Contacts of the helix formed by residues 50 - 63 (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 SER 50 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48F SER* 3.1 14.0 + - - -
49F GLY* 1.3 80.4 - - - +
51F ARG* 1.3 65.1 + - - +
52F ARG* 3.5 8.5 + - - +
53F ASP* 3.0 31.6 + - - +
54F GLN* 3.0 22.3 + - - +
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Residues in contact with ARG 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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17F VAL 3.0 29.9 + - - -
18F GLU* 3.2 17.8 + - - +
19F GLU 4.9 0.7 - - - -
20F LEU* 2.9 39.6 + - - +
21F GLN* 4.0 22.5 - - - +
22F VAL* 4.4 17.1 - - + +
49F GLY 3.8 0.4 + - - -
50F SER* 1.3 72.3 - - - +
52F ARG* 1.3 75.6 + - - +
54F GLN* 3.4 9.7 + - - +
55F ALA* 2.9 33.2 + - - +
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Residues in contact with ARG 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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24D TYR* 3.6 48.5 + - - +
27D ASP* 2.8 35.9 + - - +
78D GLU* 4.7 4.0 + - - -
14F LEU* 4.0 11.7 - - - +
17F VAL* 3.5 37.6 - - + +
18F GLU* 3.7 24.0 + - - +
50F SER* 3.1 8.3 + - - +
51F ARG* 1.3 90.1 - - - +
53F ASP* 1.3 57.9 + - - +
55F ALA* 3.4 1.6 + - - +
56F ARG* 2.9 42.6 + - - +
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Residues in contact with ASP 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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21D LYS* 4.9 8.1 + - - -
23D SER* 4.7 4.5 + - - -
24D TYR* 6.0 1.2 - - - -
46F ALA* 3.4 23.5 - - - +
47F GLY* 4.0 5.0 - - - -
48F SER* 2.7 36.7 + - - +
50F SER* 3.0 19.9 + - - +
52F ARG* 1.3 74.4 - - - +
54F GLN* 1.3 65.7 + - - +
56F ARG* 3.0 28.1 + - - +
57F GLN* 3.1 23.6 + - - +
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Residues in contact with GLN 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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22F VAL* 3.5 22.0 - - + +
23F ASP* 4.6 7.2 + - - +
26F TRP* 3.5 13.0 + - + -
43F ILE* 3.5 30.6 - - + +
44F GLN* 3.5 39.3 + - - +
46F ALA 4.5 0.4 + - - +
49F GLY* 3.0 23.5 + - - +
50F SER 3.0 15.7 + - - +
51F ARG* 3.6 5.2 - - - +
53F ASP* 1.3 74.4 - - - +
55F ALA* 1.3 58.6 + - - +
57F GLN 3.2 1.6 + - - -
58F LEU* 2.8 31.6 + - - +
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Residues in contact with ALA 55 (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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16F LEU 4.5 0.4 - - - +
17F VAL* 4.4 13.7 - - + -
20F LEU* 4.1 21.5 - - + -
22F VAL* 3.9 19.4 - - + +
51F ARG* 2.9 21.5 + - - +
52F ARG* 3.6 7.4 - - - +
54F GLN* 1.3 75.3 - - - +
56F ARG* 1.3 63.7 - - - +
58F LEU* 3.2 6.3 + - - +
59F ILE* 3.1 27.7 + - + +
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Residues in contact with ARG 56 (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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23D SER* 3.8 32.0 + - - +
24D TYR* 4.6 1.6 - - - +
27D ASP* 2.8 36.8 + - - -
40D GLU* 3.9 9.2 - - - -
44D ARG* 5.5 6.1 - - - +
13F ARG* 3.7 20.6 - - - +
17F VAL* 3.7 15.0 - - + +
52F ARG* 2.9 33.5 + - - +
53F ASP* 3.0 32.7 + - - +
54F GLN 3.2 0.2 - - - -
55F ALA* 1.3 76.3 - - - +
57F GLN* 1.3 62.9 + - - +
59F ILE* 3.2 7.4 - - - +
60F ILE* 3.1 39.9 + - + +
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Residues in contact with GLN 57 (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* 5.0 3.2 - - - +
44D ARG* 4.0 22.2 + - - +
42F ASP 5.8 0.2 - - - -
43F ILE* 4.2 12.8 - - + -
46F ALA* 3.6 33.4 - - + +
53F ASP 3.1 8.7 + - - +
54F GLN 3.8 2.5 - - - +
56F ARG* 1.3 73.9 - - - +
58F LEU* 1.3 66.9 + - - +
60F ILE* 3.4 15.7 + - - +
61F ASP* 2.9 57.6 + - - +
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Residues in contact with LEU 58 (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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20F LEU* 4.0 11.7 - - + -
22F VAL* 4.3 7.4 - - + -
25F LEU* 3.8 28.7 - - + -
26F TRP* 3.8 30.7 - - + -
29F LEU* 3.9 3.4 - - + -
35F PHE* 3.7 24.0 - - + -
43F ILE* 3.8 13.8 - - + +
54F GLN 2.8 14.2 + - - +
55F ALA 3.2 10.3 + - - +
57F GLN* 1.3 77.7 - - - +
59F ILE* 1.3 61.6 + - + +
61F ASP* 3.2 2.6 + - - +
62F LEU* 2.8 25.8 + - + -
73F PHE* 4.1 20.0 - - + -
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Residues in contact with ILE 59 (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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9F LEU* 4.3 16.2 - - + +
13F ARG* 3.9 26.9 - - - +
16F LEU* 3.8 46.7 - - + -
17F VAL* 4.0 15.9 - - + -
20F LEU* 4.4 15.0 - - + -
55F ALA 3.1 9.4 + - - +
56F ARG* 3.2 14.4 - - - +
58F LEU* 1.3 72.6 - - + +
60F ILE* 1.3 67.8 + - + +
62F LEU* 3.4 19.0 - - + +
63F GLU* 3.7 10.9 + - - +
73F PHE* 4.4 14.4 - - + -
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Residues in contact with ILE 60 (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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37D ILE* 4.0 27.6 - - + -
40D GLU* 3.7 9.6 - - - +
44D ARG* 3.8 20.2 - - - +
13F ARG* 3.4 30.3 - - - +
56F ARG* 3.1 36.2 + - + +
57F GLN* 3.8 13.7 - - - +
59F ILE* 1.3 76.9 - - + +
61F ASP* 1.3 73.1 + - - +
63F GLU* 3.2 27.0 + - - +
64F THR* 4.5 3.6 + - - +
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Residues in contact with ASP 61 (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* 3.5 34.2 + - + +
24C TYR* 5.3 2.1 + - - -
35F PHE* 3.9 18.2 - - + -
43F ILE* 3.6 21.3 - - + +
57F GLN* 2.9 42.7 + - - +
58F LEU 3.7 3.1 - - - +
60F ILE* 1.3 79.2 - - - +
62F LEU* 1.3 63.7 + - - +
64F THR* 2.8 31.5 + - - +
65F ARG* 3.4 5.9 - - - +
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Residues in contact with LEU 62 (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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1F MET* 4.1 5.6 - - + -
9F LEU* 3.9 24.2 - - + -
34F LEU* 4.2 16.8 - - + -
35F PHE* 3.9 16.8 - - + -
58F LEU* 2.8 14.5 + - + +
59F ILE* 3.4 15.9 - - - +
60F ILE 3.2 0.4 - - - -
61F ASP* 1.3 77.1 - - - +
63F GLU* 1.3 62.4 + - - +
64F THR 3.0 1.8 + - - -
65F ARG* 3.1 12.5 + - + +
69F ALA* 3.5 33.4 - - + +
70F LEU* 5.0 1.6 - - - -
73F PHE* 3.4 50.5 - - + -
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Residues in contact with GLU 63 (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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19C ASP* 3.7 1.2 - - - +
37D ILE* 4.0 12.7 - - - +
1F MET* 3.6 19.4 + - - +
6F ARG* 3.1 60.0 + - + +
9F LEU* 4.1 15.0 - - + +
10F ARG* 2.7 48.4 + - - -
59F ILE 3.8 9.7 - - - +
60F ILE* 3.4 16.8 - - - +
61F ASP 3.1 0.4 - - - -
62F LEU* 1.3 77.5 - - - +
64F THR* 1.3 60.9 + - + +
65F ARG 3.4 0.2 - - - -
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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