Contacts of the helix formed by residues 75 - 86 (chain E) in PDB entry 1IRJ
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 75 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E PHE* 3.6 1.8 - - - -
30E ASP 4.4 1.3 - - - -
31E THR* 4.2 16.1 - - - +
73E GLN 3.9 0.6 + - - -
74E LEU* 1.3 76.5 - - - +
76E PHE* 1.3 66.8 + - - +
77E GLU* 3.7 11.7 + - - +
78E GLU* 3.0 34.7 + - - +
79E PHE* 2.9 19.4 + - - +
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Residues in contact with PHE 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ILE* 3.9 20.9 - - + -
16E ILE* 3.3 53.4 - - + -
19E PHE* 3.2 40.1 - + + -
20E HIS* 4.5 12.1 - + + -
30E ASP 4.4 1.6 + - - +
75E SER* 1.3 72.0 - - - +
77E GLU* 1.3 64.7 + - - +
79E PHE* 3.1 13.5 + + - -
80E ILE* 3.2 35.7 + - + +
83F MET* 4.6 15.3 - - + -
84F ALA* 5.3 8.5 - - - -
86F LEU 5.9 1.1 - - - -
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Residues in contact with GLU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E THR* 5.3 2.6 + - - -
75E SER* 3.7 11.1 + - - +
76E PHE* 1.3 80.4 - - - +
78E GLU* 1.3 68.7 + - - +
80E ILE* 4.0 11.6 + - - +
81E MET* 4.0 14.6 + - - +
81F MET* 3.3 40.2 - - + +
84F ALA* 5.2 8.9 - - + +
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Residues in contact with GLU 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LEU* 3.5 29.1 - - - +
67E ASP* 4.1 1.1 - - - -
68E THR* 2.9 39.4 + - + +
69E ASN* 3.1 10.2 + - - +
73E GLN 3.0 9.7 - - - +
74E LEU* 3.5 5.6 - - + -
75E SER* 3.0 28.6 + - - +
77E GLU* 1.3 83.9 - - - +
79E PHE* 1.3 67.5 + - - +
81E MET* 3.4 20.4 + - - +
188E CA 2.5 31.1 - - - -
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Residues in contact with PHE 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ILE* 4.2 20.2 - - + -
18E THR* 6.1 0.2 - - + -
19E PHE* 3.8 31.0 - + + -
32E LEU* 3.8 15.9 - - + -
37E PHE* 4.3 13.0 - + - -
40E LEU* 3.8 39.3 - - + -
45E LEU* 5.5 0.7 - - + -
66E LEU* 5.1 1.1 - - - -
74E LEU* 4.7 9.8 - - + +
75E SER 2.9 12.3 + - - +
76E PHE* 3.1 18.8 + + - +
78E GLU* 1.3 76.5 - - - +
80E ILE* 1.3 68.2 + - + +
82E LEU* 2.9 45.7 + - + +
83E MET* 5.0 5.6 - - + +
8F LEU* 4.5 13.7 - - + -
12F ILE* 6.0 3.4 - - + -
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Residues in contact with ILE 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ILE* 5.0 0.9 - - + -
76E PHE* 3.2 47.3 + - + +
77E GLU* 4.1 10.3 - - - +
79E PHE* 1.3 71.2 - - + +
81E MET* 1.3 53.9 + - + +
82E LEU 2.7 5.3 + - - -
83E MET* 2.6 61.6 + - + +
80F ILE* 3.6 38.0 - - + +
81F MET* 4.7 5.4 - - - +
83F MET* 4.1 24.5 - - + -
84F ALA* 4.5 9.0 - - + +
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Residues in contact with MET 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LEU* 4.3 3.8 - - + -
68E THR* 6.2 4.0 - - + -
77E GLU 4.0 11.4 - - - +
78E GLU* 3.4 12.5 + - - +
79E PHE 3.2 0.8 + - - -
80E ILE* 1.3 77.1 - - + +
82E LEU* 1.3 64.8 + - - +
83E MET 3.1 0.2 - - - -
84E ALA* 2.8 25.3 + - - +
85E ARG* 3.4 19.8 + - - +
77F GLU* 3.8 29.6 - - - +
80F ILE* 4.2 9.9 - - + -
81F MET* 3.3 51.4 - - + +
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Residues in contact with LEU 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D CPS 5.0 4.0 - - + -
37E PHE* 4.2 22.9 - - + -
45E LEU* 3.9 28.0 - - + -
49E LEU* 4.7 6.1 - - + -
62E ILE* 4.2 21.5 - - + -
66E LEU* 3.7 19.0 - - + +
79E PHE* 2.9 27.6 + - + +
80E ILE 2.7 4.8 + - - -
81E MET* 1.3 74.9 - - - +
83E MET* 1.3 62.9 + - + +
84E ALA 3.1 0.3 + - - -
85E ARG* 3.2 12.9 + - + +
86E LEU* 2.9 47.3 + - + +
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Residues in contact with MET 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ILE* 3.5 45.3 - - + -
79E PHE* 5.0 4.7 - - + -
80E ILE* 2.6 50.6 + - + +
82E LEU* 1.3 73.4 - - + +
84E ALA* 1.3 65.7 + - - +
86E LEU* 2.9 29.2 + - + +
12F ILE* 4.0 36.6 - - + -
15F ILE* 4.9 5.2 - - - -
16F ILE* 4.5 5.5 - - - +
76F PHE* 4.4 12.5 - - + -
80F ILE* 4.2 18.8 - - + -
83F MET* 4.3 4.5 - - + -
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Residues in contact with ALA 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ILE 4.1 0.2 + - - -
81E MET* 2.8 18.3 + - + +
83E MET* 1.3 80.3 - - - +
85E ARG* 1.3 61.1 + - + +
86E LEU 2.7 17.3 + - - -
76F PHE* 4.6 11.7 - - - -
77F GLU* 3.6 37.9 - - + +
80F ILE* 4.2 8.2 - - + +
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Residues in contact with ARG 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LYS* 5.1 2.8 - - - +
389D CPS 3.8 58.9 + - + +
62E ILE* 5.9 0.9 - - - -
65E ASP* 2.7 38.2 + - - -
66E LEU* 3.7 22.6 - - - +
68E THR* 6.0 3.0 - - - +
81E MET* 3.4 27.3 + - - +
82E LEU* 3.2 10.5 + - + +
84E ALA* 1.3 81.2 - - + +
86E LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D CPS 4.2 25.1 - - + +
45E LEU* 5.0 2.7 - - + -
48E PHE* 4.2 35.0 - - + -
49E LEU* 4.0 29.8 - - + -
82E LEU* 2.9 44.7 + - + +
83E MET* 2.9 33.9 + - + +
84E ALA 2.7 9.8 + - - +
85E ARG* 1.3 80.2 - - - +
12F ILE* 4.2 15.7 - - + -
16F ILE* 3.9 18.5 - - + +
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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