Contacts of the helix formed by residues 42 - 54 (chain F) in PDB entry 4R8A
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 ASP 42 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F LEU* 1.3 73.6 - - - +
43F ASP* 1.3 85.8 + - - +
44F GLN* 2.7 45.1 + - - +
45F GLU* 2.9 26.6 + - - +
46F ARG* 2.9 29.4 + - - +
215F ARG* 3.5 25.8 + - - +
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Residues in contact with ASP 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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42F ASP* 1.3 85.8 + - - +
44F GLN* 1.3 62.9 + - - +
45F GLU 3.2 0.2 + - - -
46F ARG* 3.2 29.0 + - - +
47F ALA* 3.2 20.8 + - - +
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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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42F ASP* 2.7 29.5 + - - +
43F ASP* 1.3 77.4 - - + +
45F GLU* 1.3 71.1 + - - +
47F ALA* 3.6 10.8 - - - +
48F PHE* 3.4 21.1 + - - +
171F LEU* 4.0 15.8 - - - +
215F ARG* 5.2 1.8 - - - +
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Residues in contact with GLU 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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41F LEU* 3.3 25.7 - - + +
42F ASP* 2.9 41.5 + - - +
44F GLN* 1.3 90.2 + - - +
46F ARG* 1.3 63.8 + - - +
47F ALA 3.2 1.8 - - - -
48F PHE* 3.3 3.5 + - - +
49F ILE* 3.3 27.2 + - - +
171F LEU* 4.0 26.4 - - + +
174F ARG* 3.2 25.1 + - - -
175F LEU* 6.0 0.2 - - - -
215F ARG* 3.0 22.5 + - - -
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Residues in contact with ARG 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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38F ALA 4.0 11.6 + - - -
39F ASP* 5.4 0.8 + - - +
41F LEU* 2.4 50.5 + - + -
42F ASP* 2.9 10.9 + - - +
43F ASP* 3.2 44.1 + - - +
45F GLU* 1.3 75.2 - - - +
47F ALA* 1.3 63.4 + - - +
49F ILE* 3.5 4.4 + - - +
50F ALA* 3.2 23.6 + - - +
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Residues in contact with ALA 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 ASP 3.2 12.4 + - - +
44F GLN* 3.6 15.0 - - - +
46F ARG* 1.3 75.5 - - - +
48F PHE* 1.3 60.3 + - - +
50F ALA* 3.5 5.6 + - - +
51F ALA* 2.8 32.2 + - - +
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Residues in contact with PHE 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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26F PHE* 4.8 10.5 - + - -
30F LEU* 5.0 2.5 - - + -
44F GLN 3.4 6.1 + - - +
45F GLU 3.3 9.1 + - - +
46F ARG 3.3 0.4 - - - -
47F ALA* 1.3 79.1 - - - +
49F ILE* 1.3 66.8 + - + +
51F ALA* 3.2 1.4 + - - +
52F PHE* 2.8 41.2 + + + +
63F LEU* 4.4 10.3 - - + -
99F TRP* 3.4 52.5 - + - -
168F CYS* 4.0 25.1 - - + -
171F LEU* 3.8 41.7 - - + -
172F CYS* 4.4 11.9 - - - -
175F LEU* 4.4 11.2 - - + -
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Residues in contact with ILE 49 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F LEU* 4.0 54.6 - - + +
33F ILE* 4.4 9.4 - - + -
34F GLY* 5.2 4.5 - - - +
41F LEU* 3.6 28.5 - - + -
45F GLU 3.3 12.4 + - - +
46F ARG* 3.5 5.6 + - - +
48F PHE* 1.3 83.6 - - + +
50F ALA* 1.3 60.8 + - - +
52F PHE* 3.7 6.4 + - - +
53F ALA* 3.5 19.9 + - - +
171F LEU* 5.8 0.2 - - + -
175F LEU* 4.8 7.9 - - + -
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Residues in contact with ALA 50 (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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46F ARG 3.2 17.9 + - - +
47F ALA* 3.7 7.0 - - - +
48F PHE 3.2 0.2 - - - -
49F ILE* 1.3 75.1 - - - +
51F ALA* 1.3 64.2 + - - +
53F ALA* 3.3 14.0 + - - +
54F GLU* 3.5 18.0 + - - +
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Residues in contact with ALA 51 (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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47F ALA 2.8 19.8 + - - +
48F PHE 3.6 3.1 - - - +
50F ALA* 1.3 73.8 - - - +
52F PHE* 1.3 66.4 + - - +
54F GLU* 3.2 17.8 + - - +
55F LEU* 3.4 13.7 + - - +
97F LEU* 4.6 14.1 - - + +
99F TRP* 3.7 21.0 - - + -
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Residues in contact with PHE 52 (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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23F LEU* 3.8 10.1 - - + -
26F PHE* 3.5 35.0 - + - -
27F ARG* 4.4 9.0 - - + -
30F LEU* 3.5 20.6 - - + -
48F PHE* 2.8 23.8 + + + +
49F ILE* 3.9 7.2 - - - +
50F ALA 3.2 0.2 - - - -
51F ALA* 1.3 77.7 - - - +
53F ALA* 1.3 62.6 + - + +
55F LEU* 3.2 18.9 + - + +
60F GLN* 3.0 64.0 + - + -
63F LEU* 3.7 31.0 - - + -
64F VAL* 4.1 0.9 - - + -
99F TRP* 3.6 11.4 - + + -
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Residues in contact with ALA 53 (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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49F ILE 3.5 9.4 + - - +
50F ALA* 3.3 10.6 + - - +
51F ALA 3.2 0.6 - - - -
52F PHE* 1.3 82.2 - - + +
54F GLU* 1.3 64.0 + - + +
55F LEU 3.2 3.1 - - - +
60F GLN* 3.4 15.2 + - - +
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Residues in contact with GLU 54 (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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50F ALA 3.6 14.6 - - - +
51F ALA* 3.2 12.0 + - - +
53F ALA* 1.3 78.9 - - + +
55F LEU* 1.3 65.8 + - - +
56F PRO* 3.9 2.6 - - - +
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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