Contacts of the helix formed by residues 35 - 47 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C SER* 1.3 70.3 + - - +
36C ASP* 1.3 74.6 + - - +
38C PHE* 3.1 5.7 + - - +
39C LYS* 2.9 39.6 + - + +
58C GLY* 3.9 9.1 - - - +
61C ALA* 3.9 14.6 - - + -
62C ILE* 3.3 36.7 - - + +
65C LEU* 3.8 15.1 - - + +
82C GLU* 3.0 10.2 + - - +
83C SER* 3.3 31.5 + - - +
84C ASN* 2.7 29.4 + - - +
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Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LYS* 4.7 13.0 + - - -
18C THR* 5.5 2.9 + - - +
34C SER* 3.3 6.7 + - - +
35C LYS* 1.3 98.6 - - - +
37C ALA* 1.3 62.9 + - - +
39C LYS* 3.2 16.7 + - - +
40C GLU* 3.0 31.7 + - - +
82C GLU* 5.2 3.7 + - - +
130C ARG* 3.3 28.0 + - - +
134C HIS* 3.9 15.7 + - + +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C SER* 3.2 26.4 + - - +
36C ASP* 1.3 76.8 - - - +
38C PHE* 1.3 64.0 + - + +
40C GLU* 3.3 11.4 + - - +
41C VAL* 3.2 26.8 + - - +
67D HIS* 4.0 24.5 - - + +
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Residues in contact with PHE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU 5.2 0.9 - - - -
33C LEU* 4.0 22.0 - - + -
34C SER 3.1 23.6 + - - +
35C LYS 3.5 8.3 - - - +
37C ALA* 1.3 72.1 - - - +
39C LYS* 1.3 66.4 + - - +
41C VAL* 3.1 4.9 + - - +
42C MSE 3.1 28.8 + - + +
61C ALA* 3.9 11.2 - - + -
64C MSE 3.4 39.5 - - + -
65C LEU* 3.4 26.5 - - + -
68C THR* 4.2 5.2 - - - -
64D MSE 3.4 32.9 - - + +
67D HIS* 3.7 28.5 - + - -
68D THR* 4.0 7.6 - - - -
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LYS* 2.9 24.7 + - + +
36C ASP* 3.2 27.8 + - - +
38C PHE* 1.3 75.9 - - - +
40C GLU* 1.3 57.0 + - - +
42C MSE 3.1 5.4 + - - +
43C PHE* 2.9 50.4 + - + -
54C SER* 2.9 46.3 + - - -
55C ARG* 5.2 0.2 - - - +
57C VAL* 3.9 10.6 - - + +
58C GLY* 3.6 17.0 - - - +
61C ALA* 3.7 15.2 - - + +
130C ARG* 5.7 0.2 - - - +
134C HIS* 4.0 14.1 + - + +
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ASP* 3.0 16.3 + - - +
37C ALA* 3.6 11.1 - - - +
38C PHE 3.2 0.2 - - - -
39C LYS* 1.3 73.1 - - - +
41C VAL* 1.3 64.4 + - + +
43C PHE* 3.4 7.1 + - - +
44C ASP* 3.1 31.1 + - - +
130C ARG* 5.2 3.3 + - - -
131C HIS* 3.6 33.3 + - + +
134C HIS* 2.9 28.9 + - - +
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ALA 3.2 13.9 + - - +
38C PHE 3.1 8.3 + - - +
40C GLU* 1.3 76.5 - - + +
42C MSE 1.3 63.9 + - - +
44C ASP* 4.7 2.0 - - - -
45C GLY* 3.1 6.4 + - - -
60D THR* 4.0 3.6 - - + +
63D MSE 2.9 67.8 - - + +
64D MSE 3.8 19.5 - - + +
67D HIS* 4.0 30.5 - - + +
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Residues in contact with MSE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C PHE* 3.1 20.2 + - + +
39C LYS 3.1 7.2 + - - +
41C VAL* 1.3 74.7 - - + +
43C PHE* 1.3 57.4 + - - +
45C GLY 3.2 0.2 + - - -
46C LEU* 2.7 48.0 + - + +
47C GLY 4.8 0.2 - - - -
57C VAL* 3.5 25.6 - - + +
60C THR* 4.0 23.6 - - - -
61C ALA* 3.3 41.5 - - + -
64C MSE 5.1 7.2 - - + -
42D MSE 4.3 15.0 - - - +
46D LEU* 5.1 4.7 - - - -
60D THR* 3.8 17.9 - - + -
64D MSE 5.1 7.2 - - + -
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Residues in contact with PHE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LYS* 2.9 52.7 + - + +
40C GLU* 3.8 5.2 - - + +
42C MSE 1.3 72.6 - - - +
44C ASP* 1.3 59.9 + - - +
47C GLY* 2.8 38.7 + - - -
48C TRP* 3.6 22.8 - - + -
53C TRP* 4.0 11.9 - + - -
54C SER* 3.8 8.5 - - - -
57C VAL* 3.7 24.7 - - + -
131C HIS* 3.5 25.6 - + + -
133C GLY* 3.3 38.8 - - - -
134C HIS* 3.6 18.8 - + - -
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Residues in contact with ASP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLU* 3.1 20.5 + - - +
41C VAL* 5.0 1.0 - - - -
43C PHE* 1.3 76.6 - - - +
45C GLY* 1.3 61.3 + - - +
47C GLY* 4.7 0.7 + - - -
48C TRP* 4.3 9.3 - - - -
131C HIS* 2.7 32.5 + - - -
63D MSE 3.7 18.9 - - + +
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Residues in contact with GLY 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C VAL 3.1 10.6 + - - -
42C MSE 3.7 0.9 - - - -
44C ASP* 1.3 79.6 - - - +
46C LEU* 1.3 58.5 + - - +
47C GLY 3.6 0.2 - - - -
56D ARG* 3.5 17.5 - - - +
59D ALA* 5.7 2.8 - - - +
60D THR* 3.2 22.7 + - - -
63D MSE 3.6 17.4 - - - +
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Residues in contact with LEU 46 (chain C).
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 2.7 31.9 + - + +
45C GLY* 1.3 72.6 - - - -
47C GLY* 1.3 58.3 + - - +
53C TRP* 4.2 18.4 - - + -
57C VAL* 5.5 0.9 - - + -
42D MSE 4.3 14.4 - - - -
46D LEU* 3.4 33.0 - - + -
53D TRP* 4.0 17.2 - - + -
56D ARG* 3.2 54.2 + - - +
57D VAL* 4.0 8.7 - - + +
60D THR* 3.3 20.4 - - + +
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Residues in contact with GLY 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PHE* 2.8 26.6 + - - +
44C ASP 4.6 0.8 + - - -
45C GLY 3.6 1.4 - - - -
46C LEU* 1.3 79.1 - - - +
48C TRP* 1.3 63.7 + - - -
53C TRP* 3.1 19.1 + - - -
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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