 0.2 - - + -
24A VAL* 3.9 11.0 - - + -
32A THR* 2.8 45.5 + - + +
33A LEU* 3.4 8.5 - - - +
35A LEU* 1.3 72.9 - - + +
37A ALA* 1.3 64.2 + - - +
39A GLU* 3.2 6.8 + - - +
40A ALA* 2.8 31.6 + - - +
47A THR* 4.1 8.3 - - + -
51A PHE* 3.4 38.4 - - + -
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Residues in contact with ALA 37 (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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33A LEU 2.9 20.0 + - - +
34A CYS* 3.8 4.9 - - - +
36A ILE* 1.3 79.1 - - - +
38A ALA* 1.3 54.6 + - - +
40A ALA* 3.2 5.3 + - - -
41A GLY 2.9 9.5 + - - -
42A LEU* 2.7 32.8 + - - +
43A THR* 3.6 22.9 - - - -
44A GLU* 3.9 2.0 - - + +
47A THR* 3.2 26.5 - - - +
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Residues in contact with ALA 38 (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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34A CYS 3.4 10.9 + - - +
35A LEU* 3.8 10.5 - - + +
36A ILE 3.3 0.6 - - - -
37A ALA* 1.3 77.7 - - - +
39A GLU* 1.3 67.4 + - - +
41A GLY* 3.3 11.8 + - - -
42A LEU 3.9 7.6 + - - -
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Residues in contact with GLU 39 (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 ILE* 5.1 2.7 - - - +
35A LEU* 3.4 14.1 + - - +
36A ILE* 3.2 9.8 + - - +
37A ALA 3.2 0.4 - - - -
38A ALA* 1.3 84.3 - - - +
40A ALA* 1.3 61.7 + - - +
41A GLY* 3.5 0.3 + - - -
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Residues in contact with ALA 40 (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 GLN* 2.7 33.3 + - - +
16A ILE* 3.6 37.5 - - + +
17A LEU* 4.8 13.0 - - + -
20A ASN* 4.5 6.2 - - - +
36A ILE 2.8 18.6 + - - +
37A ALA* 3.2 7.8 + - - +
39A GLU* 1.3 77.0 - - - +
41A GLY* 1.3 56.4 + - - +
42A LEU* 4.6 3.6 - - + +
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Residues in contact with GLY 41 (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 GLN* 4.2 6.0 + - - +
37A ALA 2.9 2.8 + - - -
38A ALA 3.3 9.1 + - - -
39A GLU 3.2 3.8 - - - -
40A ALA* 1.3 80.5 - - - +
42A LEU* 1.3 71.5 + - - +
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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