Contacts of the helix formed by residues 59 - 75 (chain C) in PDB entry 3IKM
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 ALA 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C PRO* 1.4 76.3 - - + +
61C GLY* 3.2 3.2 - - - +
62C SER* 2.3 35.0 + - - +
63C GLY* 2.8 14.2 + - - -
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Residues in contact with PRO 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ALA* 1.4 92.3 - - + +
61C GLY* 1.3 64.5 - - - +
63C GLY* 3.4 1.7 + - - +
64C GLU* 3.0 27.4 + - - +
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Residues in contact with GLY 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ALA 3.2 1.4 - - - +
60C PRO* 1.3 83.4 - - - +
62C SER* 1.3 60.9 + - - +
64C GLU* 2.6 43.9 - - - +
65C GLY* 3.1 5.5 + - - -
357C THR* 4.6 6.3 - - - +
361C PHE* 4.0 18.1 - - - -
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Residues in contact with SER 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ALA* 2.3 44.9 + - - +
61C GLY* 1.3 77.8 - - - +
63C GLY* 1.3 60.8 + - - +
65C GLY* 3.2 3.0 + - - -
66C SER* 3.0 22.2 + - - -
294C PRO* 4.3 28.4 - - - +
295C TRP* 6.2 0.9 - - - -
357C THR* 5.2 7.1 - - - +
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Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ALA 2.8 14.9 + - - -
60C PRO* 3.4 3.8 + - - -
61C GLY 3.3 0.2 - - - -
62C SER* 1.3 78.1 + - - +
64C GLU* 1.3 60.5 + - - +
66C SER* 3.2 9.1 + - - -
67C GLU* 3.1 32.3 + - - +
88C ARG* 5.9 3.4 - - - -
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PRO 3.0 11.5 + - - +
61C GLY* 2.6 28.6 - - - +
63C GLY* 1.3 72.5 - - - +
65C GLY* 1.3 67.6 + - - +
67C GLU* 3.5 14.3 + - - +
68C ALA* 3.1 23.0 + - - +
357C THR* 6.0 0.6 - - + +
361C PHE* 3.0 36.7 - - - -
368C HIS* 6.0 6.5 - - + -
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Residues in contact with GLY 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLY 3.1 8.4 + - - -
62C SER 3.2 4.0 + - - -
64C GLU* 1.3 85.6 - - - +
66C SER* 1.3 56.6 + - - +
68C ALA* 3.2 8.7 - - - +
69C LEU* 2.8 30.2 + - - +
294C PRO* 6.2 1.6 - - - -
351C TYR* 5.5 1.3 - - - -
354C PHE* 4.3 0.2 - - - -
357C THR* 3.4 28.5 + - - -
368C HIS* 6.4 1.1 - - - -
370C LYS* 5.1 2.9 - - - -
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Residues in contact with SER 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C SER 3.0 11.9 + - - -
63C GLY* 3.4 11.4 - - - -
65C GLY* 1.3 73.0 - - - +
67C GLU* 1.3 56.0 + - - +
69C LEU* 3.2 1.4 + - - +
70C LEU* 2.6 44.7 + - - +
88C ARG* 3.4 29.4 + - - -
294C PRO* 6.0 3.6 - - - +
295C TRP* 5.5 3.4 - - - -
351C TYR* 4.0 19.3 + - - -
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLY* 3.1 18.5 + - - +
64C GLU* 3.9 12.9 - - - +
65C GLY 3.4 0.2 - - - -
66C SER* 1.3 74.7 - - - +
68C ALA* 1.3 57.1 + - - +
70C LEU* 4.4 3.4 - - - -
71C GLU* 2.5 46.8 + - + +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C GLU 3.1 11.6 + - - +
65C GLY* 3.2 13.0 - - - +
67C GLU* 1.3 82.3 - - - +
69C LEU* 1.3 59.5 + - - +
71C GLU* 4.3 7.0 - - - -
72C ILE* 2.7 32.0 + - + +
354C PHE* 3.8 22.0 - - + -
368C HIS* 5.6 6.3 - - + -
370C LYS* 5.3 1.3 - - - +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLY 2.8 16.1 + - - +
66C SER 4.0 2.2 - - - +
68C ALA* 1.3 73.9 - - - +
70C LEU* 1.3 58.8 + - - +
72C ILE* 4.4 6.7 - - + +
73C CYS* 3.1 26.7 + - - -
350C LEU* 3.6 29.8 - - + +
351C TYR* 3.0 55.4 - - + +
354C PHE* 3.4 27.4 - - + -
355C GLN* 3.8 9.6 - - - +
357C THR* 5.6 0.7 - - - +
372C LEU* 5.7 3.4 - - + -
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C SER* 2.6 27.9 + - - +
67C GLU* 3.9 2.9 - - - +
69C LEU* 1.3 74.3 - - - +
71C GLU* 1.3 63.0 + - - +
72C ILE 3.1 1.1 - - - -
73C CYS* 2.5 41.2 + - + +
74C GLN* 2.9 17.9 + - + +
79C LEU* 5.1 11.7 - - + -
86C LEU* 5.4 23.8 - - + +
87C SER* 6.5 0.9 - - - -
88C ARG 6.3 1.8 - - - +
91C LEU* 5.5 13.2 - - + -
351C TYR* 5.8 1.3 - - - +
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Residues in contact with GLU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C GLU* 2.5 29.2 + - + +
68C ALA* 3.6 6.2 - - - +
70C LEU* 1.3 78.5 - - - +
72C ILE* 1.3 99.8 + - - +
74C GLN* 2.8 14.1 + - + +
75C ARG* 2.7 69.9 + - - +
76C ARG* 3.7 3.7 + - - -
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ALA* 2.7 27.1 + - + +
69C LEU* 4.6 9.9 - - + +
70C LEU 3.1 0.6 - - - -
71C GLU* 1.3 102.1 - - - +
73C CYS* 1.3 53.4 + - - +
75C ARG* 2.2 26.6 - - - +
76C ARG* 3.1 54.0 - - + +
78C PHE* 5.3 0.2 - - - +
354C PHE* 5.5 6.7 - - + -
372C LEU* 5.6 4.0 - - + -
434C GLU* 3.5 22.0 - - + +
435C MET* 5.5 1.6 - - + -
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Residues in contact with CYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 3.1 29.6 - - - +
70C LEU* 2.5 25.8 + - + +
72C ILE* 1.3 71.2 - - - +
74C GLN* 1.3 61.9 + - - +
75C ARG 3.0 2.0 - - - -
78C PHE* 2.6 47.9 + - + -
79C LEU* 2.8 39.5 + - + -
350C LEU* 4.8 7.6 - - - -
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Residues in contact with GLN 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LEU* 2.9 16.5 + - + +
71C GLU* 2.8 21.6 + - - +
73C CYS* 1.3 72.7 - - - +
75C ARG* 1.3 114.4 + - + +
77C HIS* 3.4 14.9 + - - -
79C LEU* 4.2 15.1 - - + +
81C GLY 5.5 4.7 - - - +
82C SER* 4.2 19.5 + - - -
86C LEU* 5.8 4.0 - - + +
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Residues in contact with ARG 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLU* 2.7 41.6 + - - +
72C ILE* 2.2 25.3 - - - +
73C CYS 3.0 2.1 - - - -
74C GLN* 1.3 107.6 - - - +
76C ARG* 1.3 69.6 + - + +
77C HIS* 2.6 21.5 + - - -
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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