Contacts of the helix formed by residues 46 - 54 (chain B) in PDB entry 1F0K
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 MET 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLY* 3.5 40.4 - - - +
16B THR* 4.9 1.1 + - - +
20B VAL* 3.7 6.5 - - + -
21B PHE* 3.6 31.0 - - + -
45B ARG* 1.3 75.2 - - - +
47B GLU* 1.3 62.7 + - - +
48B ALA 3.1 0.2 - - - -
49B ASP* 3.2 9.4 + - - +
50B LEU* 3.1 42.3 + - + -
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Residues in contact with GLU 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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13B ALA 4.2 3.1 - - - +
14B GLY* 3.3 15.3 - - - -
15B GLY 2.8 24.0 + - - +
20B VAL* 4.4 3.6 - - + -
39B TRP* 4.1 8.7 - - - +
41B GLY* 3.6 9.6 - - - -
42B THR* 3.0 34.3 + - - +
45B ARG* 3.3 18.0 - - - +
46B MET* 1.3 73.4 + - - +
48B ALA* 1.3 66.6 + - - +
50B LEU* 3.9 4.9 - - - +
51B VAL* 3.1 44.1 + - + +
52B PRO* 3.5 0.5 - - - +
58B ILE* 3.9 18.2 - - + +
107B VAL* 5.4 1.6 - - - +
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Residues in contact with ALA 48 (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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42B THR 3.7 1.6 - - - +
43B ALA 3.1 23.3 - - - +
45B ARG 2.9 16.4 + - - +
47B GLU* 1.3 81.8 - - - +
49B ASP* 1.3 63.2 + - - +
52B PRO* 3.2 21.1 - - - +
58B ILE* 4.4 0.2 - - - -
60B PHE* 3.6 33.5 - - + -
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Residues in contact with ASP 49 (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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45B ARG 4.7 5.9 - - - +
46B MET* 3.2 8.5 + - - +
48B ALA* 1.3 86.5 - - - +
50B LEU* 1.3 64.0 + - - +
52B PRO* 3.5 7.7 - - - +
53B LYS* 3.2 37.5 + - - +
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Residues in contact with LEU 50 (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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20B VAL* 4.1 6.3 - - + -
21B PHE* 3.7 30.7 - - + -
24B LEU* 3.8 19.5 - - + -
46B MET* 3.1 34.8 + - - +
47B GLU* 4.5 2.2 - - - -
49B ASP* 1.3 76.9 - - - +
51B VAL* 1.3 65.6 + - + +
53B LYS* 3.1 26.8 + - + +
54B HIS* 3.3 30.5 + - + +
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Residues in contact with VAL 51 (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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20B VAL* 4.1 11.0 - - + -
24B LEU* 4.7 5.2 - - + -
39B TRP* 3.7 50.0 - - + +
47B GLU* 3.1 24.7 + - + +
50B LEU* 1.3 74.4 - - - +
52B PRO* 1.3 66.7 - - + +
54B HIS* 2.9 19.9 + - - +
56B ILE* 3.3 44.1 + - + +
58B ILE* 4.4 5.8 - - + -
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Residues in contact with PRO 52 (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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47B GLU 3.5 2.0 - - - +
48B ALA 3.2 28.0 - - - +
49B ASP* 3.5 8.5 - - - +
51B VAL* 1.3 94.0 - - + +
53B LYS* 1.3 55.7 + - + +
54B HIS 2.9 0.2 - - - -
55B GLY* 2.9 20.1 + - - -
56B ILE 3.7 10.5 - - - +
58B ILE* 4.0 17.3 - - + -
60B PHE* 5.8 0.2 - - + -
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Residues in contact with LYS 53 (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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49B ASP* 3.2 31.3 + - - +
50B LEU* 3.1 22.5 + - + +
52B PRO* 1.3 77.2 - - + +
54B HIS* 1.3 60.3 + - + +
55B GLY 3.3 1.7 + - - -
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Residues in contact with HIS 54 (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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24B LEU* 3.8 36.1 - - + +
28B HIS* 2.8 45.0 + + - +
31B MET* 5.7 0.2 - - - +
50B LEU* 3.3 35.3 + - + +
51B VAL 2.9 11.6 + - - +
53B LYS* 1.3 82.2 - - + +
55B GLY* 1.3 60.5 + - - +
56B ILE* 3.3 10.9 + - + +
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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