Contacts of the helix formed by residues 40 - 49 (chain F) in PDB entry 1R4N
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 GLU 40 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F SER* 2.9 10.4 + - - +
39F THR* 1.3 84.2 - - + +
41F SER* 1.3 66.5 + - - +
42F LEU 2.8 5.5 + - - -
43F GLN* 3.1 20.9 + - + +
44F PHE* 3.2 31.0 + - + +
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Residues in contact with SER 41 (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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24F LEU* 3.9 23.9 + - - +
35F PHE* 5.7 0.9 - - - -
36F GLU 3.7 8.5 + - - -
38F SER* 3.4 36.3 + - - -
39F THR 3.5 0.2 - - - -
40F GLU* 1.3 76.4 - - - +
42F LEU* 1.3 62.7 + - - +
44F PHE* 3.3 8.8 - - - +
45F LEU* 3.2 20.6 + - - +
312F THR* 6.1 0.3 - - - +
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Residues in contact with LEU 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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17F TRP* 3.5 36.1 - - + +
20F VAL* 4.5 9.2 - - + -
21F LYS* 3.9 30.7 - - + +
24F LEU* 3.9 25.0 - - + +
25F GLU* 6.4 1.3 - - + -
38F SER 4.9 0.4 + - - -
39F THR 4.5 7.5 + - - +
40F GLU 2.8 4.8 + - - -
41F SER* 1.3 71.6 - - - +
43F GLN* 1.3 70.0 + - - +
44F PHE 3.0 1.6 - - - -
45F LEU* 2.8 26.1 + - + +
46F LEU* 3.0 32.9 + - + +
71F GLY* 4.7 5.6 - - - -
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Residues in contact with GLN 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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39F THR 5.2 1.9 + - - +
40F GLU* 3.1 15.0 + - + +
42F LEU* 1.3 78.1 - - - +
44F PHE* 1.3 64.1 + - - +
46F LEU* 3.1 13.3 + - - +
47F ASP* 2.9 57.0 + - - +
73F ARG* 4.3 14.1 - - - +
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Residues in contact with PHE 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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40F GLU* 3.2 26.9 + - + +
41F SER* 3.3 14.6 - - - +
43F GLN* 1.3 77.7 - - - +
45F LEU* 1.3 68.1 + - - +
47F ASP* 2.8 5.5 + - - -
48F THR* 2.7 65.8 + - + +
49F CYS* 6.3 0.2 - - + -
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Residues in contact with LEU 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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24F LEU* 4.5 3.8 - - + -
41F SER 3.2 7.7 + - - +
42F LEU* 2.8 20.4 + - + +
44F PHE* 1.3 80.0 - - - +
46F LEU* 1.3 63.1 + - - +
47F ASP 3.3 0.3 + - - -
48F THR* 4.7 0.4 - - - -
49F CYS* 3.3 39.1 + - + +
70F SER 4.2 0.7 - - - +
71F GLY* 3.1 34.7 - - - +
72F PHE* 3.7 32.3 - - + -
73F ARG 4.8 2.8 + - - -
308F PHE* 4.1 15.9 - - + -
311F ALA* 4.0 14.1 - - + +
312F THR* 3.9 24.0 - - + -
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Residues in contact with LEU 46 (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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17F TRP* 4.0 22.7 - - + +
42F LEU* 3.0 44.1 + - + +
43F GLN* 3.3 19.1 - - - +
45F LEU* 1.3 75.8 - - - +
47F ASP* 1.3 62.0 + - - +
71F GLY* 3.2 31.6 - - - +
72F PHE 4.2 0.2 - - - +
73F ARG* 3.0 71.8 - - + +
74F GLN* 3.7 5.7 - - - +
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Residues in contact with ASP 47 (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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43F GLN* 2.9 47.0 + - - +
44F PHE* 2.8 11.6 + - - +
46F LEU* 1.3 77.4 - - - +
48F THR* 1.3 66.3 + - + +
49F CYS 3.8 0.2 - - - -
73F ARG* 4.4 5.4 + - - -
74F GLN* 3.4 24.6 - - - +
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Residues in contact with THR 48 (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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44F PHE* 2.7 67.4 + - + +
47F ASP* 1.3 80.9 - - + +
49F CYS* 1.3 59.1 + - - +
50F LYS* 3.2 14.4 + - - +
74F GLN* 4.9 0.6 - - - +
139F HIS* 3.3 13.6 + - - -
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Residues in contact with CYS 49 (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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44F PHE* 6.3 0.2 - - + -
45F LEU* 3.3 33.9 + - + +
47F ASP 3.8 0.4 - - - -
48F THR* 1.3 75.8 + - - +
50F LYS* 1.3 60.9 + - - +
51F VAL* 3.7 7.8 + - - +
72F PHE* 4.1 16.0 - - + -
73F ARG 5.1 0.2 + - - -
74F GLN* 3.4 23.0 + - - +
139F HIS* 3.4 26.5 - - - -
140F ILE* 4.8 1.6 - - - -
311F ALA* 4.1 28.3 - - - -
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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