Contacts of the helix formed by residues 39 - 48 (chain B) in PDB entry 2FE3
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 THR 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B HIS 3.9 0.2 + - - -
38B PRO* 1.3 76.5 - - - +
40B ALA* 1.3 63.8 + - - +
41B ASP* 3.4 11.5 + - - +
42B ASP* 3.0 31.7 + - - +
43B ILE* 3.2 21.7 + - - +
81B SER* 4.6 15.7 - - - +
82B SER 3.6 20.2 - - - +
83B ARG* 3.7 31.0 - - + +
84B PHE* 4.4 2.7 - - - -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 1.3 73.8 - - - +
41B ASP* 1.3 57.1 + - - +
43B ILE* 3.1 8.5 + - - +
44B TYR* 2.8 30.4 + - - +
56B VAL* 4.8 3.6 - - + -
59B VAL* 4.0 19.0 - - + +
60B TYR* 3.3 51.7 + - + +
63B LEU* 4.3 5.2 - - + -
82B SER 4.3 1.2 + - - -
84B PHE* 4.0 6.8 - - + -
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Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 3.2 10.2 - - - +
40B ALA* 1.3 80.1 - - - +
42B ASP* 1.3 56.2 + - - +
44B TYR* 3.4 7.2 + - - +
45B LYS* 2.9 38.8 + - + +
56B VAL* 4.2 23.4 - - - +
60B TYR* 5.5 2.3 + - - -
81B SER* 5.1 7.7 + - - -
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.9 11.9 + - - +
38B PRO* 3.8 15.8 - - + +
39B THR* 3.0 44.6 + - - +
41B ASP* 1.3 75.5 - - - +
43B ILE* 1.3 64.2 + - - +
45B LYS* 3.9 3.8 - - - +
46B ALA* 3.0 25.5 + - - +
83B ARG* 4.0 7.4 + - - -
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.0 15.9 - - + -
30B TYR* 3.7 28.5 - - + -
31B LEU* 4.0 23.1 - - + -
38B PRO* 4.1 5.6 - - + -
39B THR 3.2 15.2 + - - +
40B ALA* 3.1 7.9 + - - +
42B ASP* 1.3 76.5 - - - +
44B TYR* 1.3 62.8 + - - +
46B ALA* 3.2 4.8 + - - +
47B LEU* 3.1 43.0 + - + +
59B VAL* 3.9 15.7 - - + -
63B LEU* 4.1 30.7 - - + -
84B PHE* 4.9 2.5 - - + -
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Residues in contact with TYR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA 2.8 19.9 + - - +
41B ASP* 3.6 7.2 - - - +
43B ILE* 1.3 73.0 - - - +
45B LYS* 1.3 80.5 + - + +
47B LEU 3.2 0.7 + - - -
48B GLU* 2.8 51.9 + - + +
54B MET* 3.2 48.5 + - + +
55B SER* 3.9 3.5 - - - -
56B VAL* 3.7 45.1 - - + -
59B VAL* 4.2 7.8 - - + +
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Residues in contact with LYS 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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41B ASP* 2.9 24.0 + - + +
42B ASP* 4.1 3.8 - - - +
44B TYR* 1.3 93.3 - - + +
46B ALA* 1.3 62.2 + - - +
47B LEU 3.4 0.9 + - - -
48B GLU* 3.4 36.1 + - - +
49B GLY 4.9 0.7 + - - -
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Residues in contact with ALA 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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30B TYR* 3.3 39.0 - - + +
42B ASP 3.0 15.6 + - - +
43B ILE 3.2 5.4 + - - +
45B LYS* 1.3 76.7 - - - +
47B LEU* 1.3 66.8 + - + +
49B GLY* 5.1 1.1 + - - -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 6.2 0.2 - - + -
26B ALA* 3.7 44.4 - - + +
27B ILE* 3.9 10.3 - - + -
30B TYR* 4.5 11.2 - - + -
43B ILE* 3.1 36.4 + - + +
46B ALA* 1.3 89.8 - - + +
48B GLU* 1.3 61.6 + - - +
49B GLY 3.1 3.1 - - - -
50B LYS* 2.9 25.7 + - + +
51B PHE* 3.3 19.5 + - + -
54B MET* 3.7 17.3 - - + -
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 2.8 39.4 + - + +
45B LYS* 3.4 44.1 + - + +
46B ALA 3.7 0.2 - - - -
47B LEU* 1.3 77.4 - - - +
49B GLY* 1.3 77.6 + - - +
51B PHE 3.1 22.6 + - - +
52B PRO* 5.1 0.2 - - - +
54B MET* 3.3 14.6 - - + +
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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
------------------------------------------------------------
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