Contacts of the helix formed by residues 59 - 75 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60F PRO* 1.4 74.8 - - + +
61F GLY 3.3 2.6 - - - +
62F SER* 2.3 36.6 + - - +
63F GLY* 2.8 12.6 + - - -
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Residues in contact with PRO 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ALA* 1.4 93.4 - - + +
61F GLY* 1.3 65.8 + - - +
63F GLY* 3.2 3.6 + - - +
64F GLU* 2.8 26.4 + - - +
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Residues in contact with GLY 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ALA 3.3 1.0 - - - +
60F PRO* 1.3 83.4 - - - +
62F SER* 1.3 59.0 + - - +
64F GLU* 2.6 44.0 - - - +
65F GLY* 2.9 9.4 + - - -
357F THR* 4.3 6.2 - - - +
361F PHE* 5.5 7.4 - - - -
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Residues in contact with SER 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F ALA* 2.3 40.7 + - - +
61F GLY* 1.3 76.4 - - - +
63F GLY* 1.3 62.9 + - - +
65F GLY* 3.3 2.2 + - - -
66F SER* 3.1 22.5 + - - -
294F PRO* 4.4 28.7 - - - +
295F TRP* 6.2 0.9 - - - -
357F THR* 5.2 6.7 - - - -
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Residues in contact with GLY 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F ALA 2.8 14.9 + - - -
60F PRO* 3.2 5.8 + - - -
62F SER* 1.3 80.0 + - - +
64F GLU* 1.3 58.0 + - - +
66F SER* 3.4 7.8 + - - -
67F GLU* 3.1 32.6 + - - +
88F ARG* 6.0 3.1 - - - -
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F PRO 2.8 10.6 + - - +
61F GLY* 2.6 39.8 - - - +
63F GLY* 1.3 76.3 - - - +
65F GLY* 1.3 63.8 + - - +
67F GLU* 3.9 13.1 - - - +
68F ALA* 3.2 22.3 + - - +
357F THR* 5.8 0.6 - - + +
361F PHE* 4.3 19.1 - - - -
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Residues in contact with GLY 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F GLY 2.9 15.4 + - - -
62F SER 3.3 2.4 + - - -
64F GLU* 1.3 79.3 - - - +
66F SER* 1.3 57.0 + - - +
68F ALA* 3.4 6.6 - - - +
69F LEU* 3.0 28.1 + - - +
294F PRO* 6.2 2.7 - - - -
351F TYR* 6.2 0.7 - - - -
354F PHE* 4.0 0.3 - - - -
357F THR* 3.2 32.9 + - - -
368F HIS* 6.4 0.4 - - - -
370F LYS* 5.0 2.9 - - - -
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Residues in contact with SER 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F SER 3.1 12.9 + - - -
63F GLY* 3.5 11.9 - - - -
65F GLY* 1.3 74.4 - - - +
67F GLU* 1.3 56.1 + - - +
69F LEU* 3.0 2.8 + - - +
70F LEU* 2.6 44.6 + - - +
88F ARG* 3.5 27.5 + - - -
294F PRO* 6.0 3.3 - - - +
295F TRP* 5.5 3.1 - - - -
351F TYR* 4.0 19.7 + - - -
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Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F GLY 3.1 17.4 + - - +
64F GLU* 3.9 12.5 - - - +
65F GLY 3.5 0.2 - - - -
66F SER* 1.3 75.4 - - - +
68F ALA* 1.3 55.0 + - - +
70F LEU* 4.4 3.4 - - - -
71F GLU* 2.3 50.8 + - + +
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Residues in contact with ALA 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F GLU 3.2 11.8 + - - +
65F GLY* 3.4 11.4 - - - +
67F GLU* 1.3 78.5 - - - +
69F LEU* 1.3 56.1 + - - +
71F GLU* 4.2 7.4 - - - -
72F ILE* 2.7 43.2 + - + +
354F PHE* 3.7 21.3 - - + -
368F HIS* 5.2 9.2 - - + -
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F GLY 3.0 11.0 + - - +
66F SER 3.9 2.2 - - - +
68F ALA* 1.3 78.5 - - - +
70F LEU* 1.3 59.5 + - - +
72F ILE* 4.0 7.5 - - + +
73F CYS* 3.6 26.6 + - - -
350F LEU* 3.7 14.6 - - + +
351F TYR* 3.2 62.8 - - + +
354F PHE* 3.4 38.6 - - + -
355F GLN* 3.9 3.8 - - - -
357F THR* 5.6 0.4 - - - +
372F LEU* 5.6 4.0 - - + -
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Residues in contact with LEU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F SER* 2.6 27.6 + - - +
67F GLU* 4.0 2.9 - - - +
69F LEU* 1.3 72.1 - - - +
71F GLU* 1.3 63.5 + - - +
72F ILE 2.9 1.1 - - - -
73F CYS* 2.5 35.0 + - + +
74F GLN* 3.0 22.2 + - + +
79F LEU* 5.1 12.8 - - + -
86F LEU* 5.2 24.2 - - + +
87F SER* 6.5 0.9 - - - -
91F LEU* 5.5 13.7 - - + -
351F TYR* 6.0 0.9 - - - +
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Residues in contact with GLU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F GLU* 2.3 41.4 + - + +
68F ALA* 3.5 5.4 - - - +
70F LEU* 1.3 77.2 - - - +
72F ILE* 1.3 93.2 + - - +
74F GLN* 3.0 12.3 + - + +
75F ARG* 2.9 61.7 + - - +
76F ARG* 4.1 3.0 + - - -
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Residues in contact with ILE 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ALA* 2.7 33.3 + - + +
69F LEU* 4.2 11.0 - - + +
71F GLU* 1.3 97.4 + - - +
73F CYS* 1.3 54.4 + - - +
75F ARG 2.4 21.1 - - - +
76F ARG* 3.2 51.6 - - + +
354F PHE* 5.5 6.3 - - + -
372F LEU* 5.5 3.8 - - + -
434F GLU* 3.6 24.0 - - + +
435F MET* 5.8 1.3 - - + +
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Residues in contact with CYS 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F LEU* 3.6 23.8 - - - +
70F LEU* 2.5 23.5 + - + +
72F ILE* 1.3 75.6 - - - +
74F GLN* 1.3 59.1 + - - +
75F ARG 3.1 3.1 - - - -
78F PHE* 2.8 40.7 + - + -
79F LEU* 2.7 48.7 + - + -
350F LEU* 4.9 7.6 - - - -
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Residues in contact with GLN 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F LEU* 3.0 17.8 + - + +
71F GLU* 3.1 21.0 - - - +
73F CYS* 1.3 76.9 - - - +
75F ARG* 1.3 113.3 + - + +
77F HIS* 3.6 14.9 + - - -
79F LEU* 4.3 13.9 - - - +
81F GLY 5.5 3.6 - - - +
82F SER* 3.9 21.1 + - - +
86F LEU* 5.9 3.0 - - + +
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Residues in contact with ARG 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F GLU* 2.9 36.2 + - - +
72F ILE 2.4 23.4 - - - +
73F CYS 3.1 2.4 - - - -
74F GLN* 1.3 112.5 - - - +
76F ARG* 1.3 86.2 + - + +
77F HIS* 3.0 3.4 - - - -
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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