Contacts of the helix formed by residues 39 - 46 (chain F) in PDB entry 1F1H
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 ASN 39 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F LEU* 5.4 8.5 - - - -
36F HIS 5.4 1.2 + - - +
37F GLN* 3.8 14.7 + - - +
38F VAL* 1.3 77.9 - - - +
40F ALA* 1.3 68.3 + - + +
41F GLU* 3.1 16.5 - - - +
42F PHE* 2.7 44.4 + - - +
43F PHE* 3.6 14.3 + - - -
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Residues in contact with ALA 40 (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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6F LEU* 5.9 1.8 - - - +
39F ASN* 1.3 76.2 - - - +
41F GLU* 1.3 64.8 + - - +
43F PHE* 3.2 14.8 + - - +
44F GLU* 3.7 26.0 + - - +
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Residues in contact with GLU 41 (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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39F ASN* 3.1 16.6 - - - +
40F ALA* 1.3 77.8 - - - +
42F PHE* 1.3 67.2 + - - +
44F GLU* 3.0 19.9 + - - +
45F GLU* 3.0 51.2 + - + +
46F GLY 5.3 2.7 - - - +
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Residues in contact with PHE 42 (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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17F VAL* 5.1 0.7 - - + -
19F LEU* 4.1 32.3 - - + -
33F ILE* 5.6 5.6 - - + -
37F GLN 4.3 6.5 - - - +
38F VAL* 3.8 40.4 - - + -
39F ASN* 2.7 26.9 + - - +
41F GLU* 1.3 76.1 - - + +
43F PHE* 1.3 73.0 + + - +
46F GLY* 2.7 45.8 + - - -
47F LYS* 4.4 13.9 - - + -
67F LEU* 5.3 0.7 - - + -
69F PRO* 3.6 38.5 - - + +
87F ILE* 4.8 7.0 - - + -
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Residues in contact with PHE 43 (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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2F ALA* 3.8 30.7 - - + -
5F VAL* 3.7 28.5 - - + -
6F LEU* 4.2 13.2 - - + -
38F VAL* 3.9 21.8 - - + -
39F ASN 3.6 12.7 + - - -
40F ALA* 3.2 9.0 + - - +
41F GLU 3.1 1.2 + - - -
42F PHE* 1.3 89.7 - + - +
44F GLU* 1.3 63.7 + - + +
68F MET* 3.6 15.0 - - - +
69F PRO* 4.1 27.3 - - + +
71F ALA* 3.5 29.6 - - + -
87F ILE* 4.6 4.0 - - + -
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Residues in contact with GLU 44 (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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40F ALA* 3.7 27.1 + - - +
41F GLU* 3.0 7.8 + - - +
43F PHE* 1.3 81.8 - - + +
45F GLU* 1.3 64.5 + - + +
46F GLY 3.8 0.2 - - - -
68F MET* 3.9 8.6 - - - +
97F LEU* 4.2 9.5 - - - +
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Residues in contact with GLU 45 (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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41F GLU* 3.0 47.8 + - - +
44F GLU* 1.3 81.0 - - + +
46F GLY* 1.3 71.1 + - - +
48F MET* 5.6 2.4 - - - +
66F VAL* 3.4 16.8 - - - +
68F MET* 3.4 12.0 - - - +
97F LEU* 4.8 12.3 - - + +
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Residues in contact with GLY 46 (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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41F GLU* 5.3 2.6 - - - +
42F PHE* 2.7 37.3 + - - +
45F GLU* 1.3 84.6 - - - +
47F LYS* 1.3 60.4 + - - +
66F VAL* 4.5 0.7 - - - -
67F LEU 3.2 16.6 - - - -
68F MET* 3.5 5.6 - - - +
69F PRO* 3.8 7.4 - - - -
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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