Contacts of the helix formed by residues 39 - 46 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6L LEU* 5.4 7.6 - - - -
36L HIS 5.4 2.3 + - - +
37L GLN* 3.7 14.2 + - - +
38L VAL* 1.3 78.1 - - - +
40L ALA* 1.3 67.0 + - + +
41L GLU* 3.1 16.2 - - - +
42L PHE* 2.7 45.6 + - - +
43L PHE* 3.6 14.4 + - - -
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Residues in contact with ALA 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L LEU* 5.9 1.7 - - - +
39L ASN* 1.3 77.9 - - + +
41L GLU* 1.3 65.8 + - - +
43L PHE* 3.2 15.2 + - - +
44L GLU* 3.7 25.2 + - - +
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Residues in contact with GLU 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ASN* 3.1 16.6 - - - +
40L ALA* 1.3 77.5 - - - +
42L PHE* 1.3 66.9 + - - +
44L GLU* 3.0 20.1 + - - +
45L GLU* 3.0 51.5 + - + +
46L GLY 5.3 2.5 - - - +
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Residues in contact with PHE 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L VAL* 5.1 0.9 - - + -
19L LEU* 4.1 33.2 - - + -
33L ILE* 5.6 5.2 - - + -
37L GLN 4.3 7.4 - - - +
38L VAL* 3.8 39.7 - - + -
39L ASN* 2.7 26.3 + - - +
41L GLU* 1.3 75.8 - - - +
43L PHE* 1.3 72.1 + + - +
46L GLY* 2.7 44.9 + - - -
47L LYS* 4.4 13.5 - - + -
67L LEU 5.3 0.4 - - - -
69L PRO* 3.6 39.8 - - + +
87L ILE* 4.8 6.1 - - + -
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Residues in contact with PHE 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L ALA* 3.8 29.6 - - + -
5L VAL* 3.7 28.3 - - + -
6L LEU* 4.2 14.1 - - + -
38L VAL* 3.9 21.8 - - + -
39L ASN 3.6 13.4 + - - -
40L ALA* 3.2 9.5 + - - +
41L GLU 3.1 1.0 + - - -
42L PHE* 1.3 90.8 - + - +
44L GLU* 1.3 64.1 + - + +
68L MET* 3.6 15.0 - - - +
69L PRO* 4.1 29.0 - - + +
71L ALA* 3.5 30.3 - - + -
87L ILE* 4.6 4.3 - - + -
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Residues in contact with GLU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L ALA* 3.7 28.0 + - - +
41L GLU* 3.0 7.8 + - - +
43L PHE* 1.3 81.1 - - + +
45L GLU* 1.3 66.4 + - + +
68L MET* 3.9 10.0 - - - +
97L LEU* 4.2 9.4 - - - +
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Residues in contact with GLU 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349G ALA* 5.2 9.4 - - - +
41L GLU* 3.0 47.0 + - - +
44L GLU* 1.3 81.2 - - + +
46L GLY* 1.3 71.4 + - - +
48L MET* 5.6 2.1 - - - +
66L VAL* 3.4 18.2 - - - +
68L MET* 3.4 10.3 - - - +
97L LEU* 4.8 11.9 - - + +
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Residues in contact with GLY 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L GLU* 5.3 2.4 - - - +
42L PHE* 2.7 36.3 + - - +
45L GLU* 1.3 83.0 - - - +
47L LYS* 1.3 61.4 + - - +
66L VAL* 4.6 0.2 - - - -
67L LEU 3.2 17.7 - - - -
68L MET* 3.5 5.1 - - - +
69L PRO* 3.8 7.9 - - - -
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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