Contacts of the helix formed by residues 55 - 67 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B HIS* 3.6 26.3 + - - -
189B CPS 4.8 6.2 + - - +
51G LYS 5.1 1.6 - - - +
52G GLU* 2.9 18.1 + - - +
53G ASN 3.2 0.9 - - - -
54G LYS* 1.3 79.8 - - + +
56G GLU* 1.3 64.9 + - - +
57G LYS* 3.1 20.1 + - - +
58G VAL* 2.9 29.0 + - + +
59G ILE* 3.4 5.1 + - - +
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Residues in contact with GLU 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D GLN* 4.9 8.8 - - - +
72D LYS* 3.1 38.9 + - + +
38G LYS* 2.6 45.1 + - + +
53G ASN 4.8 2.3 + - - -
54G LYS 4.1 1.6 + - - -
55G ASN* 1.3 73.6 + - - +
57G LYS* 1.3 61.9 + - - +
59G ILE* 3.1 12.9 + - + +
60G GLU* 3.0 25.3 + - - +
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Residues in contact with LYS 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS 5.7 0.4 - - - +
61B HIS* 3.3 39.5 + - + +
64B GLU* 2.5 39.4 + - - -
55G ASN* 3.1 12.9 + - - +
56G GLU* 1.3 79.0 - - - +
58G VAL* 1.3 62.8 + - - +
60G GLU* 3.2 20.3 + - - +
61G HIS* 3.1 36.1 + - + +
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Residues in contact with VAL 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B HIS* 4.1 3.1 - - + -
189B CPS 3.8 31.6 - - + +
52G GLU* 3.7 36.1 - - + +
55G ASN* 2.9 36.9 + - + +
57G LYS* 1.3 75.4 - - - +
59G ILE* 1.3 63.7 + - - +
61G HIS* 3.1 18.4 + - - +
62G ILE* 3.1 14.0 + - + +
489G CPS 3.6 21.5 - - + -
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Residues in contact with ILE 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 3.9 19.9 - - + -
38G LYS* 3.9 30.7 - - + +
41G VAL* 4.0 23.6 - - + -
49G LEU* 5.1 0.2 - - + -
52G GLU* 3.4 39.0 - - + +
53G ASN* 3.9 11.9 - - - +
55G ASN 3.7 10.5 - - - +
56G GLU* 3.1 12.7 + - + +
58G VAL* 1.3 77.8 - - - +
60G GLU* 1.3 62.7 + - - +
62G ILE* 3.2 13.8 + - + +
63G MET* 3.0 20.3 + - - +
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Residues in contact with GLU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 6.2 0.4 - - + +
34D GLN* 4.5 4.0 - - - +
34G GLN* 3.3 31.2 + - - +
38G LYS* 2.6 30.4 + - - +
56G GLU* 3.0 20.4 + - - +
57G LYS* 3.4 21.6 - - - +
58G VAL 3.2 0.2 - - - -
59G ILE* 1.3 77.6 - - - +
61G HIS* 1.3 63.2 + - - +
63G MET* 3.3 4.5 + - - +
64G GLU* 3.1 34.0 + - - +
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Residues in contact with HIS 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 4.5 3.6 + - - +
57B LYS* 3.8 31.6 - - + +
58B VAL* 3.8 20.2 + - + +
61B HIS* 2.9 34.2 + - - +
189B CPS 4.3 7.0 - - + -
57G LYS* 3.1 27.5 + - + -
58G VAL* 3.1 14.8 + - - +
60G GLU* 1.3 78.1 - - + +
62G ILE* 1.3 58.2 + - - +
64G GLU* 3.3 15.1 + - - +
65G ASP* 2.8 29.6 + - - +
489G CPS 3.6 28.9 - - + +
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Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 3.8 21.3 - - + -
49G LEU* 4.2 22.0 - - + -
52G GLU* 4.3 4.7 - - + -
58G VAL 3.1 14.5 + - - +
59G ILE* 3.2 23.3 + - + +
61G HIS* 1.3 73.7 - - - +
63G MET* 1.3 59.5 + - - +
65G ASP* 3.2 1.6 + - + +
66G LEU* 2.9 35.0 + - + +
82G LEU* 4.1 20.0 - - + -
489G CPS 3.9 51.8 - - + -
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Residues in contact with MET 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU 3.6 15.9 - - - +
33G ASN 4.3 0.2 - - - -
34G GLN* 3.8 40.2 - - + +
37G PHE* 3.9 27.5 - - + -
59G ILE 3.0 12.0 + - - +
60G GLU* 3.4 12.3 - - - +
62G ILE* 1.3 77.1 - - - +
64G GLU* 1.3 60.5 + - + +
66G LEU* 3.2 4.3 + - - -
67G ASP* 2.9 32.0 + - + +
72G LYS* 3.6 35.4 - - - +
73G GLN 4.0 1.1 - - - +
74G LEU* 3.7 29.2 - - + +
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Residues in contact with GLU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 3.5 32.1 + - - +
57B LYS* 3.0 45.5 + - - +
34G GLN* 5.5 4.3 - - - +
60G GLU* 3.1 22.2 + - - +
61G HIS* 3.7 5.8 + - - +
63G MET* 1.3 76.2 - - + +
65G ASP* 1.3 66.5 + - - +
67G ASP* 3.4 22.2 + - - +
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Residues in contact with ASP 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LYS* 2.9 27.8 + - - -
55B ASN* 5.0 1.1 - - - +
61G HIS 2.8 16.8 + - - +
62G ILE 3.5 5.4 - - - +
64G GLU* 1.3 78.8 - - - +
66G LEU* 1.3 60.1 + - + +
67G ASP 3.6 0.2 + - - -
68G THR* 4.1 9.7 + - - +
85G ARG* 2.4 41.6 + - - +
489G CPS 2.5 32.9 + - + +
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Residues in contact with LEU 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 3.9 17.9 - - + -
62G ILE* 2.9 27.8 + - + +
63G MET 3.8 0.2 - - - +
65G ASP* 1.3 75.9 - - - +
67G ASP* 1.3 58.4 + - - +
68G THR* 2.8 16.1 + - - +
74G LEU* 3.6 30.7 - - + -
78G GLU* 3.4 29.6 - - - +
79G PHE* 4.3 6.3 - - - +
81G MET* 4.1 2.9 - - + +
82G LEU* 3.7 44.4 - - + +
85G ARG* 4.0 28.0 - - + +
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Residues in contact with ASP 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G MET* 2.9 20.4 + - + +
64G GLU* 3.4 16.2 + - - +
66G LEU* 1.3 72.5 - - - +
68G THR* 1.3 57.5 + - - +
69G ASN* 2.8 10.0 - - - +
70G ALA* 3.0 22.6 + - - +
71G ASP* 3.0 4.7 + - - +
72G LYS* 2.7 28.9 + - - +
73G GLN 3.6 7.2 - - - -
74G LEU* 3.5 11.9 - - + +
78G GLU* 3.7 1.8 - - - -
188G CA 2.1 31.9 - - - -
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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