Contacts of the helix formed by residues 26 - 39 (chain F) in PDB entry 5IXM
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 GLY 26 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E ARG* 3.7 7.4 - - - -
23F ASP* 3.1 28.8 + - - -
24F PRO 4.6 0.2 - - - +
25F TYR* 1.3 82.2 - - - +
27F PRO* 1.3 77.0 - - - +
28F LEU* 3.3 2.7 - - - -
29F ALA* 3.4 6.0 + - - +
30F ARG* 3.2 19.4 + - - +
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Residues in contact with PRO 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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100E ARG* 3.9 19.7 - - - +
25F TYR 4.6 0.7 - - - +
26F GLY* 1.3 81.5 - - - +
28F LEU* 1.3 65.9 + - + +
30F ARG* 3.1 13.9 + - + +
31F SER* 2.9 24.8 + - - -
125F GLN* 4.4 8.8 + - - +
128F ARG* 3.7 34.1 - - - +
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Residues in contact with LEU 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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26F GLY 3.3 1.0 - - - -
27F PRO* 1.3 80.8 - - + +
29F ALA* 1.3 59.6 + - - +
31F SER* 3.1 4.2 + - - -
32F ILE* 2.9 48.7 + - + +
57F ILE* 4.7 13.2 - - + -
60F SER* 3.8 32.3 - - - +
82F LEU* 5.7 0.9 - - + -
84F VAL* 3.9 27.6 - - + -
128F ARG* 3.7 45.9 - - + +
131F ALA* 4.6 3.6 - - + -
132F ALA 5.1 0.9 - - - +
135F LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 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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19F LEU* 4.9 2.3 - - + +
21F SER* 4.1 14.8 - - - +
23F ASP 3.3 25.9 + - - +
24F PRO* 3.7 14.4 - - + +
26F GLY 3.4 6.1 + - - +
27F PRO 3.3 0.4 - - - -
28F LEU* 1.3 78.1 - - - +
30F ARG* 1.3 58.1 + - - +
32F ILE* 3.4 13.1 + - - +
33F ARG* 2.9 42.3 + - - +
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Residues in contact with ARG 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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139E ASN 4.2 5.7 + - - -
140E GLU* 2.8 32.9 + - - +
141E ASN 4.4 1.2 - - - -
142E TRP 4.8 0.2 - - - +
143E ASN* 4.2 10.9 - - - +
174E TYR* 3.3 62.2 - - - +
24F PRO 5.3 0.4 + - - -
25F TYR* 4.3 16.2 + - - +
26F GLY 3.2 9.9 + - - +
27F PRO* 3.1 13.8 + - - +
29F ALA* 1.3 75.4 - - - +
31F SER* 1.3 59.6 + - - +
33F ARG* 3.2 9.6 + - - +
34F GLN* 2.9 47.5 + - + +
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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 PRO 2.9 12.7 + - - -
28F LEU 3.5 8.3 - - - -
30F ARG* 1.3 76.3 - - - +
32F ILE* 1.3 58.4 + - - +
34F GLN* 3.3 12.6 + - - +
35F GLN* 2.9 34.4 + - - +
125F GLN* 3.8 10.9 + - - -
128F ARG* 4.2 6.8 - - - +
129F GLU* 3.7 42.9 + - - +
132F ALA* 3.8 7.2 - - - -
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Residues in contact with ILE 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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19F LEU* 4.2 16.2 - - + -
21F SER* 6.0 0.2 - - - +
28F LEU* 2.9 39.0 + - + +
29F ALA* 3.6 11.4 - - + +
31F SER* 1.3 75.7 - - - +
33F ARG* 1.3 58.7 + - - +
35F GLN* 3.3 2.4 + - - +
36F LEU* 2.9 48.1 + - + +
55F LEU* 4.7 8.5 - - + -
57F ILE* 3.6 31.6 - - + -
84F VAL* 5.8 0.2 - - + -
132F ALA* 3.9 19.3 - - + -
135F LEU* 4.1 16.8 - - + -
136F VAL* 6.1 2.2 - - + -
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Residues in contact with ARG 33 (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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140E GLU* 4.9 19.3 + - - -
19F LEU* 3.6 39.9 + - + +
21F SER* 5.8 1.6 - - - -
24F PRO* 3.1 33.7 + - - +
25F TYR* 6.2 1.7 - - - -
29F ALA* 2.9 33.3 + - - +
30F ARG* 3.5 7.6 - - + +
32F ILE* 1.3 74.4 - - - +
34F GLN* 1.3 60.3 + - + +
36F LEU* 3.8 1.8 - - - +
37F ARG* 2.9 31.9 + - - +
43F ILE* 4.2 27.2 - - + +
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Residues in contact with GLN 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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174E TYR* 4.6 11.7 - - - -
176E ASN* 6.2 2.0 - - - +
30F ARG* 2.9 45.2 + - + +
31F SER* 3.3 11.9 + - - +
33F ARG* 1.3 76.5 - - + +
35F GLN* 1.3 60.2 + - + +
37F ARG* 3.4 10.2 + - - +
38F LEU* 2.9 28.6 + - - +
125F GLN* 5.7 1.0 + - - -
129F GLU* 5.1 9.4 - - - +
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Residues in contact with GLN 35 (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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31F SER* 2.9 20.1 + - - +
32F ILE 3.7 3.8 - - - +
34F GLN* 1.3 77.6 - - + +
36F LEU* 1.3 64.4 + - - +
38F LEU* 3.1 21.9 + - - +
39F ASN* 2.8 41.0 + - - -
129F GLU* 4.5 6.8 + - - +
132F ALA* 3.5 21.3 - - + -
133F GLN* 3.7 37.1 - - - +
136F VAL* 4.0 16.2 - - + +
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Residues in contact with LEU 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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17F LEU* 4.3 17.7 - - + -
19F LEU* 3.9 25.1 - - + -
32F ILE* 2.9 37.1 + - + +
33F ARG 3.8 3.6 - - - +
35F GLN* 1.3 75.6 - - - +
37F ARG* 1.3 60.8 + - - +
39F ASN* 3.1 9.4 + - - -
41F VAL* 2.9 55.6 + - + +
43F ILE* 4.4 11.7 - - + -
55F LEU* 4.7 7.2 - - + -
136F VAL* 4.2 18.6 - - + -
139F LEU* 4.5 17.0 - - + -
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Residues in contact with ARG 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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176E ASN* 3.8 23.2 - - - +
177E ASP* 2.7 34.1 + - - -
182E ASP* 2.4 42.2 + - - -
214E PRO* 4.4 10.5 - - - +
216E SER* 5.0 1.2 - - - -
33F ARG 2.9 19.8 + - - +
34F GLN* 3.5 8.5 - - - +
36F LEU* 1.3 79.1 - - - +
38F LEU* 1.3 59.8 + - - +
40F ASN* 3.2 17.5 + - - +
41F VAL 4.5 8.5 + - - +
43F ILE* 5.2 4.0 - - + +
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Residues in contact with LEU 38 (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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214E PRO* 5.4 12.3 - - + -
215E LEU 5.4 0.9 - - - +
216E SER* 2.1 48.2 + - - +
217E ASN 4.9 0.5 - - - +
221E SER* 4.4 20.6 - - - +
34F GLN 2.9 18.1 + - - +
35F GLN* 3.1 29.3 + - - +
37F ARG* 1.3 76.9 - - - +
39F ASN* 1.3 61.0 + - - +
40F ASN 3.2 0.7 - - - -
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Residues in contact with ASN 39 (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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216E SER* 4.4 0.4 - - - -
217E ASN 5.5 4.5 - - - +
11F PRO* 5.2 4.3 - - - +
12F THR* 4.1 16.2 + - - +
15F GLN* 4.7 6.4 + - - +
35F GLN* 2.8 38.5 + - - +
36F LEU* 3.1 5.1 + - - +
38F LEU* 1.3 83.5 - - - +
40F ASN* 1.3 72.3 + - - +
41F VAL* 3.3 15.7 + - + +
136F VAL* 3.7 28.4 - - + +
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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