Contacts of the helix formed by residues 36 - 45 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER* 3.4 16.0 + - - -
102A SO4 2.9 39.4 + - - -
28C HIS* 4.8 1.6 + - - -
77C HIS* 3.1 36.1 + - - -
78C GLU* 2.8 61.2 + - - +
79C GLY* 4.4 2.7 - - - +
35F PHE* 1.3 76.8 - - - +
37F PRO* 1.3 75.0 - - + +
38F HIS* 3.2 6.9 - - + +
39F MET* 3.1 24.1 + - + +
40F ILE* 3.1 12.9 + - - +
65F ARG* 4.5 0.9 - - - +
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Residues in contact with PRO 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 3.6 27.1 - - + +
30A ILE* 3.7 33.3 - - + +
31A SER* 3.3 27.8 - - - +
30F LEU* 4.0 17.2 - - + -
36F ARG* 1.3 94.1 - - + +
38F HIS* 1.3 63.0 + - - +
40F ILE* 3.2 10.7 + - + +
41F GLU* 3.0 23.6 + - - +
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Residues in contact with HIS 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 3.4 17.9 - - - -
24A TYR* 4.0 22.2 - + - -
27A ASP* 2.6 28.5 + - + +
24C TYR* 4.5 8.1 - + + -
78C GLU* 5.9 2.2 - - - +
38E HIS* 3.7 28.0 + + - -
42E ASP* 4.4 2.2 + - - -
36F ARG* 3.2 6.4 - - + +
37F PRO* 1.3 77.4 - - - +
39F MET* 1.3 65.9 + - + +
41F GLU* 3.3 13.9 + - - +
42F ASP* 3.1 39.2 + - - -
45F ARG* 3.9 9.7 + - - -
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Residues in contact with MET 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS* 6.5 0.7 - - + -
24C TYR* 3.6 50.0 + - + +
78C GLU* 3.3 44.0 - - + +
80C TYR* 4.5 2.5 - - - +
35F PHE* 4.1 16.4 - - + -
36F ARG* 3.1 28.6 + - + +
38F HIS* 1.3 77.0 - - + +
40F ILE* 1.3 57.8 + - - +
42F ASP* 3.1 3.5 + - - +
43F ILE* 2.9 36.2 + - + +
65F ARG* 3.6 31.0 - - - +
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Residues in contact with ILE 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 4.6 8.3 - - + -
40A GLU* 5.3 1.6 - - - +
26F TRP* 3.6 51.6 - - + +
29F LEU* 5.2 1.6 - - + -
30F LEU* 3.8 37.0 - - + +
35F PHE* 4.0 18.8 - - + -
36F ARG 3.1 14.7 + - - +
37F PRO* 3.2 9.8 + - + +
39F MET* 1.3 76.1 - - - +
41F GLU* 1.3 62.9 + - + +
43F ILE* 3.3 7.3 + - - +
44F GLN* 2.9 37.4 + - - +
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Residues in contact with GLU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 2.6 43.9 - - - +
26A MET* 3.7 17.4 - - - +
27A ASP* 3.6 15.8 - - - +
30A ILE* 5.9 2.5 - - + -
40A GLU* 3.8 15.2 - - + +
44A ARG* 3.7 14.1 + - - +
37F PRO 3.0 12.9 + - - +
38F HIS* 3.3 19.4 + - - +
39F MET 3.3 0.6 - - - -
40F ILE* 1.3 76.2 - - + +
42F ASP* 1.3 62.5 + - - +
44F GLN* 3.2 14.6 + - - +
45F ARG* 3.1 37.7 + - - +
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Residues in contact with ASP 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 2.6 43.1 + - - +
38E HIS* 4.4 4.3 + - - -
42E ASP* 4.8 5.0 - - - +
45E ARG* 4.9 10.5 + - - -
38F HIS* 3.1 20.9 + - - +
39F MET 3.1 4.0 + - - +
41F GLU* 1.3 75.1 - - - +
43F ILE* 1.3 65.0 + - + +
45F ARG* 2.6 47.0 + - - +
46F ALA* 3.3 10.6 + - - +
57F GLN* 5.5 0.6 - - - +
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Residues in contact with ILE 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 5.8 0.9 - - - +
26F TRP* 3.6 23.8 - - + -
35F PHE* 3.7 40.8 - - + -
39F MET* 2.9 22.4 + - + +
40F ILE* 3.3 6.9 + - - +
42F ASP* 1.3 76.1 - - + +
44F GLN* 1.3 61.3 + - - +
46F ALA* 3.2 21.6 + - - +
54F GLN* 3.5 30.9 - - - +
57F GLN* 4.2 7.0 - - + -
58F LEU* 3.8 17.7 - - + +
61F ASP* 3.6 21.1 - - - +
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Residues in contact with GLN 44 (chain F).
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* 2.6 42.1 + - - +
41A GLU* 4.1 5.6 - - - +
44A ARG* 3.7 18.6 - - - +
26F TRP* 3.2 31.4 + - + +
40F ILE* 2.9 21.3 + - - +
41F GLU* 3.4 20.2 - - - +
42F ASP 3.2 0.2 - - - -
43F ILE* 1.3 76.9 - - - +
45F ARG* 1.3 59.6 + - - +
46F ALA 3.4 0.2 - - - -
49F GLY* 3.7 10.6 - - - -
54F GLN* 3.5 38.5 + - - +
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Residues in contact with ARG 45 (chain F).
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* 3.7 27.5 + - - -
44A ARG* 4.2 28.6 - - - +
101A SO4 4.4 9.1 + - - -
42E ASP* 5.0 10.3 + - - -
38F HIS* 3.9 15.2 + - - -
41F GLU* 3.1 21.6 + - - +
42F ASP* 2.6 41.4 + - - +
44F GLN* 1.3 80.9 - - - +
46F ALA* 1.3 65.0 + - - +
47F GLY 3.4 10.2 + - - +
49F GLY* 4.5 4.1 + - - -
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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