Contacts of the helix formed by residues 43 - 54 (chain H) in PDB entry 1O1F
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 ASP 43 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37H ASN* 3.2 19.6 + - - -
39H ASP* 5.1 0.5 - - - +
41H ILE* 3.2 8.6 + - + +
42H ILE* 1.3 75.4 - - - +
44H LYS* 1.3 58.5 + - - +
45H ASP* 3.0 30.1 + - - +
46H ASP* 2.8 38.2 + - - +
47H LEU* 3.2 15.6 + - - +
68H ILE* 4.8 2.7 - - - -
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Residues in contact with LYS 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H ASP* 1.3 73.5 - - - +
45H ASP* 1.3 59.9 + - - +
47H LEU* 3.3 14.2 + - - +
48H ARG* 3.0 49.1 + - - +
61H ASN* 3.6 38.0 - - - +
64H LEU* 3.7 17.2 - - + +
65H ASP* 3.4 28.6 + - - +
68H ILE* 3.7 17.3 - - + +
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Residues in contact with ASP 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H ASP* 3.0 20.0 + - - +
44H LYS* 1.3 79.0 + - - +
46H ASP* 1.3 58.3 + - - +
48H ARG* 3.2 28.9 + - - +
49H GLU* 2.9 49.7 + - - +
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Residues in contact with ASP 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ILE 3.0 17.3 - - - +
35H ASP* 3.2 10.3 - - - +
36H GLN* 3.0 30.3 + - - +
37H ASN* 3.1 24.0 + - - +
42H ILE* 3.9 7.2 - - + -
43H ASP* 2.8 42.6 + - - +
45H ASP* 1.3 75.4 - - - +
47H LEU* 1.3 56.3 + - - +
49H GLU* 3.3 3.4 + - - +
50H THR* 2.8 35.0 + - - -
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Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831G TRP* 2.0 62.6 - - + -
34H ILE* 3.8 5.6 - - + -
42H ILE* 3.7 19.5 - - + +
43H ASP 3.2 15.0 + - - +
44H LYS* 3.3 11.2 + - - +
46H ASP* 1.3 77.1 - - - +
48H ARG* 1.3 58.2 + - - +
50H THR* 3.3 1.9 + - - -
51H PHE* 3.0 38.9 + - + -
64H LEU* 3.6 22.9 - - + +
67H MET* 4.5 0.2 - - + -
68H ILE* 4.0 27.1 - - + -
75H ILE* 6.3 1.8 - - + -
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Residues in contact with ARG 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H LYS* 3.0 48.2 + - - +
45H ASP* 3.4 32.4 + - - +
47H LEU* 1.3 77.9 - - - +
49H GLU* 1.3 61.2 + - + +
51H PHE* 3.3 5.6 + - - +
52H ALA* 2.9 30.4 + - + +
59H VAL* 4.1 20.9 - - + +
61H ASN* 3.8 19.6 - - - +
64H LEU* 3.8 14.1 - - + +
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H GLN* 3.0 27.0 + - - +
45H ASP* 2.9 40.4 + - - +
46H ASP* 3.9 2.4 + - - +
48H ARG* 1.3 80.4 - - + +
50H THR* 1.3 59.1 + - - +
52H ALA* 4.0 7.3 - - - +
53H ALA* 3.2 26.7 + - - +
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Residues in contact with THR 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834G LEU* 4.3 13.0 - - + -
838G ILE* 4.5 1.3 - - + -
33H VAL* 3.4 12.5 + - + +
34H ILE* 3.2 34.8 + - + -
36H GLN* 3.0 20.3 + - - +
46H ASP 2.8 17.7 + - - -
47H LEU 3.7 4.0 - - - -
49H GLU* 1.3 74.0 - - - +
51H PHE* 1.3 67.2 + - + +
53H ALA* 3.2 5.3 + - - +
54H MET* 3.1 45.0 + - + +
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Residues in contact with PHE 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830G PRO* 5.3 5.2 - - + -
831G TRP* 4.6 13.7 - + - -
834G LEU* 2.3 45.1 - - + -
34H ILE* 6.5 0.4 - - + -
47H LEU* 3.0 26.6 + - + +
48H ARG 3.3 3.8 + - - +
50H THR* 1.3 76.6 - - + +
52H ALA* 1.3 56.9 + - - +
54H MET* 3.0 17.6 + - + +
55H GLY 3.1 0.5 + - - -
56H ARG* 2.8 51.7 + - + +
59H VAL* 3.6 25.4 - - + -
63H GLU* 5.7 0.4 - - - -
64H LEU* 3.7 17.5 - - + -
67H MET* 3.8 32.5 - - + -
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ARG* 2.9 20.5 + - + +
49H GLU* 4.0 8.1 - - - +
51H PHE* 1.3 74.1 - - - +
53H ALA* 1.3 58.3 + - - +
55H GLY* 3.1 18.2 + - - -
56H ARG 3.4 17.6 + - - +
57H LEU* 5.3 6.5 - - + +
59H VAL* 5.5 0.7 - - + -
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Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H GLN* 4.5 7.2 - - - +
49H GLU 3.2 19.3 + - - +
50H THR* 3.2 7.6 + - - +
52H ALA* 1.3 75.9 - - - +
54H MET* 1.3 68.7 + - + +
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Residues in contact with MET 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834G LEU* 4.9 9.2 - - + -
837G MLY 6.0 7.4 - - + -
838G ILE* 2.2 51.8 - - + -
841G LEU* 5.4 8.7 - - + -
33H VAL* 4.4 7.4 - - + -
50H THR* 3.2 24.7 - - + +
51H PHE* 3.0 11.9 + - + +
53H ALA* 1.3 85.4 - - + +
55H GLY* 1.3 56.5 + - - +
56H ARG* 3.7 5.8 - - + +
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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