Contacts of the helix formed by residues 60 - 77 (chain E) in PDB entry 7KHI
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 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E LYS* 6.3 2.0 - - + -
13E ILE* 4.5 22.0 - - + -
22E VAL* 4.1 14.4 - - - -
54E ILE* 6.0 0.9 - - + -
57E GLY* 4.7 7.9 + - - -
59E ILE* 1.3 78.4 + - - +
61E ASN* 1.3 58.3 + - - +
62E GLN* 2.6 38.2 + - - +
63E ILE* 2.8 29.6 + - - +
64E LEU* 2.9 29.3 + - - +
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Residues in contact with ASN 61 (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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13E ILE* 5.5 4.7 - - + +
18E ASP* 5.2 9.0 + - - +
22E VAL* 4.0 25.8 - - + +
25E ARG* 3.5 23.4 + - - -
60E ASN* 1.3 76.9 - - - +
62E GLN* 1.3 71.9 + - - +
64E LEU* 3.6 3.2 - - - +
65E ASP* 2.7 45.9 + - - +
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Residues in contact with GLN 62 (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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13E ILE* 6.1 1.0 - - - +
60E ASN* 2.6 17.8 + - - +
61E ASN* 1.3 87.1 + - - +
63E ILE* 1.3 62.1 + - + +
65E ASP* 3.3 5.7 + - - +
66E VAL* 3.0 31.6 + - - +
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Residues in contact with ILE 63 (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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57E GLY 5.0 2.5 - - - +
58E LEU 3.2 25.8 - - - +
59E ILE* 4.3 3.8 - - + -
60E ASN* 2.8 37.8 + - - +
62E GLN* 1.3 76.0 - - + +
64E LEU* 1.3 66.7 + - - +
66E VAL* 3.0 14.9 - - + +
67E ARG* 2.9 33.4 + - + +
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Residues in contact with LEU 64 (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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22E VAL* 4.7 15.0 - - + +
25E ARG* 3.3 57.0 - - + +
26E ARG* 4.8 7.2 - - + +
29E GLN* 4.4 22.7 - - - +
59E ILE* 3.9 21.7 - - + +
60E ASN 2.9 21.2 + - - +
61E ASN* 3.6 6.1 - - - +
63E ILE* 1.3 77.3 - - - +
65E ASP* 1.3 56.9 + - - +
67E ARG* 4.0 3.6 - - + +
68E GLU* 2.9 35.1 + - + +
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Residues in contact with ASP 65 (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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25E ARG* 3.9 24.3 + - - +
61E ASN* 2.7 36.7 + - - +
62E GLN* 3.3 5.8 + - - +
64E LEU* 1.3 76.8 - - - +
66E VAL* 1.3 63.3 + - - +
68E GLU* 3.3 10.2 + - - +
69E ARG* 3.0 32.5 + - - +
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Residues in contact with VAL 66 (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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62E GLN 3.0 16.4 + - - +
63E ILE* 3.0 36.1 - - + +
65E ASP* 1.3 79.1 - - - +
67E ARG* 1.3 59.6 + - + +
69E ARG* 3.3 4.6 + - - +
70E GLN* 2.9 29.7 + - + +
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Residues in contact with ARG 67 (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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26E ARG* 5.3 11.0 - - - +
29E GLN* 5.8 0.4 - - - -
35E LYS* 4.8 15.7 - - - +
36E ASP* 5.5 4.9 + - - -
38E LEU* 3.7 37.6 - - - +
63E ILE* 2.9 25.0 + - + +
64E LEU* 4.1 3.8 - - + +
66E VAL* 1.3 78.4 - - + +
68E GLU* 1.3 58.1 + - - +
70E GLN* 3.3 9.1 + - + +
71E GLU* 2.9 55.8 + - + +
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Residues in contact with GLU 68 (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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25E ARG* 5.5 8.5 + - - +
29E GLN* 5.6 6.5 - - - +
64E LEU* 2.9 25.5 + - + +
65E ASP* 3.7 9.6 - - - +
67E ARG* 1.3 76.1 - - - +
69E ARG* 1.3 72.9 + - - +
71E GLU* 3.3 15.5 + - - +
72E GLN* 2.9 37.4 + - - +
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Residues in contact with ARG 69 (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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65E ASP* 3.0 22.2 + - - +
66E VAL* 3.9 4.9 - - - +
68E GLU* 1.3 83.7 + - - +
70E GLN* 1.3 59.0 + - - +
72E GLN* 3.7 17.7 - - - +
73E GLN* 2.9 37.5 + - + +
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Residues in contact with GLN 70 (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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66E VAL* 2.9 17.2 + - + +
67E ARG* 3.3 15.9 - - + +
69E ARG* 1.3 77.2 - - - +
71E GLU* 1.3 59.3 + - + +
73E GLN* 3.8 4.3 - - - +
74E GLU* 2.9 56.4 + - + +
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Residues in contact with GLU 71 (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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29E GLN* 4.3 16.4 + - - +
35E LYS* 3.6 37.9 - - - +
67E ARG* 2.9 41.0 + - + +
68E GLU* 3.8 12.7 - - - +
70E GLN* 1.3 77.8 - - + +
72E GLN* 1.3 58.3 + - - +
74E GLU* 3.4 6.5 + - - +
75E GLN* 2.9 36.5 + - - +
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Residues in contact with GLN 72 (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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68E GLU* 2.9 28.2 + - - +
69E ARG* 3.7 17.5 - - - +
70E GLN 3.2 0.2 - - - -
71E GLU* 1.3 76.3 - - - +
73E GLN* 1.3 96.1 + - - +
75E GLN* 3.2 5.9 + - - +
76E GLU* 2.9 40.1 + - - +
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Residues in contact with GLN 73 (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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69E ARG* 2.9 25.6 + - + +
70E GLN* 4.1 5.2 - - - +
72E GLN* 1.3 109.0 + - - +
74E GLU* 1.3 64.0 + - + +
76E GLU* 3.4 21.1 + - - +
77E ALA* 3.7 6.9 + - - +
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Residues in contact with GLU 74 (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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70E GLN* 2.9 50.8 + - + +
71E GLU* 3.7 6.7 - - - +
73E GLN* 1.3 78.5 - - - +
75E GLN* 1.3 61.6 + - - +
77E ALA* 3.1 25.1 + - - +
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Residues in contact with GLN 75 (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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71E GLU* 2.9 21.3 + - - +
72E GLN* 3.9 4.3 - - - +
74E GLU* 1.3 74.2 - - - +
76E GLU* 1.3 64.0 + - - +
77E ALA 3.2 8.2 + - - +
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Residues in contact with GLU 76 (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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72E GLN* 2.9 28.8 + - - +
73E GLN* 3.5 22.7 - - - +
74E GLU 3.2 0.2 - - - -
75E GLN* 1.3 77.7 - - - +
77E ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 77 (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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73E GLN 3.7 5.9 + - - +
74E GLU* 3.1 21.2 + - - +
75E GLN 3.5 7.5 - - - +
76E GLU* 1.3 84.8 - - - +
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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