Contacts of the helix formed by residues 35 - 47 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A SER* 1.3 69.9 + - - +
36A ASP* 1.3 75.5 + - - +
38A PHE* 3.2 6.0 + - - +
39A LYS* 2.9 40.8 + - + +
58A GLY* 4.0 8.7 - - - +
61A ALA* 4.1 12.6 - - + -
62A ILE* 3.5 33.2 - - + +
65A LEU* 3.9 15.8 - - + +
82A GLU 3.0 10.3 + - - +
83A SER* 3.4 24.6 + - - +
84A ASN* 2.7 36.7 + - - +
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Residues in contact with ASP 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 LYS* 3.9 19.8 + - - -
18A THR* 5.0 5.1 + - - +
34A SER* 3.3 7.2 + - - +
35A LYS* 1.3 96.4 - - - +
37A ALA* 1.3 57.6 + - - +
39A LYS* 3.2 14.6 + - - +
40A GLU* 2.9 44.8 + - - +
82A GLU* 4.8 3.3 + - - +
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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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34A SER* 3.3 25.9 + - - +
35A LYS 3.3 0.4 - - - -
36A ASP* 1.3 77.1 - - - +
38A PHE* 1.3 62.4 + - - +
40A GLU* 3.3 16.5 + - - +
41A VAL* 3.2 26.3 + - - +
67B HIS* 4.0 24.6 - - + +
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Residues in contact with PHE 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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32A LEU 5.3 0.2 - - - -
33A LEU* 3.8 23.8 - - + -
34A SER 3.1 27.2 + - - +
35A LYS 3.5 7.2 - - - +
37A ALA* 1.3 71.9 - - - +
39A LYS* 1.3 66.3 + - - +
41A VAL* 3.2 4.7 + - - +
42A MSE 3.1 28.2 + - + +
61A ALA* 3.7 13.2 - - + -
64A MSE 3.5 34.1 - - + -
65A LEU* 3.5 24.9 - - + -
68A THR* 4.2 4.3 - - - -
64B MSE 3.3 36.1 - - + +
67B HIS* 3.6 29.4 - + - -
68B THR* 4.0 5.2 - - - -
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Residues in contact with LYS 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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35A LYS* 2.9 30.9 + - + +
36A ASP* 3.2 23.8 + - - +
38A PHE* 1.3 75.7 - - - +
40A GLU* 1.3 56.8 + - + +
42A MSE 3.2 5.2 + - - +
43A PHE* 2.8 57.9 + - + -
54A SER* 3.4 33.6 + - - -
55A ARG* 5.6 0.6 - - - +
57A VAL* 3.9 10.4 - - + +
58A GLY* 3.7 17.6 - - - +
61A ALA* 3.7 15.0 - - + +
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Residues in contact with GLU 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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36A ASP* 2.9 34.6 + - + +
37A ALA* 3.6 13.0 + - - +
38A PHE 3.2 0.2 - - - -
39A LYS* 1.3 74.3 - - + +
41A VAL* 1.3 66.1 + - + +
43A PHE* 4.0 10.5 - - + +
44A ASP* 3.0 34.9 + - - +
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Residues in contact with VAL 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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37A ALA 3.2 14.1 + - - +
38A PHE 3.2 7.0 + - - +
40A GLU* 1.3 76.2 - - + +
42A MSE 1.3 58.5 + - - +
44A ASP* 3.4 2.8 + - - -
45A GLY* 3.1 10.2 + - - -
60B THR* 3.9 3.1 - - + +
63B MSE 2.9 62.2 - - + +
64B MSE 3.8 28.3 - - + +
67B HIS* 4.2 28.5 - - + +
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Residues in contact with MSE 42 (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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38A PHE* 3.1 16.0 + - + +
39A LYS 3.2 5.4 + - - +
41A VAL* 1.3 74.8 - - - +
43A PHE* 1.3 60.4 + - - +
46A LEU* 2.8 40.4 + - + +
57A VAL* 3.6 35.7 - - + +
60A THR* 3.8 24.7 - - - +
61A ALA* 3.6 26.5 - - + +
64A MSE 5.2 5.6 - - + -
42B MSE 4.1 17.0 - - - +
46B LEU* 4.8 6.5 - - - -
60B THR* 3.8 20.2 - - + -
64B MSE 5.0 8.1 - - + -
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Residues in contact with PHE 43 (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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39A LYS* 2.8 46.9 + - + +
40A GLU* 4.0 9.9 - - + +
41A VAL 3.4 0.2 - - - -
42A MSE 1.3 71.7 - - - +
44A ASP* 1.3 62.7 + - - +
47A GLY* 2.8 46.9 + - - +
48A TRP* 4.1 19.6 - + + -
53A TRP* 3.9 9.4 - + - -
54A SER* 3.5 35.4 - - - -
57A VAL* 3.7 29.6 - - + -
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Residues in contact with ASP 44 (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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40A GLU* 3.0 25.2 + - - +
41A VAL* 3.6 6.4 - - - +
43A PHE* 1.3 80.7 - - - +
45A GLY* 1.3 57.9 + - - +
47A GLY 4.9 0.3 + - - -
63B MSE 3.6 15.1 - - + +
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Residues in contact with GLY 45 (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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41A VAL 3.1 9.9 + - - -
42A MSE 3.9 0.4 - - - -
43A PHE 3.3 0.2 - - - -
44A ASP* 1.3 77.4 - - - +
46A LEU* 1.3 60.7 + - - +
47A GLY 3.8 0.2 - - - -
56B ARG* 4.3 10.7 + - - +
59B ALA* 5.7 2.6 - - - +
60B THR* 3.2 24.5 + - - -
63B MSE 3.5 17.9 - - - +
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Residues in contact with LEU 46 (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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42A MSE 2.8 22.1 + - + +
45A GLY* 1.3 78.9 - - - +
47A GLY* 1.3 59.1 + - - +
53A TRP* 3.9 24.6 - - + -
57A VAL* 5.6 0.2 - - + -
42B MSE 4.6 13.2 - - - -
46B LEU* 3.6 31.4 - - + -
53B TRP* 4.1 16.3 - - + -
56B ARG* 2.8 55.0 + - + +
57B VAL* 4.0 7.9 - - + +
60B THR* 3.4 20.6 - - + +
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Residues in contact with GLY 47 (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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43A PHE* 2.8 33.1 + - - +
44A ASP 4.7 0.2 - - - -
45A GLY 3.8 0.6 - - - -
46A LEU* 1.3 74.6 - - - +
48A TRP* 1.3 64.5 + - - -
53A TRP* 2.9 21.5 + - - -
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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