Contacts of the helix formed by residues 28 - 37 (chain F) in PDB entry 2GLJ
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 28 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F GLU 3.5 5.5 + - - -
24F VAL* 3.6 8.3 - - - -
25F PHE* 2.7 20.7 + - - +
27F LEU* 1.3 86.0 - - - +
29F ASP* 1.3 60.2 + - - -
31F PHE* 3.5 1.0 - - - +
32F LYS* 3.0 33.7 - - - +
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Residues in contact with ASP 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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24F VAL 4.5 1.1 + - - -
25F PHE* 3.1 11.0 + - + +
28F GLY* 1.3 68.5 - - - -
30F ARG* 1.3 55.5 + - - +
31F PHE 2.5 18.1 + - - -
32F LYS* 2.9 6.7 + - - +
33F ASN* 2.9 26.8 + - + +
34F PHE 3.5 1.4 + - - -
271F TYR* 4.6 5.5 - - - -
272F THR* 5.4 3.2 - - - +
275F GLU* 3.5 26.9 - - - +
449F LYS* 5.7 1.1 - - - +
452F ILE* 4.1 26.0 - - + +
453F TYR* 3.6 34.8 + - - +
456F LYS* 4.1 16.9 + - - +
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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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167C ASP 5.8 1.8 + - - -
168C ASN* 5.7 3.6 + - - +
25F PHE 3.3 4.1 + - - +
26F ALA 3.1 17.5 - - - +
27F LEU* 3.1 21.9 - - - +
29F ASP* 1.3 74.7 - - - +
31F PHE* 1.3 68.1 + - - +
33F ASN* 5.3 0.7 - - - -
34F PHE* 2.9 61.4 - - + +
250F ARG* 5.7 0.6 - - - +
251F ASP* 2.6 45.9 + - - +
259F VAL* 4.1 9.2 - - + -
449F LYS* 3.0 39.7 - - + +
452F ILE* 5.8 3.5 - - + +
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Residues in contact with PHE 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 LEU* 3.0 20.4 - - + +
28F GLY 3.5 1.6 - - - +
29F ASP 2.5 5.7 + - - -
30F ARG* 1.3 80.6 - - - +
32F LYS* 1.3 74.1 + - + +
34F PHE* 3.0 19.1 - + - +
35F ILE* 2.7 47.2 + - + +
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Residues in contact with LYS 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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28F GLY* 3.0 30.7 + - - +
29F ASP* 2.9 10.0 + - - +
31F PHE* 1.3 96.5 - - + +
33F ASN* 1.3 51.2 + - - +
35F ILE* 2.9 9.3 - - - +
36F SER* 2.8 32.6 + - - -
271F TYR* 2.9 23.9 + - + +
275F GLU* 3.0 35.0 + - - +
456F LYS* 4.7 2.6 - - - +
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Residues in contact with ASN 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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29F ASP* 2.9 20.2 + - + +
30F ARG* 5.3 0.6 - - - -
32F LYS* 1.3 70.0 - - - +
34F PHE* 1.3 58.2 + - - +
35F ILE 2.5 17.7 + - - -
36F SER* 2.5 18.4 + - - -
37F ASN* 2.7 27.6 + - - +
259F VAL* 5.2 6.3 - - - +
264F GLN* 5.2 2.9 + - - -
267F ARG* 4.9 2.0 + - - +
268F ILE* 3.9 24.6 - - - +
271F TYR* 3.5 33.8 - - + +
447F SER* 5.2 1.0 + - - -
452F ILE* 3.8 26.6 - - + +
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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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167C ASP 5.7 2.9 - - - -
29F ASP 3.5 1.4 + - - -
30F ARG* 2.9 60.0 - - + +
31F PHE* 3.0 32.5 - + - +
33F ASN* 1.3 83.3 + - - +
35F ILE* 1.3 52.9 + - + +
37F ASN* 3.6 6.0 - - - +
38F CYS* 2.7 29.8 - - - -
248F LYS* 5.8 5.6 - - + -
249F ALA* 2.9 30.8 - - - +
250F ARG* 3.3 17.0 - - - -
259F VAL* 4.0 22.4 - - + -
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Residues in contact with ILE 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 PHE* 2.7 28.5 + - + +
32F LYS* 2.9 19.5 - - - +
33F ASN 2.5 4.6 + - - -
34F PHE* 1.3 78.7 - - + +
36F SER* 1.3 67.0 + - - +
37F ASN 3.4 0.9 - - - -
38F CYS* 3.1 22.5 + - + +
39F LYS* 3.3 48.4 + - + +
248F LYS* 5.7 5.6 - - - +
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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 LYS 2.8 12.8 + - - -
33F ASN* 2.5 18.3 + - - -
35F ILE* 1.3 75.1 - - - +
37F ASN* 1.3 57.5 + - - -
38F CYS 2.7 7.4 + - - -
39F LYS* 5.6 0.7 - - - -
40F THR* 2.6 33.8 + - - -
45F VAL* 5.0 10.9 - - - +
48F LEU* 5.7 7.8 - - - +
49F ILE* 5.8 1.6 - - - +
267F ARG* 5.7 4.8 - - - +
271F TYR* 3.7 30.7 - - - +
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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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33F ASN* 2.7 42.7 + - - +
34F PHE* 3.6 6.8 - - - +
36F SER* 1.3 72.9 + - - +
38F CYS* 1.3 57.3 + - - +
40F THR 3.7 15.0 - - - +
41F GLU* 3.8 12.6 - - - +
249F ALA* 3.4 25.7 + - - +
259F VAL* 5.4 1.9 - - - +
261F GLY* 4.0 9.3 - - - -
262F TYR 3.6 28.1 + - - +
263F GLY 5.4 0.2 - - - -
264F GLN* 4.8 14.0 + - - +
267F ARG* 4.6 16.4 - - + +
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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