Contacts of the helix formed by residues 39 - 46 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E LEU* 5.4 8.5 - - - -
36E HIS 5.4 1.8 + - - +
37E GLN* 3.8 13.6 + - - +
38E VAL* 1.3 78.1 - - - +
40E ALA* 1.3 67.6 + - + +
41E GLU* 3.1 15.9 - - - +
42E PHE* 2.7 44.2 + - - +
43E PHE* 3.6 14.3 + - - -
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Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 5.9 1.5 - - - +
39E ASN* 1.3 76.5 - - + +
41E GLU* 1.3 65.2 + - - +
43E PHE* 3.2 14.7 + - - +
44E GLU* 3.7 25.9 + - - +
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Residues in contact with GLU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ASN* 3.1 17.2 - - - +
40E ALA* 1.3 78.3 - - - +
42E PHE* 1.3 66.2 + - - +
44E GLU* 3.0 19.7 + - - +
45E GLU* 3.0 52.2 + - + +
46E GLY 5.3 2.9 - - - +
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Residues in contact with PHE 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E VAL* 5.1 0.7 - - + -
19E LEU* 4.1 33.2 - - + -
33E ILE* 5.6 4.9 - - + -
37E GLN 4.3 7.0 - - - +
38E VAL* 3.8 40.2 - - + -
39E ASN* 2.7 27.8 + - - +
41E GLU* 1.3 76.1 - - - +
43E PHE* 1.3 72.6 + + - +
46E GLY* 2.7 45.4 + - - -
47E LYS* 4.4 13.2 - - + -
67E LEU* 5.3 0.4 - - + -
69E PRO* 3.6 38.7 - - + +
87E ILE* 4.8 6.5 - - + -
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Residues in contact with PHE 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ALA* 3.8 30.1 - - + -
5E VAL* 3.7 28.0 - - + -
6E LEU* 4.2 14.4 - - + -
38E VAL* 3.9 21.5 - - + -
39E ASN 3.6 13.0 + - - -
40E ALA* 3.2 9.4 + - - +
41E GLU 3.1 1.4 + - - -
42E PHE* 1.3 91.2 - + - +
44E GLU* 1.3 64.5 + - + +
68E MET* 3.6 15.3 - - - +
69E PRO* 4.1 27.3 - - + +
71E ALA* 3.5 29.8 - - + -
87E ILE* 4.6 4.0 - - + -
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Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ALA* 3.7 27.2 + - - +
41E GLU* 3.0 7.8 + - - +
43E PHE* 1.3 82.0 - - + +
45E GLU* 1.3 64.7 + - + +
46E GLY 3.8 0.2 - - - -
68E MET* 3.9 9.3 - - - +
97E LEU* 4.2 9.4 - - - +
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Residues in contact with GLU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D ALA* 5.2 9.7 - - - +
41E GLU* 3.0 47.6 + - - +
44E GLU* 1.3 80.4 - - + +
46E GLY* 1.3 71.9 + - - +
48E MET* 5.6 2.3 - - - +
66E VAL* 3.4 17.7 - - - +
68E MET* 3.4 11.6 - - - +
97E LEU* 4.8 11.9 - - + +
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Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E GLU* 5.3 2.4 - - - +
42E PHE* 2.7 38.2 + - - +
45E GLU* 1.3 84.1 - - - +
47E LYS* 1.3 60.1 + - - +
67E LEU 3.2 17.5 - - - -
68E MET* 3.5 4.9 - - - +
69E PRO* 3.8 7.0 - - - -
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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