Contacts of the helix formed by residues 58 - 78 (chain B) in PDB entry 4NKU
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 SER 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B LYS* 3.3 5.8 + - - +
57B ILE* 1.3 78.6 - - - +
59B ASP* 1.3 59.2 + - - +
60B LYS* 3.4 12.2 + - - +
61B GLU* 2.9 26.4 + - - +
62B PHE* 2.8 26.2 + - - +
98B LYS* 4.7 14.7 - - - +
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE 3.8 1.0 + - - -
58B SER* 1.3 73.9 - - - +
60B LYS* 1.3 60.5 + - - +
62B PHE* 3.6 11.2 - - + +
63B LYS* 2.8 62.8 + - - +
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A ALA* 6.2 6.3 - - + -
58B SER* 3.1 9.6 - - - +
59B ASP* 1.3 81.1 + - - +
61B GLU* 1.3 67.2 + - + +
63B LYS* 3.2 8.5 + - - +
64B GLU* 3.0 49.2 + - + +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.5 19.7 - - + +
58B SER* 2.9 18.9 + - - +
60B LYS* 1.3 73.4 - - + +
62B PHE* 1.3 66.1 + - - +
64B GLU* 3.3 15.6 + - + +
65B LYS* 3.0 51.7 + - - +
98B LYS* 3.7 13.5 - - - +
99B ASN* 2.7 47.9 + - - -
100B SER 3.8 1.0 + - - -
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Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE* 4.0 21.5 - - + +
58B SER 2.8 17.6 + - - +
59B ASP* 3.6 13.0 - - + +
61B GLU* 1.3 79.2 - - - +
63B LYS* 1.3 75.6 + - - +
65B LYS* 3.2 3.7 + - - +
66B ARG* 3.0 57.5 + - + +
91B LEU* 4.0 35.4 - - + -
94B GLY* 5.9 4.0 - - - -
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASP* 2.8 52.6 + - - +
60B LYS* 3.5 7.2 - - - +
62B PHE* 1.3 86.6 - - - +
64B GLU* 1.3 57.4 + - + +
66B ARG* 3.4 7.9 + - + +
67B ALA* 3.0 28.1 + - - +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 3.0 49.0 + - + +
61B GLU* 3.7 19.3 - - + +
62B PHE 3.2 0.2 - - - -
63B LYS* 1.3 79.5 - - + +
65B LYS* 1.3 59.3 + - + +
67B ALA* 3.2 8.3 + - - +
68B ALA* 3.0 26.3 + - - +
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE* 4.4 0.4 - - + -
61B GLU* 3.0 50.1 + - + +
62B PHE 4.0 3.1 - - - +
64B GLU* 1.3 77.0 - - + +
66B ARG* 1.3 60.2 + - - +
68B ALA* 3.3 3.2 + - - +
69B LEU 3.0 22.5 + - - -
91B LEU* 3.6 41.5 - - + -
99B ASN* 4.8 3.0 - - - +
100B SER* 3.5 23.4 + - - +
102B MET* 3.4 27.2 - - + +
157B PHE* 4.4 30.3 - - + +
158B GLN 5.0 1.0 - - - +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 3.0 43.6 + - + +
63B LYS* 3.7 7.9 - - - +
65B LYS* 1.3 77.2 - - - +
67B ALA* 1.3 59.6 + - - +
69B LEU* 3.5 25.3 + - + +
70B ASP* 3.0 39.6 + - - +
87B ALA* 4.3 5.7 - - - +
91B LEU* 3.9 39.6 + - - +
92B GLU* 3.1 35.6 + - - -
102B MET* 5.5 2.8 - - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS 3.0 14.5 + - - +
64B GLU* 3.2 11.6 + - - +
66B ARG* 1.3 74.1 - - - +
68B ALA* 1.3 61.4 + - - +
70B ASP* 3.4 9.4 + - - +
71B THR* 2.8 33.9 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLU 3.0 12.9 + - - +
65B LYS* 3.3 10.5 + - - +
67B ALA* 1.3 75.6 - - - +
69B LEU* 1.3 59.9 + - - +
71B THR* 3.3 6.8 + - - -
72B LEU* 2.9 36.2 + - + +
102B MET* 4.3 1.8 - - - -
130B PHE* 6.5 1.1 - - + -
157B PHE* 3.8 33.2 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LYS 3.0 14.2 + - - +
66B ARG* 3.6 29.8 - - + +
68B ALA* 1.3 76.5 - - - +
70B ASP* 1.3 65.1 + - - +
72B LEU* 3.3 5.2 + - - -
73B ARG* 2.9 50.5 + - - +
85B LEU* 3.8 20.9 - - + +
87B ALA* 3.7 26.0 - - + +
92B GLU* 5.5 0.4 - - - +
102B MET* 4.0 9.1 - - + +
104B LEU* 3.6 24.0 - - + -
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Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG* 3.0 26.1 + - - +
67B ALA* 3.7 8.6 - - - +
69B LEU* 1.3 79.2 - - - +
71B THR* 1.3 62.7 + - - +
73B ARG* 3.4 25.5 + - - +
74B LEU* 3.2 30.9 + - + +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ALA* 2.8 22.1 + - - +
68B ALA* 3.6 7.7 - - - -
69B LEU 3.2 0.2 - - - -
70B ASP* 1.3 78.2 - - - +
72B LEU* 1.3 62.9 + - - +
74B LEU* 3.3 14.9 + - + +
75B CYS* 3.1 20.4 + - + +
130B PHE* 4.5 20.0 - - + -
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ALA* 2.9 25.1 + - + +
69B LEU* 3.3 1.3 + - - +
71B THR* 1.3 75.7 - - - +
73B ARG* 1.3 57.1 + - - +
75B CYS* 3.2 6.6 + - - +
76B LEU* 3.0 27.5 + - - +
85B LEU* 3.6 15.3 - - + -
102B MET* 5.5 1.1 - - - -
104B LEU* 3.6 27.1 - - + -
121B PHE* 3.8 6.7 - - + -
125B LEU* 3.5 31.4 - - + -
130B PHE* 4.0 17.0 - - + -
145B LEU* 3.8 17.0 - - + -
157B PHE* 4.3 12.1 - - + -
159B CYS* 4.2 13.0 - - - -
161B ILE* 4.6 4.0 - - + -
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 2.9 43.5 + - - +
70B ASP* 3.6 28.7 + - - +
72B LEU* 1.3 76.8 - - - +
74B LEU* 1.3 57.5 + - + +
76B LEU* 3.2 5.6 + - + +
77B LYS* 3.0 37.8 + - + +
84B GLU* 6.2 0.4 - - - +
85B LEU* 2.8 49.3 + - + +
86B VAL* 4.7 2.8 - - - +
87B ALA 4.9 1.0 - - - +
401B MG 4.2 13.0 - - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ASP* 3.2 18.0 + - + +
71B THR* 3.5 14.6 - - + +
73B ARG* 1.3 79.2 - - + +
75B CYS* 1.3 61.2 + - - +
77B LYS* 3.2 6.5 + - + +
78B ARG* 3.2 35.9 + - - +
401B MG 3.3 21.1 - - - -
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Residues in contact with CYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR* 3.1 13.6 + - + +
72B LEU* 3.2 10.5 + - - +
74B LEU* 1.3 73.2 - - - +
76B LEU* 1.3 64.9 + - - +
78B ARG* 3.3 32.5 + - - +
79B ILE* 3.5 13.7 + - - +
121B PHE* 3.9 7.6 - - + -
124B GLU* 3.3 30.5 - - - -
125B LEU* 3.6 29.4 - - + -
128B GLU* 4.9 4.7 - - + -
130B PHE* 5.5 2.2 - - + -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU 3.0 12.7 + - - +
73B ARG* 3.2 11.0 + - + +
75B CYS* 1.3 75.2 - - - +
77B LYS* 1.3 58.1 + - + +
79B ILE* 2.9 9.3 + - + +
80B SER 2.9 25.8 + - - +
83B ALA* 3.7 22.0 - - + +
84B GLU 3.6 33.2 - - - +
85B LEU* 3.7 12.6 - - + +
106B VAL* 4.2 9.0 - - + -
117B ILE* 3.7 29.8 - - + -
121B PHE* 3.6 34.9 - - + -
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ARG* 3.0 28.0 + - + +
74B LEU* 3.7 7.2 - - + +
75B CYS 3.2 0.4 - - - -
76B LEU* 1.3 78.5 - - + +
78B ARG* 1.3 60.0 + - + +
79B ILE 3.2 0.4 + - - -
80B SER 3.5 22.6 + - - +
81B PRO* 3.0 28.8 + - + +
82B ASP 4.3 1.6 + - - -
83B ALA 2.9 27.1 + - - +
84B GLU* 4.7 7.0 - - - +
401B MG 3.7 17.5 - - - -
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR 5.7 0.4 + - - -
74B LEU* 3.2 28.3 + - - +
75B CYS* 3.8 24.2 - - - +
76B LEU 3.2 1.4 - - - -
77B LYS* 1.3 78.1 - - - +
79B ILE* 1.3 63.9 + - + +
124B GLU* 3.3 14.2 + - - +
128B GLU* 2.6 35.4 + - - +
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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