Contacts of the helix formed by residues 35 - 47 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B SER* 1.3 69.9 + - - +
36B ASP* 1.3 76.2 + - - +
38B PHE* 3.2 6.7 + - - +
39B LYS* 2.9 42.0 + - + +
58B GLY* 4.1 6.1 - - - +
61B ALA* 3.8 12.5 - - + +
62B ILE* 3.5 35.2 - - + +
65B LEU* 3.9 17.0 - - + +
82B GLU 3.0 10.3 + - - +
83B SER* 3.3 26.6 + - - +
84B ASN* 2.7 34.5 + - - +
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 4.7 9.7 + - - -
18B THR* 5.7 1.6 + - - +
34B SER* 3.3 5.8 + - - +
35B LYS* 1.3 91.2 - - - +
37B ALA* 1.3 58.0 + - - +
39B LYS* 3.2 23.0 + - - +
40B GLU* 2.9 38.8 + - - +
82B GLU* 5.1 4.8 + - - +
130B ARG* 2.8 36.7 + - - +
134B HIS* 3.7 11.9 + - + +
194B BEZ 4.1 6.1 - - - +
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 3.9 23.1 - - + +
34B SER* 3.2 27.5 + - - +
36B ASP* 1.3 75.8 - - - +
38B PHE* 1.3 64.1 + - - +
40B GLU* 3.3 10.2 + - - +
41B VAL* 3.1 27.1 + - - +
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Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MSE 3.6 30.2 - - + +
67A HIS* 3.6 32.1 - + - -
68A THR* 4.1 5.4 - - - -
33B LEU* 3.9 24.7 - - + -
34B SER 3.1 24.5 + - - +
35B LYS 3.4 8.5 - - - +
37B ALA* 1.3 72.3 - - - +
39B LYS* 1.3 65.5 + - - +
41B VAL* 3.3 4.9 + - - +
42B MSE 3.1 29.1 + - + +
61B ALA* 3.8 13.0 - - + +
64B MSE 3.5 39.9 - - + -
65B LEU* 3.6 24.5 - - + -
68B THR* 4.3 4.5 - - - -
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS* 2.9 28.8 + - + +
36B ASP* 3.2 26.7 + - - +
38B PHE* 1.3 74.6 - - - +
40B GLU* 1.3 52.3 + - - +
42B MSE 3.0 5.0 + - - +
43B PHE* 2.8 48.1 + - + -
54B SER* 3.0 42.4 + - - -
55B ARG* 5.3 0.6 - - - +
57B VAL* 3.9 11.1 - - + +
58B GLY* 3.7 17.5 - - - +
61B ALA* 3.6 16.2 - - + -
130B ARG* 5.6 0.8 - - - +
134B HIS* 3.7 22.2 + - + +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ASP* 2.9 25.7 + - - +
37B ALA* 3.7 8.7 - - - +
38B PHE 3.2 0.2 - - - -
39B LYS* 1.3 73.0 - - - +
41B VAL* 1.3 64.0 + - - +
43B PHE* 3.3 6.4 + - + +
44B ASP* 3.0 33.4 + - - +
130B ARG* 4.6 3.6 + - - -
131B HIS* 3.6 32.9 + - + +
134B HIS* 2.8 31.4 + - + +
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 4.1 2.7 - - - +
63A MSE 3.0 44.7 - - + +
64A MSE 3.8 29.2 - - + +
67A HIS* 4.0 31.0 - - + +
37B ALA 3.1 15.8 + - - +
38B PHE 3.3 6.9 + - - +
40B GLU* 1.3 75.2 - - + +
42B MSE 1.3 63.8 + - - +
44B ASP* 3.4 2.6 + - - -
45B GLY* 3.0 18.0 + - - -
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Residues in contact with MSE 42 (chain B).
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 4.1 17.3 - - - +
46A LEU* 4.6 7.2 - - - -
60A THR* 3.9 20.2 - - + -
64A MSE 5.0 7.2 - - + -
38B PHE* 3.1 19.9 + - + +
39B LYS 3.0 7.4 + - - +
41B VAL* 1.3 74.4 - - - +
43B PHE* 1.3 60.9 + - - +
46B LEU* 2.8 41.3 + - + +
47B GLY 4.9 0.2 - - - -
57B VAL* 3.7 35.2 - - + +
60B THR* 3.8 23.6 - - - -
61B ALA* 3.7 22.0 - - + +
64B MSE 5.1 6.7 - - + -
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Residues in contact with PHE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS* 2.8 47.1 + - + +
40B GLU* 3.3 6.3 + - + +
42B MSE 1.3 72.7 - - - +
44B ASP* 1.3 58.4 + - - +
47B GLY* 2.8 41.0 + - - +
48B TRP* 3.7 19.5 - - + -
53B TRP* 4.1 11.9 - + - -
54B SER* 3.9 8.3 - - - -
57B VAL* 3.9 24.2 - - + -
131B HIS* 3.7 33.9 - + + -
133B GLY* 3.2 32.8 - - - -
134B HIS* 3.6 22.4 - + - -
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A MSE 3.9 12.2 - - + +
40B GLU* 3.0 22.1 + - - +
41B VAL* 3.7 6.0 - - - +
43B PHE* 1.3 79.5 - - - +
45B GLY* 1.3 60.0 + - - +
47B GLY 4.6 1.2 + - - -
131B HIS* 2.9 30.2 + - - -
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Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ARG* 4.4 11.6 + - - +
59A ALA* 5.6 2.6 - - - +
60A THR* 3.2 23.8 + - - -
63A MSE 3.5 18.6 - - - +
41B VAL 3.0 11.5 + - - -
42B MSE 3.8 0.7 - - - -
44B ASP* 1.3 77.2 - - - +
46B LEU* 1.3 59.0 + - - +
47B GLY 3.8 0.2 - - - -
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Residues in contact with LEU 46 (chain B).
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 4.8 3.8 - - - -
46A LEU* 3.6 31.4 - - + -
53A TRP* 3.9 24.2 - - + -
56A ARG* 2.9 51.7 + - + +
57A VAL* 3.9 7.0 - - + +
60A THR* 3.3 25.4 - - + +
42B MSE 2.8 30.3 + - + +
45B GLY* 1.3 72.2 - - - -
47B GLY* 1.3 60.9 + - - +
53B TRP* 4.3 17.7 - - + -
57B VAL* 5.5 0.9 - - + -
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Residues in contact with GLY 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B MSE 4.3 0.5 - - - +
43B PHE* 2.8 32.1 + - - +
44B ASP 4.5 1.0 + - - -
45B GLY 3.8 0.8 - - - -
46B LEU* 1.3 75.7 - - - +
48B TRP* 1.3 64.2 + - - +
53B 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