Contacts of the helix formed by residues 58 - 78 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LYS* 3.4 4.1 + - - +
57A ILE* 1.3 80.0 - - - +
59A ASP* 1.3 59.9 + - - +
60A LYS* 3.8 12.9 + - - +
61A GLU* 3.1 26.2 + - - +
62A PHE* 3.0 27.8 + - - +
98A LYS* 4.7 10.1 - - - +
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE 4.0 0.4 + - - -
58A SER* 1.3 73.3 - - - +
60A LYS* 1.3 56.6 + - - +
62A PHE* 3.4 12.8 + - - +
63A LYS* 2.9 38.7 + - + +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A SER* 3.8 9.6 + - - +
59A ASP* 1.3 76.4 - - - +
61A GLU* 1.3 66.1 + - + +
63A LYS* 3.3 7.7 + - - +
64A GLU* 3.0 46.8 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 3.5 22.7 - - + +
58A SER* 3.1 18.7 + - - +
60A LYS* 1.3 79.9 - - + +
62A PHE* 1.3 62.0 + - - +
64A GLU* 3.3 17.5 + - + +
65A LYS* 3.0 52.7 + - - +
98A LYS* 3.7 8.3 - - - +
99A ASN* 3.0 43.3 + - - +
100A SER 3.6 2.4 + - - -
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Residues in contact with PHE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 3.9 17.4 - - + +
58A SER 3.0 17.4 + - - +
59A ASP* 3.6 15.9 - - - +
61A GLU* 1.3 78.8 - - - +
63A LYS* 1.3 64.9 + - + +
65A LYS* 3.3 5.2 + - - +
66A ARG* 3.0 64.1 + - + +
91A LEU* 3.6 38.8 - - + -
94A GLY* 5.9 3.6 - - - -
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Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 2.9 30.4 + - + +
60A LYS* 3.7 7.0 - - - +
62A PHE* 1.3 83.3 - - + +
64A GLU* 1.3 57.3 + - - +
66A ARG* 3.3 12.8 - - + +
67A ALA* 3.0 26.9 + - - +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LYS* 3.0 43.0 + - - +
61A GLU* 3.5 21.8 - - + +
62A PHE 3.2 0.2 - - - -
63A LYS* 1.3 75.5 - - - +
65A LYS* 1.3 62.4 + - + +
67A ALA* 3.2 7.8 + - - +
68A ALA* 2.9 26.2 + - - +
152A GLY 5.8 3.1 - - - +
153A PHE* 3.8 16.1 - - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 4.4 0.9 - - + -
61A GLU* 3.0 47.6 + - + +
62A PHE 3.3 3.6 + - - +
64A GLU* 1.3 75.7 - - + +
66A ARG* 1.3 61.6 + - - +
68A ALA* 3.3 6.1 + - + -
69A LEU* 3.0 24.1 + - - +
91A LEU* 3.5 36.6 - - + -
99A ASN 5.1 0.2 - - - -
100A SER* 3.2 21.2 + - - -
102A MET* 3.3 36.4 - - + +
157A PHE* 4.9 13.3 - - + +
158A GLN 5.1 4.8 + - - +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.0 53.4 + - + +
63A LYS* 3.3 20.4 - - + +
65A LYS* 1.3 78.3 - - - +
67A ALA* 1.3 57.8 + - - +
69A LEU* 3.3 26.0 + - + +
70A ASP* 3.0 37.3 + - - +
87A ALA* 5.7 1.4 - - - +
91A LEU* 4.2 10.5 + - - +
92A GLU* 3.3 31.7 + - - +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LYS 3.0 13.1 + - - +
64A GLU* 3.2 9.6 + - - +
66A ARG* 1.3 73.6 - - - +
68A ALA* 1.3 66.6 + - - +
70A ASP* 3.2 13.9 + - - +
71A THR* 3.0 27.2 + - - -
153A PHE* 3.7 12.3 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU 2.9 13.3 + - - +
65A LYS* 3.6 8.7 - - - +
66A ARG 3.3 0.2 - - - -
67A ALA* 1.3 77.0 - - - +
69A LEU* 1.3 58.3 + - - +
71A THR* 3.2 2.8 + - - -
72A LEU* 2.9 35.7 + - + +
102A MET* 4.0 4.9 - - - -
153A PHE* 3.3 23.0 - - + -
157A PHE* 3.6 35.0 - - + -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS 3.0 12.8 + - - +
66A ARG* 3.5 30.1 - - + +
68A ALA* 1.3 77.8 - - - +
70A ASP* 1.3 58.2 + - - +
72A LEU* 3.3 5.5 + - - -
73A ARG* 2.9 61.9 + - - +
85A LEU* 4.0 18.8 - - + +
87A ALA* 4.0 22.4 - - + +
102A MET* 4.1 12.0 - - + +
104A LEU* 3.9 22.0 - - + -
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 3.0 22.1 + - - +
67A ALA* 3.2 15.7 + - - +
69A LEU* 1.3 78.0 - - - +
71A THR* 1.3 60.7 + - - +
73A ARG* 3.4 20.5 + - - +
74A LEU* 3.2 32.4 + - + +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA 3.0 13.8 + - - -
68A ALA 3.6 7.6 - - - -
70A ASP* 1.3 76.6 - - - +
72A LEU* 1.3 63.5 + - - +
74A LEU* 3.4 11.0 + - - +
75A CYS* 3.1 20.8 + - + +
130A PHE* 4.3 11.9 - - + -
151A ASN* 3.8 22.4 - - + +
153A PHE* 3.4 23.0 - - + -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 2.9 22.4 + - + +
69A LEU* 3.9 1.3 - - - +
71A THR* 1.3 74.9 - - - +
73A ARG* 1.3 60.8 + - - +
75A CYS* 3.3 6.1 + - + +
76A LEU* 3.0 27.4 + - - +
85A LEU* 3.5 16.6 - - + +
102A MET* 5.4 0.9 - - - -
104A LEU* 3.8 24.0 - - + -
121A PHE* 3.8 7.9 - - + -
125A LEU* 3.6 30.1 - - + -
130A PHE* 3.8 24.0 - - + -
145A LEU* 3.9 13.2 - - + -
157A PHE* 4.2 15.3 - - + -
159A CYS* 4.1 13.5 - - - -
161A ILE* 4.9 1.8 - - + -
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 2.9 50.4 + - - +
70A ASP* 3.6 20.3 + - - +
72A LEU* 1.3 76.2 - - - +
74A LEU* 1.3 64.4 + - + +
76A LEU* 3.1 5.2 + - + +
77A LYS* 3.0 43.7 + - + +
84A GLU* 6.1 0.2 - - - +
85A LEU* 2.8 49.3 + - + +
86A VAL* 4.6 3.6 - - - +
87A ALA 5.0 0.6 - - - +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASP* 3.2 22.9 + - + +
71A THR* 3.6 9.9 - - - +
73A ARG* 1.3 80.4 - - + +
75A CYS* 1.3 62.2 + - - +
77A LYS* 3.3 17.9 + - + +
78A ARG* 3.3 17.5 + - - +
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Residues in contact with CYS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 3.1 15.4 + - + +
72A LEU* 3.5 9.9 - - + +
73A ARG 3.2 0.2 - - - -
74A LEU* 1.3 77.5 - - - +
76A LEU* 1.3 62.2 + - - +
78A ARG* 3.2 25.3 + - - +
79A ILE* 3.8 7.3 + - - +
121A PHE* 4.0 4.9 - - + -
124A GLU* 4.1 24.0 - - - -
125A LEU* 3.5 31.0 - - + -
128A GLU* 4.3 20.4 - - + -
130A PHE* 6.0 1.8 - - + -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU 3.0 14.1 + - - +
73A ARG* 3.1 8.9 + - + +
75A CYS* 1.3 76.5 - - - +
77A LYS* 1.3 60.2 + - + +
79A ILE* 2.9 22.3 + - + +
80A SER 3.1 9.9 + - - +
83A ALA* 3.8 22.7 - - + +
84A GLU 3.7 31.6 - - - +
85A LEU* 3.8 11.4 - - + +
106A VAL* 4.1 13.0 - - + -
117A ILE* 3.8 27.6 - - + -
121A PHE* 3.6 35.1 - - + -
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG* 3.0 33.6 + - + +
74A LEU* 3.8 11.0 - - + +
75A CYS 3.3 0.6 - - - -
76A LEU* 1.3 76.3 - - + +
78A ARG* 1.3 60.1 + - - +
79A ILE 3.2 0.7 + - - -
80A SER 3.6 23.0 + - - +
81A PRO* 3.4 24.2 + - + +
83A ALA 2.9 26.1 + - - +
84A GLU* 4.4 10.0 - - - +
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU 3.3 13.3 + - - +
75A CYS* 3.2 17.0 + - - +
76A LEU 3.1 0.8 - - - -
77A LYS* 1.3 77.3 - - - +
79A ILE* 1.3 67.3 + - + +
124A GLU* 4.2 25.7 + - - +
128A GLU* 5.4 4.7 + - - -
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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