Contacts of the helix formed by residues 25 - 32 (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 LEU 25 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F LEU* 4.0 25.6 - - + -
21F GLN 3.7 11.4 - - - +
22F VAL* 3.0 12.0 + - + +
24F GLN* 1.3 78.1 - - - +
26F TRP* 1.3 67.5 + - + +
27F ASP 3.3 2.9 - - - -
28F ALA* 3.1 13.0 + - - +
29F LEU* 3.1 22.9 + - + +
58F LEU* 3.8 27.6 - - + -
73F PHE* 4.1 8.7 - - + -
76F CYS* 3.7 40.2 - - + +
77F LEU* 4.2 4.3 - - + -
80F THR* 3.8 10.8 - - + +
82F GLN* 4.1 4.5 - - - +
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Residues in contact with TRP 26 (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* 3.6 26.5 - - + -
41A GLU* 3.0 27.0 + - - -
22F VAL* 3.3 29.3 + - + -
23F ASP* 3.8 4.2 + - - +
24F GLN 3.6 1.0 - - - -
25F LEU* 1.3 78.0 - - - +
27F ASP* 1.3 62.6 + - - +
29F LEU* 3.4 28.8 + - + +
30F LEU* 3.0 27.0 + - - +
35F PHE* 5.4 0.9 - + - -
40F ILE* 3.6 31.9 - - + +
43F ILE* 3.6 32.8 - - + -
44F GLN* 3.2 29.8 + - + +
54F GLN* 3.5 22.5 + - + -
58F LEU* 3.8 19.5 - - + -
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Residues in contact with ASP 27 (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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36A THR* 5.6 2.6 - - - -
37A ILE* 3.7 34.4 + - - +
38A SER* 4.9 2.6 + - - -
24F GLN 4.6 6.5 + - - +
25F LEU 3.3 0.8 - - - -
26F TRP* 1.3 78.4 - - - +
28F ALA* 1.3 58.7 + - - +
30F LEU* 3.3 9.2 + - - +
31F SER* 2.9 30.2 + - - -
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Residues in contact with ALA 28 (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 GLN 4.9 1.2 + - - -
25F LEU 3.1 9.9 + - - +
27F ASP* 1.3 78.3 - - - +
29F LEU* 1.3 62.8 + - - +
31F SER* 2.7 25.7 + - - -
32F ARG 3.1 5.7 + - - -
76F CYS* 3.5 37.1 - - + +
79F ASP* 4.3 10.1 - - + +
80F THR* 4.0 19.1 - - + -
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Residues in contact with LEU 29 (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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25F LEU* 3.1 26.1 + - + +
26F TRP* 3.4 40.4 + - + +
28F ALA* 1.3 77.0 - - - +
30F LEU* 1.3 60.8 + - - +
32F ARG 3.3 1.9 + - - -
33F GLU 3.1 2.8 + - - -
34F LEU* 2.9 47.9 + - + +
35F PHE* 4.3 21.3 - - + +
40F ILE* 5.2 2.7 - - + -
58F LEU* 3.9 15.3 - - + -
73F PHE* 4.0 19.3 - - + -
76F CYS* 3.8 21.5 - - + -
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Residues in contact with LEU 30 (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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30A ILE* 4.0 17.3 - - + -
37A ILE* 3.9 27.8 - - + -
26F TRP 3.0 21.7 + - - +
27F ASP* 3.6 9.2 - - - +
29F LEU* 1.3 73.9 - - - +
31F SER* 1.3 58.9 + - - +
33F GLU* 2.7 28.6 + - - +
35F PHE 3.5 22.2 - - - +
37F PRO* 4.0 24.5 - - + -
40F ILE* 3.8 16.4 - - + +
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Residues in contact with SER 31 (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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27F ASP 2.9 18.2 + - - -
28F ALA* 2.7 22.0 + - - -
30F LEU* 1.3 71.7 - - - +
32F ARG* 1.3 70.0 + - - +
33F GLU* 3.5 8.0 + - - +
79F ASP* 4.7 4.5 + - - -
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Residues in contact with ARG 32 (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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81C LYS* 5.1 0.3 + - - -
28F ALA 3.1 6.7 + - - +
29F LEU 4.1 2.2 - - - +
30F LEU 3.1 1.0 - - - -
31F SER* 1.3 88.7 + - - +
33F GLU* 1.3 71.1 + - - +
34F LEU* 3.1 7.7 + - + +
72F LEU* 3.8 48.1 - - + +
75F SER* 3.8 20.3 + - - -
76F CYS* 3.5 28.1 - - - +
79F ASP* 2.8 38.3 + - - -
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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