Contacts of the helix formed by residues 24 - 36 (chain A) in PDB entry 3HOT
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 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS 4.4 0.4 + - - -
23A LYS* 1.3 72.4 - - - +
25A ALA* 1.3 66.4 + - - +
26A ALA* 4.0 6.3 - - - +
27A GLU* 3.1 27.6 + - - +
28A SER* 2.8 25.6 + - - -
50A PHE* 3.4 3.8 - - - -
30D A 4.7 7.1 + - - +
31D A 3.7 17.7 - - - +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A THR* 1.3 71.6 - - - +
26A ALA* 1.3 53.3 + - - +
28A SER* 3.1 5.3 + - - -
29A HIS* 2.8 37.1 + - - +
43A VAL* 5.0 1.8 - - + +
46A CYS* 4.5 6.4 - - + +
47A GLU* 3.8 37.2 - - + +
50A PHE* 3.2 26.9 - - + -
31D A 3.2 17.6 + - - +
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Residues in contact with ALA 26 (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 THR* 3.3 2.6 - - - +
25A ALA* 1.3 73.5 - - - +
27A GLU* 1.3 59.0 + - - +
29A HIS* 2.8 25.7 + - - +
30A ARG* 3.1 28.8 + - - +
43A VAL* 4.6 10.3 - - + +
30D A 3.3 35.7 - - + +
31D A 2.9 15.3 + - - +
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Residues in contact with GLU 27 (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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23A LYS* 2.9 22.8 + - + +
24A THR* 3.1 21.9 + - - +
26A ALA* 1.3 77.4 - - - +
28A SER* 1.3 55.4 + - - +
30A ARG* 2.8 38.3 + - - +
31A MET* 2.9 27.9 + - - +
30D A 4.9 3.3 + - - +
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Residues in contact with SER 28 (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 LEU* 4.3 15.7 - - - +
18A CYS* 3.0 41.4 + - - +
23A LYS* 3.6 9.1 + - - +
24A THR 2.8 21.1 + - - -
25A ALA* 3.2 7.6 - - - -
26A ALA 2.8 0.6 + - - -
27A GLU* 1.3 76.7 - - - +
29A HIS* 1.3 63.5 + - - -
30A ARG 3.3 0.4 - - - -
31A MET* 3.0 19.5 - - - +
32A LEU* 3.3 9.7 + - - +
46A CYS* 5.4 0.2 - - - -
50A PHE* 4.0 5.2 - - - -
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Residues in contact with HIS 29 (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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25A ALA 2.8 15.5 + - - +
26A ALA* 2.8 10.4 + - - +
28A SER* 1.3 71.6 - - - +
30A ARG* 1.3 69.4 + - + +
32A LEU* 3.1 12.5 + - - +
33A VAL* 3.1 33.6 + - + +
38A GLU* 5.7 1.6 + - - -
40A VAL* 4.3 13.5 - - + +
41A PRO 3.1 27.6 + - - -
42A THR* 3.9 2.3 + - - -
43A VAL* 3.4 36.6 + - + +
46A CYS* 4.3 16.5 - - - -
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Residues in contact with ARG 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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26A ALA* 3.1 32.6 + - - +
27A GLU* 2.8 46.2 + - - +
29A HIS* 1.3 83.1 - - + +
31A MET* 1.3 67.2 + - - +
33A VAL* 3.4 16.1 - - + +
34A GLU* 3.2 21.7 + - - +
30D A 3.4 32.2 + - - -
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Residues in contact with MET 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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17A PHE* 5.4 3.8 - - + -
18A CYS* 3.7 12.6 - - - -
21A LEU* 5.5 4.3 - - + -
23A LYS* 3.0 33.2 - - + +
27A GLU* 2.9 27.9 + - - +
28A SER* 3.0 9.6 - - - +
30A ARG* 1.3 76.5 - - - +
32A LEU* 1.3 65.4 + - - +
34A GLU* 2.8 24.1 + - - +
35A ALA* 2.9 12.6 + - - +
17B PHE* 3.6 32.8 - - + -
21B LEU* 3.8 17.3 - - + -
31B MET* 5.6 2.9 - - + -
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Residues in contact with LEU 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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11A THR* 4.6 10.5 - - + +
14A VAL* 3.5 34.3 - - + -
15A LEU* 4.1 26.0 - - + -
18A CYS* 5.6 0.2 - - - -
28A SER 3.3 8.0 + - - +
29A HIS* 3.1 12.3 + - - +
31A MET* 1.3 79.5 - - - +
33A VAL* 1.3 58.2 + - - +
35A ALA* 3.1 1.2 + - - +
36A PHE* 2.8 47.3 + - + +
37A GLY 4.6 0.2 - - - +
40A VAL* 3.5 34.3 - - + -
41A PRO* 5.3 2.5 - - + +
46A CYS* 4.5 11.9 - - - -
17B PHE* 4.0 12.6 - - + -
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Residues in contact with VAL 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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29A HIS* 3.1 18.3 + - + +
30A ARG* 3.4 25.1 - - + +
31A MET 3.2 0.4 - - - -
32A LEU* 1.3 79.8 - - - +
34A GLU* 1.3 62.6 + - + +
37A GLY* 2.9 32.6 + - - +
38A GLU* 3.4 46.2 - - - +
40A VAL* 4.1 10.1 - - + +
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Residues in contact with GLU 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 ARG 3.2 10.5 + - - +
31A MET* 2.8 20.1 + - - +
33A VAL* 1.3 81.5 - - + +
35A ALA* 1.3 64.9 + - - +
37A GLY 4.7 0.5 + - - -
20B HIS 4.9 3.3 - - - +
21B LEU* 3.3 28.6 - - + +
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Residues in contact with ALA 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 MET 2.9 6.3 + - - +
32A LEU 3.8 1.6 - - - +
34A GLU* 1.3 81.0 - - - +
36A PHE* 1.3 62.5 + - + +
17B PHE* 3.4 39.0 - - + -
20B HIS* 3.1 42.4 + - + +
21B LEU* 3.5 16.6 - - + -
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Residues in contact with PHE 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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5A VAL* 4.1 31.5 + - - +
6A PRO* 4.3 31.6 - - + +
11A THR* 6.0 2.2 - - - -
14A VAL* 4.3 9.2 - - + -
32A LEU* 2.8 35.0 + - + +
35A ALA* 1.3 84.5 - - - +
37A GLY* 1.3 59.6 + - - +
39A GLN* 5.4 1.1 + - - +
40A VAL* 5.0 5.4 - - + -
13B THR* 6.3 0.4 - - + -
16B ILE* 4.2 11.4 - - + -
17B PHE* 3.5 45.1 - + + -
20B HIS* 3.7 24.7 - + - -
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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