Contacts of the helix formed by residues 24 - 37 (chain F) in PDB entry 3G3B
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 24 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F ASP* 3.5 9.9 - - - -
19F ASN* 3.9 10.5 + - - +
22F GLY 4.0 1.6 + - - -
23F TYR* 1.3 75.2 - - - +
25F LEU* 1.3 66.6 + - - +
27F ASN* 2.9 38.0 + - - +
28F TRP* 3.4 2.8 - - - -
120F VAL* 3.9 5.5 - - - +
121F GLN* 3.1 30.6 + - - +
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Residues in contact with LEU 25 (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 ALA 3.9 6.5 - - - +
12F MET* 3.8 16.2 - - + -
13F LYS* 3.7 47.3 - - + +
17F LEU* 4.4 4.0 - - + -
18F ASP* 3.0 42.0 + - + +
23F TYR 3.9 0.2 + - - -
24F SER* 1.3 71.7 - - - +
26F GLY* 1.3 62.6 + - - +
27F ASN 3.0 1.4 + - - -
28F TRP* 3.0 19.9 + - + +
29F VAL* 3.4 15.9 + - + +
121F GLN* 4.0 4.4 + - - +
124F ILE* 3.5 32.8 - - + -
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Residues in contact with GLY 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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24F SER 3.1 1.6 + - - -
25F LEU* 1.3 79.2 - - - +
27F ASN* 1.3 56.2 + - - +
29F VAL* 3.7 2.6 + - - +
30F CYS* 2.9 30.3 + - - +
120F VAL* 3.6 24.2 - - - +
121F GLN* 3.2 13.6 + - - -
123F TRP* 3.9 6.7 - - - +
124F ILE* 3.7 15.1 - - - +
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Residues in contact with ASN 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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23F TYR* 3.9 12.6 - - + +
24F SER* 2.9 47.2 + - - +
26F GLY* 1.3 77.9 - - - +
28F TRP* 1.3 57.9 + - + +
30F CYS* 3.3 3.9 + - - +
31F ALA* 2.9 30.1 + - - +
105F MET* 3.7 15.5 - - - -
111F TRP* 3.2 36.2 + - - +
116F LYS* 5.2 1.2 - - - -
120F VAL* 3.7 22.5 - - - +
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Residues in contact with TRP 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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12F MET* 3.8 24.1 - - + +
17F LEU* 2.8 54.6 + - + -
20F TYR* 3.8 32.3 - + + -
23F TYR* 3.4 25.1 + + + +
24F SER 3.4 14.1 - - - -
25F LEU* 3.0 12.0 + - - +
27F ASN* 1.3 71.2 - - - +
29F VAL* 1.3 66.7 + - - +
31F ALA* 3.2 4.4 + - - +
32F ALA* 3.0 24.1 + - - +
56F LEU* 4.3 9.9 - - + +
95F ALA* 4.3 16.4 - - + -
99F VAL* 3.5 37.2 - - + -
105F MET* 3.7 24.7 - - + -
108F TRP* 4.7 3.4 - + - -
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Residues in contact with VAL 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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5F ARG* 4.0 22.9 - - + +
8F LEU* 4.6 3.1 - - + -
9F ALA* 3.9 24.7 - - + +
12F MET* 3.7 19.5 - - - -
25F LEU* 3.5 15.5 - - + +
26F GLY 3.8 6.5 - - - +
28F TRP* 1.3 73.6 - - - +
30F CYS* 1.3 62.5 + - - +
32F ALA* 3.3 4.5 + - - +
33F LYS 3.1 17.8 + - - -
38F PHE* 3.6 22.6 - - + -
123F TRP* 3.9 24.7 - - + +
124F ILE* 4.2 7.9 - - + -
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Residues in contact with CYS 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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26F GLY 2.9 23.0 + - - +
27F ASN* 3.3 5.1 + - - +
29F VAL* 1.3 74.3 - - - +
31F ALA* 1.3 60.5 + - - +
33F LYS* 3.2 8.4 - - - +
34F PHE* 3.2 40.2 - - - -
114F ARG 4.4 1.3 - - - -
115F CYS* 2.0 50.3 - - + -
118F THR* 5.5 0.4 - - - -
120F VAL* 5.3 1.1 - - + -
123F TRP* 3.4 36.1 - - + +
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Residues in contact with ALA 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 ASN 2.9 17.7 + - - +
28F TRP 3.2 4.7 + - - +
30F CYS* 1.3 76.6 - - - +
32F ALA* 1.3 53.2 + - - +
34F PHE* 3.3 4.1 + - - +
35F GLU* 2.8 38.6 + - - +
56F LEU* 4.0 14.1 - - + -
105F MET* 3.8 19.1 - - + -
108F TRP* 4.9 7.9 - - + -
111F TRP* 4.0 23.7 + - + +
115F CYS* 4.0 0.4 - - - -
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Residues in contact with ALA 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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8F LEU* 3.7 25.8 - - + -
12F MET* 4.2 5.4 - - + -
28F TRP 3.0 15.9 + - - +
29F VAL 3.6 4.5 - - - +
31F ALA* 1.3 71.4 - - - +
33F LYS* 1.3 60.4 + - - +
36F SER* 2.8 35.2 + - - -
37F ASN 3.2 1.7 + - - -
38F PHE* 4.1 3.6 - - + -
55F ILE* 3.5 24.0 - - + +
56F LEU* 3.6 9.7 - - + +
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Residues in contact with LYS 33 (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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29F VAL 3.1 8.1 + - - +
30F CYS 3.2 11.7 - - - +
32F ALA* 1.3 74.6 - - - +
34F PHE* 1.3 72.7 + - + +
37F ASN* 2.5 66.6 + - - +
38F PHE* 3.5 34.4 - - + -
123F TRP* 3.6 25.1 - - + -
132G TRP* 5.5 4.8 + - + +
135G PHE* 6.1 2.4 - - - -
140G LEU* 3.7 27.8 - - - +
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Residues in contact with PHE 34 (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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30F CYS* 3.2 43.7 + - - +
31F ALA* 3.3 4.4 + - - +
33F LYS* 1.3 86.4 - - + +
35F GLU* 1.3 70.4 + - - +
37F ASN 5.0 0.2 + - - -
110F ALA* 4.0 24.2 - - + +
111F TRP 5.2 0.7 - - - +
114F ARG* 3.2 63.3 - - + -
115F CYS* 3.9 5.6 - - - -
123F TRP* 4.0 13.9 - + - -
131G PRO 5.5 0.7 - - - -
140G LEU* 4.1 23.6 - - + -
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Residues in contact with GLU 35 (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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31F ALA 2.8 20.8 + - - +
34F PHE* 1.3 81.4 - - - +
36F SER* 1.3 57.6 + - - +
42F ALA* 5.5 0.2 - - - +
55F ILE 3.4 17.9 - - - +
56F LEU* 3.8 10.1 - - - +
57F GLN* 3.5 32.2 + - + +
108F TRP* 3.4 42.7 - - + +
109F VAL 4.8 0.3 + - - -
110F ALA* 3.7 25.3 + - - +
111F TRP 4.7 0.7 + - - -
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Residues in contact with SER 36 (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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32F ALA 2.8 12.7 + - - -
35F GLU* 1.3 72.2 - - - +
37F ASN* 1.3 67.9 + - - +
38F PHE 3.3 7.8 + - - -
39F ASN* 3.2 30.6 + - - +
42F ALA* 3.9 11.6 - - - +
54F GLY 3.5 17.5 - - - -
55F ILE* 2.9 32.1 + - - +
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Residues in contact with ASN 37 (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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2F VAL* 4.1 12.0 - - - +
32F ALA 3.2 0.2 + - - -
33F LYS* 2.5 60.9 + - - +
35F GLU 3.9 0.2 - - - -
36F SER* 1.3 73.6 - - - +
38F PHE* 1.3 71.9 + - - +
39F ASN* 3.3 2.0 + - + +
47H THR* 4.1 23.6 - - - +
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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