Contacts of the helix formed by residues 55 - 67 (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 ASN 55 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D HIS* 3.6 15.6 + - - -
289D CPS 5.0 7.4 + - - +
51E LYS 4.0 2.2 + - - +
52E GLU* 2.6 23.9 + - - +
53E ASN 4.6 1.1 - - - -
54E LYS* 1.3 74.2 - - + +
56E GLU* 1.3 64.3 + - - +
57E LYS* 3.1 12.6 + - - +
58E VAL* 2.6 53.8 + - + +
59E ILE* 3.4 6.3 + - - +
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Residues in contact with GLU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 4.0 10.7 - - - +
72B LYS* 2.7 52.2 + - - +
38E LYS* 3.2 36.8 + - + +
53E ASN 4.8 2.1 + - - -
54E LYS 4.1 2.0 + - - -
55E ASN* 1.3 71.4 - - - +
57E LYS* 1.3 63.6 + - + +
59E ILE* 3.2 11.3 + - + +
60E GLU* 3.2 26.1 + - - +
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Residues in contact with LYS 57 (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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60D GLU 5.9 0.6 + - - -
61D HIS* 3.6 32.7 - - + +
64D GLU* 4.7 23.4 + - - +
55E ASN* 3.1 10.8 + - - +
56E GLU* 1.3 78.4 - - + +
58E VAL* 1.3 62.9 + - - +
60E GLU* 3.1 21.2 + - - +
61E HIS* 3.0 32.2 + - + +
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Residues in contact with VAL 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D HIS* 4.0 2.5 - - + -
289D CPS 3.6 35.4 - - + +
389D CPS 3.7 21.8 - - + -
52E GLU* 3.8 34.5 - - + +
55E ASN* 2.6 47.3 + - + +
57E LYS* 1.3 73.9 - - - +
59E ILE* 1.3 61.9 + - - +
61E HIS* 3.1 18.2 + - - +
62E ILE* 3.1 13.0 + - + +
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Residues in contact with ILE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 3.8 19.2 - - + -
38E LYS* 3.8 33.0 - - + +
41E VAL* 3.9 25.1 - - + -
49E LEU* 5.1 0.7 - - + -
52E GLU* 3.6 35.4 - - + +
53E ASN* 4.0 11.0 - - - +
55E ASN 3.4 9.6 + - - +
56E GLU* 3.2 12.6 + - + +
58E VAL* 1.3 76.2 - - - +
60E GLU* 1.3 63.7 + - - +
62E ILE* 3.1 14.6 + - + +
63E MET* 3.0 20.0 + - + +
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 4.3 3.3 - - - +
57D LYS* 6.0 3.0 - - + +
34E GLN* 3.2 30.3 + - - +
38E LYS* 2.6 33.6 + - - +
56E GLU* 3.2 17.4 + - - +
57E LYS* 3.1 23.2 + - - +
59E ILE* 1.3 73.9 - - - +
61E HIS* 1.3 66.9 + - - +
63E MET* 3.2 5.1 + - - +
64E GLU* 3.0 37.4 + - - +
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Residues in contact with HIS 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ASN* 4.8 2.9 + - - +
57D LYS* 3.7 30.3 - - + -
58D VAL* 3.8 19.5 + - + +
61D HIS* 2.7 37.3 + + + +
289D CPS 4.5 6.7 - - + -
389D CPS 3.5 29.2 - - + +
57E LYS* 3.0 22.3 + - + -
58E VAL* 3.1 14.3 + - + +
60E GLU* 1.3 78.1 - - + +
62E ILE* 1.3 58.9 + - - +
64E GLU* 3.4 17.7 + - - +
65E ASP* 2.9 29.3 + - - +
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Residues in contact with ILE 62 (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 3.8 52.9 - - + -
37E PHE* 3.9 19.5 - - + -
49E LEU* 4.3 14.4 - - + -
52E GLU* 4.3 5.6 - - + -
58E VAL 3.1 15.6 + - - +
59E ILE* 3.1 28.7 + - + +
61E HIS* 1.3 77.8 - - - +
63E MET* 1.3 62.7 + - - +
65E ASP* 3.3 2.1 + - + +
66E LEU* 3.0 36.5 + - + +
82E LEU* 4.2 13.9 - - + -
85E ARG* 5.9 1.1 - - - -
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Residues in contact with MET 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU 3.6 20.9 - - - +
34E GLN* 3.8 39.0 - - + +
37E PHE* 3.8 27.3 - - + -
59E ILE 3.0 12.5 + - - +
60E GLU* 3.4 12.6 - - - +
62E ILE* 1.3 76.6 - - - +
64E GLU* 1.3 61.0 + - + +
66E LEU 3.2 2.3 + - - -
67E ASP* 2.9 33.1 + - + +
72E LYS* 3.6 30.3 - - - +
73E GLN 3.8 2.2 - - - +
74E LEU* 3.7 30.1 - - + +
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Residues in contact with GLU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ASN* 3.2 31.4 + - - +
57D LYS* 3.0 43.4 + - - +
34E GLN* 5.7 2.0 - - - +
60E GLU* 3.0 23.8 + - + +
61E HIS* 3.6 16.9 + - - +
63E MET* 1.3 79.2 - - + +
65E ASP* 1.3 62.6 + - - +
67E ASP* 3.3 23.7 + - - +
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Residues in contact with ASP 65 (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* 2.7 42.5 + - - +
55D ASN* 5.0 1.5 - - - +
389D CPS 3.5 17.1 + - + +
61E HIS 2.9 17.8 + - - +
62E ILE* 3.3 4.9 + - + +
64E GLU* 1.3 77.5 - - - +
66E LEU* 1.3 61.5 + - + +
67E ASP 4.4 0.3 - - - -
68E THR* 4.4 10.9 + - - +
85E ARG* 2.7 43.6 + - - +
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Residues in contact with LEU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 4.0 18.4 - - + -
62E ILE* 3.0 35.4 + - + +
63E MET 3.8 2.9 - - - +
65E ASP* 1.3 73.7 - - + +
67E ASP* 1.3 60.3 + - - +
68E THR* 2.8 17.6 + - - +
74E LEU* 3.8 16.6 - - + -
78E GLU* 3.5 30.6 - - - +
79E PHE* 4.5 4.3 - - - +
81E MET* 4.2 3.3 - - + +
82E LEU* 3.7 44.2 - - + +
85E ARG* 3.7 29.4 - - - +
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Residues in contact with ASP 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E MET* 2.9 20.5 + - + +
64E GLU* 3.3 18.4 + - - +
65E ASP 4.4 0.4 - - - -
66E LEU* 1.3 72.0 - - - +
68E THR* 1.3 58.7 + - - +
69E ASN* 2.9 8.1 - - - +
70E ALA* 3.0 23.4 + - - +
71E ASP* 2.9 9.0 + - - +
72E LYS* 2.8 29.8 + - - +
73E GLN 3.7 5.4 - - - -
74E LEU* 3.6 10.0 - - + +
78E GLU* 3.6 3.1 - - - -
188E CA 2.2 32.9 - - - -
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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