Contacts of the helix formed by residues 59 - 77 (chain T) in PDB entry 5KHU
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 LEU 59 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58T ASP* 3.8 29.4 - - - +
60T GLU* 3.8 25.8 - - - +
62T ILE* 4.6 15.7 - - - +
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Residues in contact with GLU 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T LEU* 3.8 25.8 - - - +
61T LEU* 3.8 28.7 - - - +
63T LYS* 4.6 14.1 - - - +
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Residues in contact with LEU 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T GLU* 3.8 29.2 - - - +
62T ILE* 3.8 26.0 - - - +
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Residues in contact with ILE 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T LEU* 4.6 14.6 - - - +
61T LEU* 3.8 25.6 - - - +
63T LYS* 3.8 28.9 - - - +
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Residues in contact with LYS 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T GLU* 4.6 15.5 - - - +
62T ILE* 3.8 29.2 - - - +
64T TYR* 3.8 26.5 - - - +
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Residues in contact with TYR 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63T LYS* 3.8 28.3 - - - +
65T LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64T TYR* 3.8 29.4 - - - +
66T ASN* 3.8 27.1 - - - +
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Residues in contact with ASN 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65T LEU* 3.8 29.4 - - - +
67T ASN* 3.8 24.5 - - - +
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Residues in contact with ASN 67 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66T ASN* 3.8 24.7 - - - +
68T VAL* 3.8 28.9 - - - +
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Residues in contact with VAL 68 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67T ASN* 3.8 29.4 - - - +
69T VAL* 3.8 26.7 - - - +
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Residues in contact with VAL 69 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68T VAL* 3.8 28.5 - - - +
70T GLU* 3.8 29.2 - - - +
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Residues in contact with GLU 70 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69T VAL* 3.8 25.4 - - - +
71T GLN* 3.8 28.9 - - - +
73T LYS* 4.7 15.5 - - - +
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Residues in contact with GLN 71 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70T GLU* 3.8 29.2 - - - +
72T LEU* 3.8 25.8 - - - +
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Residues in contact with LEU 72 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71T GLN* 3.8 28.9 - - - +
73T LYS* 3.8 26.7 - - - +
75T TRP* 4.4 19.3 - - - +
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Residues in contact with LYS 73 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70T GLU* 4.7 16.6 - - - +
72T LEU* 3.8 25.6 - - - +
74T ASP* 3.8 28.5 - - - +
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Residues in contact with ASP 74 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73T LYS* 3.8 26.7 - - - +
75T TRP* 3.8 28.7 - - - +
77T TYR* 4.2 19.5 - - - +
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Residues in contact with TRP 75 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72T LEU* 4.4 16.6 - - - +
74T ASP* 3.8 28.5 - - - +
76T LEU* 3.8 25.1 - - - +
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Residues in contact with LEU 76 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75T TRP* 3.8 29.4 - - - +
77T TYR* 3.8 24.5 - - - +
79T CYS* 4.7 15.0 - - - +
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Residues in contact with TYR 77 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74T ASP* 4.2 18.4 - - - +
76T LEU* 3.8 27.4 - - - +
78T LYS* 3.8 29.2 - - - +
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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