Contacts of the helix formed by residues 60 - 69 (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 LYS 60 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H ASN 3.9 10.3 + - - +
59H VAL* 1.3 75.2 - - - +
61H ASN* 1.3 62.1 + - - +
62H GLU* 3.5 24.9 - - - +
63H GLU* 3.0 55.7 + - + +
64H LEU* 3.6 8.0 - - - +
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Residues in contact with ASN 61 (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* 3.6 27.6 - - - +
48H ARG* 3.8 23.6 - - - +
59H VAL 5.0 2.7 + - - +
60H LYS* 1.3 73.1 - - - +
62H GLU* 1.3 65.7 + - - +
64H LEU* 3.1 12.0 + - - +
65H ASP* 2.9 36.2 + - - +
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Residues in contact with GLU 62 (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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60H LYS* 3.2 31.6 - - + +
61H ASN* 1.3 86.7 + - - +
63H GLU* 1.3 56.6 + - + +
65H ASP* 3.7 11.8 - - - +
66H ALA* 3.0 28.1 + - - +
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Residues in contact with GLU 63 (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* 6.0 1.5 - - + +
51H PHE* 5.7 0.5 - - - -
56H ARG* 3.4 26.9 + - - -
58H ASN 4.4 0.3 - - - +
59H VAL* 3.9 9.1 - - + +
60H LYS* 3.0 58.2 + - + +
62H GLU* 1.3 74.3 - - - +
64H LEU* 1.3 65.3 + - - +
66H ALA* 3.1 7.6 + - - +
67H MET* 3.1 43.7 + - + +
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Residues in contact with LEU 64 (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* 3.7 24.2 - - + -
47H LEU* 3.6 28.2 - - + +
48H ARG* 3.8 38.4 - - + +
51H PHE* 3.7 27.4 - - + -
59H VAL* 3.9 9.2 - - + +
60H LYS 3.6 9.6 - - - +
61H ASN* 3.4 21.3 - - - +
63H GLU* 1.3 76.7 - - - +
65H ASP* 1.3 57.1 + - - +
67H MET* 3.2 9.5 + - - +
68H ILE* 3.1 34.7 + - - +
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Residues in contact with ASP 65 (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* 3.4 28.8 + - - +
61H ASN* 2.9 27.3 + - - +
62H GLU* 3.7 10.8 - - - +
63H GLU 3.3 0.2 - - - -
64H LEU* 1.3 77.1 - - - +
66H ALA* 1.3 55.6 + - - +
68H ILE* 3.3 9.8 + - - +
69H LYS* 2.9 30.7 + - - +
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Residues in contact with ALA 66 (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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62H GLU 3.0 16.9 + - - +
63H GLU* 3.1 8.0 + - - +
65H ASP* 1.3 73.4 - - - +
67H MET* 1.3 64.7 + - + +
69H LYS* 3.4 17.5 + - + +
70H GLU* 3.2 24.1 + - - +
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Residues in contact with MET 67 (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* 3.5 35.7 - - + -
831G TRP* 2.1 67.1 - - + +
47H LEU* 4.5 1.3 - - + -
51H PHE* 3.8 26.0 - - + -
63H GLU* 3.1 34.5 + - + +
64H LEU* 3.5 9.6 - - - +
66H ALA* 1.3 78.3 - - + +
68H ILE* 1.3 62.4 + - - +
70H GLU* 3.2 27.5 + - - +
71H ALA* 4.1 2.6 + - - +
75H ILE* 5.2 3.4 - - - +
83H MET* 4.6 5.2 - - - +
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Residues in contact with ILE 68 (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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42H ILE 5.7 1.3 - - - +
43H ASP* 4.8 2.2 - - - -
44H LYS* 3.7 41.1 - - + +
47H LEU* 4.0 11.7 - - + -
64H LEU 3.1 17.4 + - - +
65H ASP* 3.8 9.6 - - - +
67H MET* 1.3 76.7 - - - +
69H LYS* 1.3 56.8 + - - +
70H GLU 3.2 0.2 - - - -
71H ALA* 3.1 30.5 + - - +
73H GLY 5.1 5.3 - - - +
75H ILE* 5.5 13.0 - - + -
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Residues in contact with LYS 69 (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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65H ASP 2.9 17.7 + - - +
66H ALA* 3.6 13.2 - - + +
67H MET 3.2 0.2 - - - -
68H ILE* 1.3 75.9 - - - +
70H GLU* 1.3 61.4 + - + +
71H ALA 3.3 6.1 + - - +
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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