Contacts of the helix formed by residues 59 - 69 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ASN* 4.3 6.1 + - - +
57B GLN* 3.1 0.8 - - - +
58B LEU* 1.3 82.6 - - - +
60B LEU* 1.3 62.8 + - - +
61B ASP* 3.1 8.1 - - - -
62B LEU* 3.3 39.0 + - + +
63B ILE* 3.5 11.7 + - - +
331B PHE* 3.3 22.1 - - + -
335B SER* 3.6 34.8 - - - +
338B ARG* 3.7 17.9 - - - -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 4.1 23.3 - - + -
84A LYS* 3.4 47.8 - - + +
87A ALA* 4.3 7.4 - - + -
88A ASN* 5.2 2.5 - - + -
56B ASN 4.8 2.9 - - - +
57B GLN* 3.6 43.9 + - + +
59B CYS* 1.3 75.9 - - - +
61B ASP* 1.3 54.9 + - - +
63B ILE* 2.8 13.5 + - + +
64B GLU* 2.8 37.8 + - + +
280B MET 4.7 1.8 - - - +
281B GLY 4.0 20.4 - - - +
282B LEU* 4.5 4.7 - - + -
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 3.8 10.7 - - - +
57B GLN 5.2 0.2 + - - -
58B LEU 3.7 2.7 - - - +
59B CYS* 3.1 19.9 - - - -
60B LEU* 1.3 75.3 + - - +
62B LEU* 1.3 69.3 + - - +
64B GLU* 3.2 19.7 + - - +
65B ASP* 2.6 43.6 + - - +
338B ARG* 3.0 29.7 + - - -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B CYS* 3.3 38.4 - - + +
60B LEU 3.1 0.4 - - - -
61B ASP* 1.3 86.5 + - - +
63B ILE* 1.3 58.9 + - - +
65B ASP* 3.6 13.8 + - + +
66B TRP* 3.3 19.6 + - - +
327B PHE* 3.8 9.8 - - + -
330B ASN* 4.5 17.5 - - - +
331B PHE* 4.3 17.9 - - + -
334B GLU* 3.7 22.9 - - + +
338B ARG* 3.5 26.2 - - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 3.3 30.1 - - + -
59B CYS 3.8 12.3 - - - +
60B LEU* 2.8 14.1 + - + +
62B LEU* 1.3 75.8 - - - +
64B GLU* 1.3 61.2 + - - +
66B TRP* 3.1 6.6 + - - +
67B ILE* 2.8 40.7 + - + +
280B MET* 3.5 40.4 - - + +
282B LEU* 4.1 17.3 - - + -
317B PHE* 4.9 1.1 - - + -
321B MET* 4.3 14.8 - - + -
327B PHE* 4.2 15.7 - - + -
331B PHE* 4.5 4.9 - - + -
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A SER 5.4 3.3 + - - -
83A PHE* 4.1 23.5 + - + +
84A LYS* 2.8 44.3 + - - +
60B LEU 2.8 14.3 + - - +
61B ASP* 3.2 15.2 - - - +
63B ILE* 1.3 73.8 - - - +
65B ASP* 1.3 66.8 + - - +
66B TRP 3.1 0.5 + - - -
67B ILE* 3.2 11.2 + - - +
68B LYS* 3.1 36.9 + - - +
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Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASP* 2.6 32.1 + - - +
62B LEU* 3.6 17.3 + - + +
64B GLU* 1.3 77.7 - - - +
66B TRP* 1.3 61.6 + - - +
68B LYS* 3.4 20.3 + - - +
69B ARG* 3.3 45.9 + - - +
70B ASN* 5.7 0.2 - - - -
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Residues in contact with TRP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU 3.3 11.7 + - - +
63B ILE* 3.1 10.5 + - - +
64B GLU 3.0 0.4 - - - -
65B ASP* 1.3 77.4 - - - +
67B ILE* 1.3 66.4 + - + +
68B LYS 2.8 14.7 + - - -
70B ASN* 2.5 52.4 + - + +
71B PRO* 2.9 29.5 - - + +
72B LYS 4.4 13.7 - - - -
73B GLY* 4.8 3.4 - - - -
317B PHE* 4.5 11.9 - + - -
320B ALA* 3.8 15.0 - - + -
321B MET* 3.2 57.9 - - + -
324B ASP* 3.4 19.1 + - + -
327B PHE* 3.6 31.0 - + + +
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Residues in contact with ILE 67 (chain B).
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* 3.2 23.8 - - + +
83A PHE* 3.4 54.7 - - + -
63B ILE* 2.8 27.8 + - + +
64B GLU* 3.2 7.6 + - - +
66B TRP* 1.3 79.1 - - + +
68B LYS* 1.3 64.4 + - + +
71B PRO 3.4 3.8 - - - +
72B LYS* 3.5 21.3 - - - +
74B SER* 4.8 3.1 - - - +
317B PHE* 3.8 25.4 - - + -
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLU* 3.1 27.1 - - - +
65B ASP* 3.4 20.3 + - - +
66B TRP 2.8 1.8 + - - -
67B ILE* 1.3 77.7 - - + +
69B ARG* 1.3 61.2 + - + +
71B PRO 2.5 20.3 - - - +
72B LYS* 3.9 5.0 - - - +
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ASP* 3.3 35.4 + - - +
68B LYS* 1.3 79.0 - - + +
70B ASN* 1.3 57.0 + - + +
71B PRO* 2.7 25.3 - - - +
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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