Contacts of the helix formed by residues 36 - 45 (chain E) in PDB entry 4RHW
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 ARG 36 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A HIS* 4.9 1.2 + - - -
77A HIS* 3.2 34.7 + - - -
78A GLU* 2.9 59.9 + - - +
79A GLY* 4.4 2.9 - - - +
31C SER* 3.2 16.2 + - - -
102C SO4 2.9 40.8 + - - -
35E PHE* 1.3 75.4 - - - +
37E PRO* 1.3 75.2 - - + +
38E HIS* 3.3 7.1 - - + +
39E MET* 3.1 27.4 + - + +
40E ILE* 3.2 11.6 + - - +
65E ARG* 4.5 1.5 - - - +
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Residues in contact with PRO 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASP* 3.6 28.3 - - + +
30C ILE* 3.8 29.3 - - + +
31C SER* 3.5 27.4 - - - +
30E LEU* 4.0 12.8 - - + -
36E ARG* 1.3 92.0 - - + +
38E HIS* 1.3 62.9 + - - +
40E ILE* 3.0 22.1 + - + +
41E GLU* 3.1 16.1 + - - +
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Residues in contact with HIS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 4.6 5.8 - + + -
78A GLU* 6.1 1.1 - - - +
23C SER* 3.3 20.6 - - - -
24C TYR* 4.0 21.5 - + - -
27C ASP* 2.7 28.6 + - + +
36E ARG* 3.3 6.0 - - + +
37E PRO* 1.3 75.3 - - - +
39E MET* 1.3 65.4 + - + +
41E GLU* 3.1 14.8 + - - +
42E ASP* 3.0 37.3 + - - -
45E ARG* 3.8 15.2 + - - -
38F HIS* 3.7 29.0 + + + -
42F ASP* 4.4 3.2 + - - -
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Residues in contact with MET 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 6.3 1.3 - - + -
24A TYR* 3.7 48.3 + - + +
78A GLU* 3.3 43.5 - - + +
80A TYR* 4.3 2.5 - - - +
35E PHE* 4.1 15.5 - - + -
36E ARG* 3.1 31.3 + - + +
38E HIS* 1.3 75.9 - - + +
40E ILE* 1.3 57.6 + - - +
42E ASP* 3.2 4.2 + - - +
43E ILE* 3.0 33.9 + - + +
61E ASP* 6.2 0.2 - - - +
65E ARG* 3.5 31.0 - - - +
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Residues in contact with ILE 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ILE* 4.6 8.7 - - + -
40C GLU* 5.3 0.7 - - - +
26E TRP* 3.6 50.7 - - + +
29E LEU* 5.1 1.1 - - + -
30E LEU* 3.9 34.1 - - + +
35E PHE* 3.8 21.3 - - + -
36E ARG 3.2 16.0 + - - +
37E PRO* 3.0 10.2 + - + +
39E MET* 1.3 74.8 - - - +
41E GLU* 1.3 66.6 + - + +
43E ILE* 3.2 7.8 + - + +
44E GLN* 2.9 37.5 + - - +
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Residues in contact with GLU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C SER* 2.6 44.0 - - - +
26C MET* 3.7 25.4 - - - +
27C ASP* 3.7 14.6 - - - +
30C ILE* 6.1 2.2 - - + -
40C GLU* 3.8 15.5 - - + +
44C ARG* 5.5 3.2 - - - +
37E PRO* 3.1 13.1 + - + +
38E HIS* 3.1 20.4 + - - +
40E ILE* 1.3 75.0 - - + +
42E ASP* 1.3 63.4 + - - +
44E GLN* 3.3 12.8 + - - +
45E ARG* 3.1 42.6 + - - +
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Residues in contact with ASP 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER* 5.1 0.7 + - - -
24A TYR* 2.6 43.0 + - - +
38E HIS* 3.0 20.8 + - - +
39E MET 3.5 4.0 - - - +
41E GLU* 1.3 74.1 - - - +
43E ILE* 1.3 64.9 + - + +
45E ARG* 2.7 44.4 + - - +
46E ALA* 3.2 11.6 + - - +
57E GLN* 5.7 0.2 - - - -
61E ASP* 6.1 0.4 - - - +
38F HIS* 4.4 4.3 + - - -
42F ASP* 4.8 5.4 - - - +
45F ARG* 5.0 9.6 + - - -
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Residues in contact with ILE 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 6.0 0.4 - - - +
26E TRP* 3.5 27.1 - - + -
35E PHE* 3.9 39.0 - - + -
39E MET* 3.0 21.0 + - + +
40E ILE* 3.7 9.4 - - - +
42E ASP* 1.3 75.2 - - + +
44E GLN* 1.3 62.6 + - - +
46E ALA* 3.1 21.7 + - - +
54E GLN* 3.5 31.3 - - - +
57E GLN* 4.2 8.3 - - + +
58E LEU* 3.9 14.1 - - - +
61E ASP* 3.7 20.6 - - + +
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Residues in contact with GLN 44 (chain E).
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* 2.6 41.6 + - - +
41C GLU* 3.9 7.6 - - - +
44C ARG* 3.6 33.7 + - - +
26E TRP* 3.3 29.2 + - + +
40E ILE* 2.9 19.2 + - - +
41E GLU* 3.4 23.4 - - - +
43E ILE* 1.3 75.9 - - - +
45E ARG* 1.3 59.8 + - - +
49E GLY* 3.7 9.2 - - - -
54E GLN* 3.3 38.3 - - - +
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Residues in contact with ARG 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C SER* 3.7 27.8 + - - -
44C ARG* 3.5 28.0 - - - +
101C SO4 4.4 10.1 + - - -
38E HIS* 3.8 16.0 + - - -
41E GLU* 3.1 22.0 + - - +
42E ASP* 2.7 40.2 + - - +
44E GLN* 1.3 77.2 - - - +
46E ALA* 1.3 65.7 + - - +
47E GLY 3.3 10.4 + - - +
49E GLY* 4.5 4.1 + - - -
42F ASP* 4.9 10.7 + - - -
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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