Contacts of the helix formed by residues 59 - 67 (chain A) in PDB entry 1IAX
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 CYS 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASN* 4.3 5.6 + - - +
57A GLN 3.1 1.0 - - - -
58A LEU* 1.3 86.2 - - - +
60A LEU* 1.3 65.6 + - - +
61A ASP* 3.1 8.1 - - - -
62A LEU* 3.0 42.8 + - + +
63A ILE* 3.4 4.4 + - - +
331A PHE* 3.7 23.1 - - + -
335A SER* 3.5 37.9 - - - +
338A ARG* 3.9 10.5 - - - -
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Residues in contact with LEU 60 (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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56A ASN 4.9 3.3 + - - +
57A GLN* 3.3 32.3 + - + +
58A LEU 3.7 0.2 - - - -
59A CYS* 1.3 75.3 - - - +
61A ASP* 1.3 67.1 + - - +
63A ILE* 3.0 26.8 + - + +
64A GLU* 3.0 18.4 + - - +
280A MET 5.0 1.1 - - - +
281A GLY 4.5 14.4 - - - +
282A LEU* 4.7 0.2 - - + -
83B PHE* 3.5 32.3 - - + -
84B LYS* 3.4 52.0 - - + +
87B ALA* 4.4 7.2 - - + -
88B ASN* 5.1 4.3 - - + -
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Residues in contact with ASP 61 (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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57A GLN 5.0 0.4 + - - -
58A LEU 3.3 8.3 - - - +
59A CYS* 3.5 1.6 - - - -
60A LEU* 1.3 78.9 - - - +
62A LEU* 1.3 70.2 + - - +
64A GLU* 3.3 16.6 + - - +
65A ASP* 3.0 35.4 + - - +
338A ARG* 2.5 41.8 + - - -
84B LYS* 4.2 10.2 - - - +
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Residues in contact with LEU 62 (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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59A CYS* 3.0 40.0 + - + +
61A ASP* 1.3 94.3 - - - +
63A ILE* 1.3 61.4 + - - +
65A ASP* 3.4 11.6 + - - +
66A TRP* 3.1 21.8 + - - +
327A PHE* 3.9 6.5 - - + -
330A ASN* 4.4 16.4 - - - +
331A PHE* 4.1 22.9 - - + -
334A GLU* 3.5 23.8 - - + +
338A ARG* 3.5 20.4 - - - +
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Residues in contact with ILE 63 (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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59A CYS 3.4 4.5 + - - +
60A LEU* 3.0 17.9 + - + +
62A LEU* 1.3 74.0 - - - +
64A GLU* 1.3 60.3 + - - +
66A TRP* 3.2 3.2 + - - +
67A ILE* 2.8 39.5 + - + +
280A MET* 3.5 25.4 - - - +
282A LEU* 4.2 10.5 - - + -
317A PHE* 4.5 0.7 - - + -
321A MET* 3.7 35.4 - - + -
327A PHE* 4.0 11.9 - - + -
331A PHE* 3.7 24.5 - - + -
83B PHE* 3.9 23.6 - - + -
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Residues in contact with GLU 64 (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 LEU 3.0 13.8 + - - +
61A ASP* 3.7 13.4 - - - +
63A ILE* 1.3 71.9 - - - +
65A ASP* 1.3 70.5 + - - +
67A ILE* 3.0 24.2 + - - +
68A LYS* 3.4 19.1 - - - +
82B SER 5.1 3.5 + - - -
83B PHE* 4.3 28.7 + - + +
84B LYS* 3.3 42.4 + - + +
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Residues in contact with ASP 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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61A ASP* 3.0 28.6 + - - +
62A LEU* 3.4 16.1 - - - +
64A GLU* 1.3 77.1 - - - +
66A TRP* 1.3 64.4 + - - +
68A LYS* 2.9 38.8 + - - +
69A ARG* 4.4 15.3 + - - +
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Residues in contact with TRP 66 (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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62A LEU 3.1 5.7 + - - +
63A ILE 3.5 6.7 - - - +
64A GLU 3.2 0.2 - - - -
65A ASP* 1.3 74.1 - - - +
67A ILE* 1.3 65.2 + - + +
68A LYS 2.7 16.4 + - - -
69A ARG* 3.0 28.2 + - + +
70A ASN* 2.9 29.7 + - - -
71A PRO* 4.2 5.2 - - + -
73A GLY* 4.9 10.3 - - - -
317A PHE* 4.2 17.0 - + - -
320A ALA* 3.4 23.8 - - + -
321A MET* 3.4 46.4 - - + -
324A ASP* 3.2 25.3 + - - -
327A PHE* 3.3 40.4 - + + +
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Residues in contact with ILE 67 (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 ILE* 2.8 33.5 + - + +
64A GLU* 3.0 13.4 + - - +
66A TRP* 1.3 88.6 - - + +
68A LYS* 1.3 56.6 - - + +
69A ARG 3.3 4.2 + - - +
73A GLY* 6.1 5.1 - - - -
317A PHE* 4.1 14.4 - - + -
75B ILE* 4.1 26.2 - - + +
83B PHE* 3.5 46.2 - - + -
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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