Contacts of the helix formed by residues 40 - 54 (chain F) in PDB entry 3F0D
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 40 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F ILE* 3.5 22.5 - - + +
22F ILE* 3.5 2.3 - - - -
23F GLY 2.8 21.0 + - - -
24F GLY* 2.8 29.8 + - - -
38F ASP* 3.3 19.4 + - - +
39F ALA* 1.3 72.4 - - - +
41F VAL* 1.3 63.4 + - - +
42F LEU 3.4 3.8 + - - -
43F LEU* 3.2 23.0 + - - +
44F HIS* 3.0 28.0 + - - -
75F SER* 3.7 11.2 - - - +
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Residues in contact with VAL 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ASP* 3.4 49.1 - - + +
11F VAL* 3.8 3.1 - - - +
12F HIS* 3.9 9.4 - - + -
22F ILE* 4.8 9.9 - - + -
33F LEU* 3.8 20.1 - - + +
39F ALA 2.8 7.1 + - - +
40F ASP* 1.3 72.3 + - - +
42F LEU* 1.3 64.8 + - - +
44F HIS 3.5 0.2 + - - -
45F ALA* 3.1 18.9 + - - +
100F ILE* 5.2 0.9 - - + -
148F ILE* 3.6 33.7 - - + +
150F ALA* 3.6 15.9 - - + +
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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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22F ILE* 3.9 11.4 - - + -
23F GLY* 3.7 21.8 - - - -
40F ASP* 3.2 8.1 + - - +
41F VAL* 1.3 81.1 - - - +
43F LEU* 1.3 65.8 + - - +
45F ALA* 3.3 2.9 + - + +
46F ILE* 3.1 29.8 + - + +
98F SER* 3.4 32.3 - - - +
99F THR 4.7 0.9 - - - +
100F ILE* 3.9 18.4 - - + -
114F MET* 3.8 20.4 - - - -
118F ILE* 3.9 16.8 - - + -
131F VAL* 4.0 9.6 - - + -
150F ALA* 3.8 14.6 - - + -
151F GLN 5.0 0.4 - - - +
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Residues in contact with LEU 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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23F GLY* 3.8 11.4 - - - -
24F GLY 3.8 4.0 - - - +
40F ASP* 3.2 34.5 + - - +
42F LEU* 1.3 76.3 - - - +
44F HIS* 1.3 58.8 + - - +
46F ILE* 3.4 5.1 + - + +
47F THR* 2.8 33.6 + - - -
75F SER* 3.9 16.4 - - - +
76F ARG* 3.6 42.0 - - + +
79F LEU* 4.0 18.0 - - + +
117F ASN* 6.2 1.3 - - + -
118F ILE* 3.7 32.1 - - + -
121F ASP* 5.7 0.2 - - - +
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Residues in contact with HIS 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LYS* 5.8 0.2 - - - +
10F ASP* 3.0 19.4 + - - +
12F HIS* 3.4 7.8 + + - -
37F SER* 3.3 22.2 + - - -
39F ALA* 3.9 11.0 - - - -
40F ASP 3.0 16.1 + - - +
41F VAL 3.7 0.7 - - - +
42F LEU 3.2 0.2 - - - -
43F LEU* 1.3 77.3 - - - +
45F ALA* 1.3 55.1 + - - +
47F THR* 3.3 3.5 + - - -
48F ASP* 2.9 32.9 + - - +
59F ILE* 3.9 30.6 - - + +
75F SER* 2.9 29.5 + - - -
78F LEU* 4.7 5.8 - - + +
163F ZN 2.0 33.6 - - - -
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Residues in contact with ALA 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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8F GLY* 3.5 19.8 - - - -
9F TYR 4.4 2.5 - - - +
10F ASP* 4.1 9.3 - - - +
41F VAL 3.1 17.0 + - - +
42F LEU* 3.3 4.9 + - + +
44F HIS* 1.3 77.3 - - - +
46F ILE* 1.3 57.1 + - - +
48F ASP* 3.3 1.4 + - - -
49F ALA 3.0 23.4 + - - -
150F ALA* 3.7 31.4 - - + +
151F GLN 4.2 0.2 - - - -
152F ALA* 3.6 15.4 - - + +
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Residues in contact with ILE 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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42F LEU* 3.1 29.5 + - + +
43F LEU* 3.8 7.0 - - + +
45F ALA* 1.3 72.5 - - - +
47F THR* 1.3 67.1 + - - +
49F ALA* 3.2 4.1 + - + +
50F LEU* 3.0 41.2 + - + +
79F LEU* 4.0 11.7 - - + -
96F VAL* 3.9 32.1 - - + -
98F SER* 4.4 7.4 - - - +
118F ILE* 3.6 35.0 - - + -
122F LEU* 4.5 5.2 - - + -
131F VAL* 5.5 0.2 - - + -
152F ALA* 3.8 18.8 - - + -
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Residues in contact with THR 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 LEU 2.8 22.2 + - - -
44F HIS* 3.5 5.9 - - - -
46F ILE* 1.3 76.1 - - - +
48F ASP* 1.3 58.0 + - - +
50F LEU* 3.2 3.8 + - - +
51F PHE* 3.0 55.1 + - + -
59F ILE* 3.8 22.5 - - + +
63F PHE* 4.4 4.7 - - + -
75F SER 5.2 0.5 + - - -
78F LEU* 4.8 2.3 - - - +
79F LEU* 3.5 25.5 + - - +
82F CYS* 3.7 18.6 - - + -
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Residues in contact with ASP 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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132D LYS* 3.5 29.1 - - - +
134D LYS* 3.9 20.4 + - - +
8F GLY* 4.2 7.2 - - - -
9F TYR 4.3 5.9 - - - +
44F HIS* 2.9 15.1 + - - +
45F ALA* 3.8 5.6 - - - +
46F ILE 3.2 0.2 - - - -
47F THR* 1.3 78.3 - - - +
49F ALA* 1.3 55.6 + - - +
51F PHE* 3.5 2.1 + - - +
52F GLY 2.9 24.6 + - - -
58F ASP* 3.3 13.4 - - - +
59F ILE* 2.8 48.2 + - - +
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Residues in contact with ALA 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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6F GLY* 3.4 19.7 - - - +
7F GLN 3.7 13.2 - - - +
8F GLY* 3.6 13.8 - - - +
45F ALA 3.0 14.2 + - - +
46F ILE* 3.2 8.0 + - - +
48F ASP* 1.3 75.4 - - - +
50F LEU* 1.3 57.2 + - - +
52F GLY 3.4 0.2 + - - -
53F ALA* 2.9 26.0 + - - +
152F ALA* 3.9 14.8 - - + +
153F ALA 4.2 0.4 - - - -
154F ALA* 4.0 14.0 - - + +
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Residues in contact with LEU 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 ILE* 3.0 30.7 + - + +
47F THR 3.6 6.1 - - - +
49F ALA* 1.3 74.1 - - - +
51F PHE* 1.3 66.5 + - - +
53F ALA* 3.3 3.7 + - - +
54F ALA* 3.1 24.9 + - - +
79F LEU* 4.1 2.7 - - + -
82F CYS* 3.7 20.9 - - - -
83F ALA 5.4 0.7 - - - +
86F VAL* 3.8 11.2 - - + +
93F ILE* 3.7 36.3 - - + -
96F VAL* 4.6 1.6 - - + -
122F LEU* 3.9 29.4 - - + -
154F ALA* 3.8 21.5 - - + -
156F VAL* 4.2 8.9 - - + +
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Residues in contact with PHE 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 THR* 3.0 42.2 + - + +
48F ASP* 3.9 3.1 - - - +
50F LEU* 1.3 76.0 - - - +
52F GLY* 1.3 57.1 + - - +
54F ALA* 3.4 1.7 + - - -
55F ALA 3.0 7.3 + - - -
56F LEU* 2.9 42.5 + - + -
57F GLY 3.7 18.2 + - - +
58F ASP* 4.0 17.3 - - - -
59F ILE* 4.0 5.2 - - - -
62F HIS* 3.4 51.8 - + + -
63F PHE* 4.0 12.8 - + - -
82F CYS* 3.7 32.3 - - + -
85F ARG* 4.2 11.2 - - + -
86F VAL* 4.8 1.6 - - + -
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Residues in contact with GLY 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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95D ASN* 4.6 3.1 + - - -
96D VAL 5.0 0.2 - - - +
97D ASP* 3.2 37.4 - - - +
130D ASN* 3.4 20.8 - - - +
132D LYS* 4.4 0.4 - - - -
5F ILE 4.2 0.3 - - - +
6F GLY* 4.2 0.2 - - - -
48F ASP 2.9 15.0 + - - -
49F ALA 3.7 0.4 - - - -
51F PHE* 1.3 77.2 - - - +
53F ALA* 1.3 61.9 - - - +
55F ALA* 3.2 10.4 + - - +
57F GLY 4.2 0.2 + - - -
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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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95D ASN* 4.5 2.1 + - - -
4F ARG* 3.1 32.3 + - - +
5F ILE 3.4 14.8 - - - -
6F GLY* 3.6 15.1 - - - +
49F ALA 2.9 17.2 + - - +
50F LEU* 3.3 5.6 + - - +
52F GLY* 1.3 76.7 - - - +
54F ALA* 1.3 59.1 + - - +
55F ALA* 3.3 1.3 + - - +
154F ALA 4.1 4.5 - - - +
156F VAL* 3.8 28.8 - - + +
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Residues in contact with ALA 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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127D ASP* 4.8 1.4 - - - +
4F ARG* 5.4 0.2 - - - -
50F LEU 3.1 16.7 + - - +
51F PHE 4.0 0.4 - - - +
53F ALA* 1.3 75.2 - - - +
55F ALA* 1.3 70.0 + - - +
56F LEU* 3.4 32.7 + - + +
86F VAL* 4.2 11.2 - - + -
89F ALA* 5.0 0.3 - - - +
91F PHE* 3.7 40.0 - - + -
156F VAL* 4.6 0.9 - - + +
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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
------------------------------------------------------------
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