Contacts of the helix formed by residues 35 - 47 (chain D) in PDB entry 2RHM
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 LYS 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D SER* 1.3 70.3 + - - +
36D ASP* 1.3 78.1 + - - +
38D PHE* 3.1 6.0 + - - +
39D LYS* 2.9 36.2 + - + +
58D GLY* 4.1 11.1 - - - +
61D ALA* 3.7 16.3 - - + +
62D ILE* 3.6 24.4 - - + +
65D LEU* 3.8 15.6 - - + +
82D GLU* 3.0 10.6 + - - +
83D SER* 3.4 25.4 + - - +
84D ASN* 2.8 34.5 + - - +
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Residues in contact with ASP 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS* 4.6 11.3 + - - -
34D SER* 3.3 6.0 + - - +
35D LYS* 1.3 92.2 - - - +
37D ALA* 1.3 61.6 + - - +
39D LYS* 3.2 24.6 + - - +
40D GLU* 3.0 33.3 + - - +
82D GLU* 5.0 4.5 + - - +
84D ASN* 6.0 0.2 - - - -
130D ARG* 3.0 31.1 + - - +
134D HIS* 3.5 9.9 + - + +
194D BEZ 4.3 6.2 - - - +
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C HIS* 3.9 24.6 - - + +
34D SER* 3.2 27.0 + - - +
36D ASP* 1.3 77.5 - - - +
38D PHE* 1.3 62.3 + - - +
40D GLU* 3.3 13.4 + - - +
41D VAL* 3.2 26.9 + - - +
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Residues in contact with PHE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C MSE 3.6 29.9 - - + +
67C HIS* 3.6 30.5 - + - -
68C THR* 4.0 5.4 - - - -
32D LEU 5.2 0.2 - - - -
33D LEU* 3.9 24.7 - - + -
34D SER 3.1 25.7 + - - +
35D LYS 3.4 8.5 - - - +
37D ALA* 1.3 75.6 - - - +
39D LYS* 1.3 65.9 + - - +
41D VAL* 3.3 5.3 + - - +
42D MSE 3.2 27.1 + - + +
61D ALA* 3.8 12.3 - - + +
64D MSE 3.4 40.4 - - + -
65D LEU* 3.5 25.1 - - + -
68D THR* 4.3 5.2 - - - -
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Residues in contact with LYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LYS* 2.9 23.8 + - + +
36D ASP* 3.2 28.1 + - - +
38D PHE* 1.3 77.0 - - - +
40D GLU* 1.3 51.6 + - - +
42D MSE 3.1 4.2 + - - +
43D PHE* 2.7 49.7 + - + -
54D SER* 3.0 41.5 + - - -
55D ARG* 5.4 0.4 - - - +
57D VAL* 3.8 12.1 - - + +
58D GLY* 3.6 18.1 - - - +
61D ALA* 3.7 16.1 - - + +
130D ARG* 5.1 2.2 - - - +
134D HIS* 3.2 24.2 + - + +
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ASP* 3.0 22.8 + - - +
37D ALA* 3.7 12.4 - - - +
38D PHE 3.2 0.2 - - - -
39D LYS* 1.3 72.7 - - - +
41D VAL* 1.3 67.0 + - + +
43D PHE* 3.8 6.7 - - + +
44D ASP* 2.9 34.2 + - - +
129D ALA 4.9 4.3 - - - +
130D ARG* 5.5 1.4 + - - -
131D HIS* 3.8 39.1 + - + +
134D HIS* 3.8 16.7 + - - +
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR* 4.0 4.1 - - + +
63C MSE 3.0 60.7 - - + +
64C MSE 3.9 27.6 - - + +
67C HIS* 4.0 29.4 - - + +
37D ALA 3.2 16.2 + - - +
38D PHE 3.7 6.1 - - - +
39D LYS 3.3 0.4 - - - -
40D GLU* 1.3 75.8 - - + +
42D MSE 1.3 57.7 + - - +
44D ASP* 4.7 1.8 - - - -
45D GLY* 3.0 11.6 + - - -
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Residues in contact with MSE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C MSE 4.3 13.0 - - - -
46C LEU* 4.3 13.9 - - - -
60C THR* 3.8 20.6 - - + -
64C MSE 5.1 8.1 - - + -
38D PHE* 3.2 17.4 + - + +
39D LYS 3.1 6.3 + - - +
41D VAL* 1.3 75.3 - - - +
43D PHE* 1.3 60.3 + - - +
46D LEU* 2.8 41.1 + - + +
47D GLY 4.9 0.2 - - - -
57D VAL* 3.7 24.2 - - + +
60D THR* 3.8 23.1 - - + -
61D ALA* 3.7 34.3 - - + +
64D MSE 5.1 6.1 - - + -
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Residues in contact with PHE 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LYS* 2.7 47.9 + - - +
40D GLU* 3.8 6.3 - - - +
42D MSE 1.3 73.4 - - - +
44D ASP* 1.3 58.6 + - - +
47D GLY* 2.8 38.3 + - - +
48D TRP* 3.8 18.3 - - + -
53D TRP* 4.0 13.0 - + - -
54D SER* 4.0 6.5 - - - -
57D VAL* 3.8 22.0 - - + -
131D HIS* 3.5 35.2 - + + -
133D GLY* 3.3 32.1 - - - -
134D HIS* 3.6 24.9 - + - -
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Residues in contact with ASP 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C MSE 3.9 12.6 - - + +
40D GLU* 2.9 24.2 + - - +
41D VAL* 3.8 4.2 - - - +
43D PHE* 1.3 77.0 - - - +
45D GLY* 1.3 60.6 + - - +
47D GLY 4.7 0.9 + - - -
48D TRP* 5.9 0.2 - - - -
131D HIS* 2.8 29.8 + - - -
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Residues in contact with GLY 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ARG* 4.6 7.6 + - - +
59C ALA* 5.8 2.0 - - - +
60C THR* 3.2 23.7 + - - -
63C MSE 3.5 19.0 - - - +
41D VAL 3.0 12.2 + - - -
44D ASP* 1.3 78.9 - - - +
46D LEU* 1.3 59.1 - - - +
47D GLY 3.7 0.2 - - - -
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C MSE 5.1 2.2 - - - -
46C LEU* 3.4 32.8 - - + -
53C TRP* 4.2 20.9 - - + -
56C ARG* 3.0 57.4 + - + +
57C VAL* 4.0 8.1 - - + +
60C THR* 3.4 27.8 - - + +
42D MSE 2.8 23.0 + - + +
45D GLY* 1.3 77.1 - - - +
47D GLY* 1.3 60.0 + - - +
53D TRP* 4.1 18.4 - - + -
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Residues in contact with GLY 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D MSE 4.3 0.2 - - - +
43D PHE* 2.8 27.3 + - - +
44D ASP 4.5 1.0 + - - -
45D GLY 3.7 1.2 - - - -
46D LEU* 1.3 80.7 - - - +
48D TRP* 1.3 65.0 + - - +
53D TRP* 3.0 19.6 + - - -
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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