Contacts of the helix formed by residues 64 - 82 (chain A) in PDB entry 2ILU
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 PRO 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA 3.9 6.3 - - - +
63A LEU* 1.3 85.2 - - + +
65A ALA* 1.3 68.4 + - - +
66A ILE* 4.0 16.8 - - + -
67A GLU* 2.8 48.4 + - - +
68A ARG 3.3 5.9 + - - -
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Residues in contact with ALA 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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63A LEU 3.3 2.6 + - - -
64A PRO* 1.3 70.3 - - - +
66A ILE* 1.3 57.3 + - - +
68A ARG* 3.0 34.2 + - - +
69A ALA 2.9 24.8 + - - -
119A ALA* 3.1 40.2 - - - +
120A ARG* 6.0 0.2 - - + -
122A TYR* 4.5 8.1 - - + +
168A LEU* 4.1 2.5 - - - +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO* 4.0 16.8 - - + -
65A ALA* 1.3 77.3 - - - +
67A GLU* 1.3 65.8 + - + +
69A ALA* 3.2 10.2 + - + +
70A SER* 2.9 25.7 + - - -
73A ARG* 4.7 13.9 - - - +
119A ALA* 3.8 10.8 - - + +
120A ARG* 3.7 50.4 - - + +
481A SO4 5.0 5.4 - - - +
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.8 25.0 - - + +
64A PRO* 2.8 47.6 + - + +
66A ILE* 1.3 78.9 - - + +
68A ARG* 1.3 63.8 + - - +
70A SER* 3.1 23.1 + - - -
71A TRP* 3.1 16.6 + - + +
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.4 51.5 + - + +
61A GLU* 3.0 22.6 + - - +
63A LEU* 2.8 36.8 + - + -
64A PRO 3.3 1.5 + - - +
65A ALA* 3.0 21.3 + - - +
67A GLU* 1.3 72.8 - - - +
69A ALA* 1.3 67.3 + - - +
71A TRP* 3.1 14.7 + - - +
72A LEU* 3.1 16.3 + - - +
122A TYR* 3.2 22.8 + - - -
167A LEU 3.3 17.5 - - - +
168A LEU* 2.8 32.8 + - - +
169A THR 3.6 5.7 + - - -
170A GLY* 3.4 10.3 - - - +
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Residues in contact with ALA 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 ALA 2.9 12.0 + - - +
66A ILE* 3.2 11.6 + - + +
68A ARG* 1.3 75.8 - - - +
70A SER* 1.3 63.8 + - - +
72A LEU* 3.1 6.9 + - - +
73A ARG* 2.9 35.3 + - - +
116A ALA* 3.1 36.2 - - + +
119A ALA* 3.8 6.3 - - + -
168A LEU* 3.8 12.0 - - + +
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Residues in contact with SER 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 ILE* 2.9 13.1 + - - -
67A GLU* 3.1 15.7 + - - -
69A ALA* 1.3 76.1 - - - +
71A TRP* 1.3 64.6 + - - +
73A ARG* 3.1 15.2 + - - +
74A LYS* 3.2 28.7 + - - +
481A SO4 2.8 36.0 + - - -
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Residues in contact with TRP 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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60A TRP* 3.5 24.6 - + + -
63A LEU* 4.4 9.7 - - + +
67A GLU* 3.1 23.8 + - - +
68A ARG* 3.1 8.3 + - - +
70A SER* 1.3 78.6 + - - +
72A LEU* 1.3 64.0 + - + +
74A LYS* 3.0 46.2 + - + +
75A ILE* 3.2 17.0 + - - +
195A ILE* 3.3 32.0 - - + +
196A GLY 3.6 19.5 - - - -
197A LEU* 3.7 26.7 - - + -
198A PRO* 3.7 23.3 - - + +
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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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60A TRP* 5.8 0.7 - - + -
68A ARG 3.1 12.2 + - - +
69A ALA 3.1 7.2 + - - +
71A TRP* 1.3 76.3 - - + +
73A ARG* 1.3 63.3 + - - +
75A ILE* 3.2 8.6 + - + +
76A SER 3.1 17.7 + - - -
112A ILE* 3.4 29.6 - - + +
113A ASP* 5.2 0.2 - - - -
115A MET 4.9 0.2 - - - -
116A ALA* 4.1 17.9 - - + +
163A MET* 4.1 28.0 - - + -
164A ALA* 3.8 22.4 - - - +
167A LEU* 4.1 21.1 - - + -
168A LEU* 3.9 31.6 - - + +
197A LEU* 6.2 0.4 - - + -
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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
----------------------------------------------------------
66A ILE* 4.7 10.9 - - - +
69A ALA* 2.9 31.7 + - - +
70A SER 3.1 7.3 + - - +
72A LEU* 1.3 75.9 - - - +
74A LYS* 1.3 57.5 + - - +
76A SER* 2.7 22.5 + - - -
77A ALA* 2.9 18.1 + - - +
113A ASP* 3.5 21.5 + - - +
116A ALA* 4.2 29.1 + - + +
117A GLU* 4.6 12.9 - - - +
120A ARG* 6.1 0.4 - - - +
481A SO4 3.2 39.1 + - - +
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Residues in contact with LYS 74 (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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70A SER* 3.2 25.6 + - - +
71A TRP* 3.0 51.8 + - + +
73A ARG* 1.3 75.4 - - + +
75A ILE* 1.3 58.0 + - - +
77A ALA* 3.3 7.7 + - - +
78A GLY 2.9 23.6 + - - -
195A ILE* 3.7 31.7 + - + +
481A SO4 5.4 2.0 - - - +
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Residues in contact with ILE 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 TRP 3.6 9.0 - - - +
72A LEU* 3.2 16.2 + - + +
74A LYS* 1.3 74.5 - - - +
76A SER* 1.3 65.0 + - - +
78A GLY* 3.1 2.1 + - - -
79A ILE* 3.0 23.5 + - + +
112A ILE* 4.3 11.4 - - + -
163A MET* 3.8 25.4 - - + -
188A PHE* 3.8 26.9 - - + -
191A ILE* 3.7 15.8 - - + +
192A VAL* 3.9 15.5 - - + -
195A ILE* 3.1 25.8 - - + -
197A LEU* 4.5 15.0 - - + -
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Residues in contact with SER 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 3.1 10.0 + - - -
73A ARG* 2.7 20.1 + - - -
75A ILE* 1.3 75.0 - - - +
77A ALA* 1.3 62.1 + - - +
79A ILE* 3.2 12.7 + - - +
80A ARG* 3.1 31.7 + - - +
109A ALA* 3.5 17.5 - - - +
112A ILE* 4.2 10.6 - - - +
113A ASP* 2.9 36.9 + - - -
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Residues in contact with ALA 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 2.9 17.7 + - - +
74A LYS* 3.5 9.0 - - - +
76A SER* 1.3 79.0 + - - +
78A GLY* 1.3 59.9 + - - +
80A ARG* 3.4 13.1 + - - +
81A GLU* 3.2 35.5 + - - +
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Residues in contact with GLY 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 LYS 2.9 14.5 + - - -
75A ILE 3.1 4.4 + - - -
77A ALA* 1.3 77.4 - - - +
79A ILE* 1.3 61.6 + - - +
81A GLU* 3.3 13.7 + - - +
82A ARG* 3.3 19.2 + - - +
191A ILE* 3.6 25.0 - - - +
195A ILE* 5.3 3.6 - - - -
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Residues in contact with ILE 79 (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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75A ILE* 3.0 19.0 + - + +
76A SER* 3.2 9.2 + - - +
78A GLY* 1.3 75.5 - - - +
80A ARG* 1.3 58.0 + - - +
82A ARG 3.1 5.4 + - - -
83A ALA* 2.9 24.8 + - - -
86A ILE* 4.2 2.2 - - + +
105A VAL* 3.6 31.6 - - + +
108A THR* 4.3 3.4 - - - +
109A ALA* 4.3 6.7 - - + -
112A ILE* 3.8 28.7 - - + -
156A PHE* 3.6 36.1 - - + -
188A PHE* 4.0 13.0 - - + -
191A ILE* 3.6 18.3 - - + +
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Residues in contact with ARG 80 (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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76A SER* 3.1 25.1 + - - +
77A ALA* 3.8 11.8 - - - +
78A GLY 3.4 0.2 - - - -
79A ILE* 1.3 75.9 - - - +
81A GLU* 1.3 63.6 + - + +
82A ARG 3.0 1.2 + - - -
83A ALA* 3.1 21.2 + - - +
105A VAL* 5.6 1.1 - - + -
106A ALA* 5.2 3.8 + - - +
109A ALA* 3.3 25.2 + - + +
110A ASP* 2.8 29.7 + - - +
113A ASP* 2.9 29.9 + - - +
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Residues in contact with GLU 81 (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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77A ALA* 3.2 26.5 + - - +
78A GLY* 3.6 12.1 + - - +
79A ILE 3.3 0.2 - - - -
80A ARG* 1.3 77.8 - - + +
82A ARG* 1.3 64.3 - - + +
83A ALA 3.6 0.4 + - - -
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Residues in contact with ARG 82 (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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78A GLY 3.3 12.7 + - - +
79A ILE 3.1 6.9 + - - +
80A ARG 3.0 0.6 - - - -
81A GLU* 1.3 86.7 - - + +
83A ALA* 1.3 63.6 + - - +
84A SER* 3.4 3.4 - - - -
85A GLU* 3.3 41.0 + - + +
86A ILE* 3.0 30.1 + - + +
187A ALA* 3.4 30.7 + - - +
190A LYS* 3.4 25.3 - - - +
191A ILE* 3.7 11.7 - - - +
194A GLU* 2.5 36.1 + - - -
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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
------------------------------------------------------------
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