Contacts of the helix formed by residues 37 - 47 (chain B) in PDB entry 3FTN
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 CYS 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA 4.1 0.2 + - - -
36B PRO* 1.3 73.8 - - - +
38B THR* 1.3 71.3 + - - +
39B SER* 3.2 32.5 - - - +
40B ASP* 3.0 24.3 + - + +
41B ILE* 3.6 7.5 + - - +
58B GLY* 6.0 0.8 - - - -
59B HIS* 3.5 17.7 - - + +
60B GLU* 3.3 15.6 + - - +
150B ASP* 3.6 17.7 - - - -
151B MET* 4.3 11.4 - - - -
334B PHE* 5.4 0.2 - - - -
337B MET* 4.1 3.4 - - - -
346B LYS* 3.7 3.1 - - - +
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B CYS* 1.3 77.7 - - - +
39B SER* 1.3 66.4 + - - +
41B ILE* 2.9 22.5 + - - +
42B HIS* 3.2 27.1 + - - -
267B TYR* 6.1 1.0 - - - +
337B MET* 3.6 24.1 - - + +
340B LYS* 5.4 11.7 - - + -
346B LYS* 4.8 1.5 - - - +
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B CYS* 3.0 13.1 - - - -
38B THR* 1.3 83.6 + - - +
40B ASP* 1.3 63.9 + - - +
42B HIS* 3.4 7.5 + - - +
43B THR* 3.1 24.4 + - - -
59B HIS* 3.1 29.9 - - - -
110B TRP* 4.3 10.5 - - - -
267B TYR* 3.9 31.1 - - - -
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B CYS 3.0 14.8 + - - +
39B SER* 1.3 80.6 + - - +
41B ILE* 1.3 61.2 + - - +
43B THR* 3.3 7.5 + - - -
44B VAL* 2.9 33.8 + - - +
57B LEU* 3.7 15.3 - - + +
58B GLY* 2.8 35.0 + - - -
59B HIS* 3.9 10.3 + - - -
110B TRP* 4.8 1.2 - - - -
113B SER* 2.8 27.5 + - - +
120B PHE* 4.6 2.8 - - + -
334B PHE* 3.9 18.4 - - + -
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Residues in contact with ILE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B CYS 4.0 5.6 - - - +
38B THR* 2.9 15.4 + - - +
40B ASP* 1.3 77.7 - - - +
42B HIS* 1.3 60.3 + - + +
44B VAL 3.4 0.3 + - - -
45B PHE* 2.9 47.1 + - + +
46B GLU* 5.0 0.5 - - - +
334B PHE* 3.6 38.1 - - + +
337B MET* 3.8 21.1 - - + +
338B LYS* 3.6 39.5 - - + +
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 3.2 24.1 + - - -
39B SER* 3.5 7.1 - - - +
41B ILE* 1.3 82.4 - - + +
43B THR* 1.3 62.7 + - - +
46B GLU* 2.9 55.2 + - - +
47B GLY 3.3 3.1 + - - -
48B ALA* 3.5 17.8 + - + -
266B ASN* 5.8 0.4 - - - -
267B TYR* 3.8 43.0 + + + -
269B GLY* 4.7 7.5 + - - -
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B MET* 3.7 28.1 - - + +
39B SER 3.1 12.7 + - - -
40B ASP* 3.3 14.0 + - - -
42B HIS* 1.3 78.1 - - - +
44B VAL* 1.3 65.0 + - + +
47B GLY* 3.3 20.3 + - - -
48B ALA* 4.1 8.9 - - - +
49B ILE* 3.6 42.8 - - + +
50B GLY 4.7 1.3 - - - +
52B ARG* 5.0 0.4 - - + -
55B MET* 4.3 10.1 - - + -
57B LEU* 5.3 1.8 - - + -
110B TRP* 4.8 5.2 - - - -
113B SER 4.8 2.6 + - - +
267B TYR* 4.8 1.6 + - - -
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B MET* 3.7 28.3 - - + -
8B SER 4.9 0.9 - - - +
9B ILE* 3.5 5.9 - - - +
10B GLY 2.6 40.7 + - - +
11B LYS 4.3 2.5 - - - +
12B VAL* 3.5 28.5 - - + -
40B ASP 2.9 19.2 + - - +
43B THR* 1.3 79.8 - - + +
45B PHE* 1.3 83.3 + - + +
46B GLU 3.6 0.2 - - - -
57B LEU* 3.8 22.0 - - + -
334B PHE* 4.1 1.8 - - + -
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Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 5.0 5.1 - - - +
10B GLY* 3.7 29.6 - - - +
12B VAL* 4.9 5.8 - - + -
41B ILE* 2.9 31.8 + - + +
44B VAL* 1.3 93.0 - - + +
46B GLU* 1.3 66.5 + - + +
47B GLY 3.7 0.7 - - - -
334B PHE* 3.8 23.6 - + - -
335B MET* 4.4 12.1 - - + -
338B LYS* 3.6 42.0 - - + -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 5.2 1.8 - - - -
41B ILE 5.0 0.2 - - - +
42B HIS* 2.9 43.8 + - - +
45B PHE* 1.3 84.4 - - + +
47B GLY* 1.3 67.5 + - - +
48B ALA* 3.1 5.9 + - + +
269B GLY 3.8 20.5 - - - +
270B SER* 4.5 8.6 - - - -
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Residues in contact with GLY 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.8 29.7 - - - +
42B HIS 3.3 0.2 + - - -
43B THR 3.3 17.6 + - - -
45B PHE 3.7 0.6 - - - -
46B GLU* 1.3 77.8 - - - +
48B ALA* 1.3 62.1 + - - +
49B ILE 3.2 4.8 + - - -
50B GLY* 3.3 15.6 + - - -
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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