Contacts of the helix formed by residues 25 - 36 (chain F) in PDB entry 3SF4
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 VAL 25 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C THR* 4.8 9.9 - - + -
323C ASN* 4.0 23.6 - - + +
23F MET* 3.2 24.1 - - + -
24F GLN* 1.3 76.0 - - - +
26F ASP* 1.3 70.7 + - - +
27F SER* 4.1 6.5 - - - +
28F VAL* 2.7 41.5 + - + -
29F GLN* 2.8 11.1 + - - -
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Residues in contact with ASP 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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319C TRP* 2.4 41.3 + - + -
323C ASN* 3.3 18.8 + - - +
356C THR* 5.0 7.4 - - + -
360C ASN* 4.8 5.1 + - - -
24F GLN 3.2 7.2 + - - -
25F VAL* 1.3 75.0 - - - +
27F SER* 1.3 64.5 + - - -
29F GLN* 3.5 5.7 + - - +
30F ARG* 3.1 29.3 + - - +
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Residues in contact with SER 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C TYR* 4.5 5.3 + - - -
283C ASN* 3.9 3.0 + - - +
316C ARG* 5.1 0.9 + - - -
319C TRP* 3.7 30.6 - - - -
320C SER* 3.9 23.0 + - - -
323C ASN* 2.9 28.3 + - - +
25F VAL* 2.9 6.8 + - - +
26F ASP* 1.3 80.3 - - - +
28F VAL* 1.3 63.5 + - - +
30F ARG* 3.6 3.3 + - - +
31F TRP* 3.1 25.3 + - - +
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Residues in contact with VAL 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ASN* 3.5 22.2 - - - +
286C THR* 3.8 32.8 - - + +
287C LEU* 3.8 36.3 - - + -
298C HIS* 6.3 0.2 - - - +
23F MET* 4.0 8.5 - - + +
25F VAL* 2.7 26.4 + - + +
27F SER* 1.3 76.5 - - - +
29F GLN* 1.3 59.4 + - - +
31F TRP* 3.2 7.1 + - + +
32F MET* 2.9 31.1 + - - +
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Residues in contact with GLN 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F MET 4.7 2.6 + - - +
24F GLN* 3.5 33.5 - - - +
25F VAL 2.8 15.3 + - - +
26F ASP* 3.9 6.2 - - - +
28F VAL* 1.3 75.6 - - - +
30F ARG* 1.3 66.2 + - - +
32F MET* 3.2 10.2 + - + +
33F GLU* 3.0 48.4 + - + +
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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
----------------------------------------------------------
316C ARG* 3.1 34.9 - - - +
319C TRP* 3.8 18.5 - - + -
350C ASP* 5.8 2.0 + - - -
26F ASP 3.1 17.6 + - - +
27F SER 3.7 5.4 - - - +
29F GLN* 1.3 76.2 - - - +
31F TRP* 1.3 64.2 + - - +
33F GLU* 3.4 22.0 + - - +
34F ASP* 2.7 66.2 + - - -
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Residues in contact with TRP 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ILE* 3.9 21.5 - - + -
258C TYR* 4.0 3.4 - - - -
279C TYR* 3.7 20.4 - + + -
280C SER* 3.6 41.8 + - - +
283C ASN* 3.3 45.3 - - + +
284C THR* 4.2 0.4 - - - -
287C LEU* 4.0 15.7 - - + -
316C ARG* 4.1 9.8 - - - +
27F SER 3.1 12.7 + - - +
28F VAL* 3.3 9.6 - - + +
29F GLN 3.2 0.2 - - - -
30F ARG* 1.3 80.9 - - - +
32F MET* 1.3 84.2 + - + +
34F ASP* 3.3 6.0 + - + +
35F LEU* 2.9 60.0 + - + +
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Residues in contact with MET 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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246C ILE* 3.9 27.8 - - + +
247C PHE* 3.5 27.0 - - + -
251C PHE* 5.4 2.7 - - + -
287C LEU* 4.6 13.7 - - + -
23F MET 4.8 7.0 - - - +
28F VAL* 2.9 31.3 + - - +
29F GLN* 3.6 9.0 - - + +
31F TRP* 1.3 89.0 - - + +
33F GLU* 1.3 56.8 + - + +
35F LEU* 3.4 7.1 - - - +
36F LYS* 2.7 38.4 + - - +
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Residues in contact with GLU 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 GLN* 3.0 45.4 + - + +
30F ARG* 3.5 22.7 + - - +
32F MET* 1.3 78.0 - - + +
34F ASP* 1.3 64.2 - - - +
36F LYS* 3.5 25.4 - - - +
37F LEU* 3.9 14.2 + - - +
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Residues in contact with ASP 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ARG* 3.0 21.0 + - - -
30F ARG* 2.7 37.8 + - - -
31F TRP* 3.6 7.4 - - + +
32F MET 3.2 0.4 - - - -
33F GLU* 1.3 76.4 - - - +
35F LEU* 1.3 67.5 + - - +
37F LEU* 3.2 15.5 + - - +
38F MET* 3.3 25.7 + - + +
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Residues in contact with LEU 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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206C TYR* 2.7 26.6 + - - +
243C ASN* 3.3 26.7 - - - +
246C ILE* 4.1 9.6 - - + -
247C PHE* 4.0 15.7 - - + -
258C TYR* 3.8 8.3 - - - +
280C SER* 4.8 4.3 - - - +
31F TRP* 2.9 62.9 + - + +
32F MET* 3.4 9.6 - - - +
34F ASP* 1.3 78.3 - - - +
36F LYS* 1.3 55.9 + - - +
38F MET* 2.8 36.6 + - - +
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Residues in contact with LYS 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C TYR* 3.7 15.4 - - - +
207C LEU* 3.8 11.1 - - - +
211C PHE* 6.2 2.9 - - + -
247C PHE* 3.6 34.5 - - + -
32F MET* 2.7 19.6 + - - +
33F GLU* 3.5 19.1 - - + +
35F LEU* 1.3 72.2 - - - +
37F LEU* 1.3 66.3 + - + +
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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