Contacts of the helix formed by residues 78 - 85 (chain C) in PDB entry 1IXR
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 GLY 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B LEU* 3.0 35.4 + - - -
158B PHE* 5.1 6.3 - - - -
187B LEU* 4.3 7.6 - - - +
76C LYS* 2.5 9.6 + - - -
77C PRO* 1.3 74.9 - - - +
79C ASP* 1.3 58.0 + - - -
80C LEU 3.3 2.2 - - - -
81C ALA* 3.4 8.1 - - - +
82C ALA* 3.1 25.3 + - - +
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PHE* 5.4 1.2 - - - -
191B ARG* 5.2 4.0 - - - +
73C ALA 5.2 2.8 - - - +
74C ILE* 4.5 16.6 - - + -
75C GLU* 3.5 9.4 + - - +
76C LYS* 2.6 60.7 + - - +
77C PRO 3.5 0.2 - - - -
78C GLY* 1.3 72.7 - - - +
80C LEU* 1.3 53.4 + - - +
82C ALA* 3.4 9.2 - - - +
83C ILE* 2.7 39.2 + - + +
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ILE* 4.3 28.2 - - + +
77C PRO* 3.0 31.9 - - + +
79C ASP* 1.3 74.3 - - - +
81C ALA* 1.3 67.2 + - + +
82C ALA 3.0 1.3 - - - -
83C ILE* 2.5 33.6 + - + +
84C LEU* 2.6 36.1 + - + +
96C ILE* 6.4 2.9 - - + -
106C ALA* 3.8 20.0 - - + +
109C HIS* 3.6 24.9 - - + +
110C LEU* 4.3 16.6 - - + -
119C MET* 5.6 1.8 - - + -
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 4.2 5.4 - - + -
187B LEU* 4.7 8.7 - - + -
78C GLY* 3.4 18.6 - - - +
80C LEU* 1.3 82.0 - - - +
82C ALA* 1.3 50.7 + - - +
84C LEU* 2.8 16.1 + - - +
85C ALA* 2.4 42.0 + - - +
119C MET* 3.2 31.4 - - + -
134C LEU* 4.8 5.6 - - + -
136C LEU* 5.6 0.4 - - - +
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PHE* 6.4 0.7 - - + -
187B LEU* 4.0 30.2 - - + +
191B ARG* 5.8 5.4 - - + -
78C GLY 3.1 10.8 + - - +
79C ASP* 3.4 13.9 - - - +
80C LEU 3.0 0.4 - - - -
81C ALA* 1.3 74.6 - - - +
83C ILE* 1.3 61.3 + - + +
84C LEU 3.0 6.1 + - - -
85C ALA* 3.7 18.2 + - - +
86C ASN 4.5 1.9 - - - +
87C SER* 4.2 6.6 + - - -
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Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ARG* 4.1 14.4 - - + +
69C THR* 4.0 31.4 - - + +
73C ALA 6.0 0.2 - - - +
74C ILE* 4.8 7.6 - - + -
79C ASP* 2.7 28.5 - - + +
80C LEU* 2.5 26.5 + - + +
82C ALA* 1.3 74.3 - - + +
84C LEU* 1.3 56.8 + - + +
87C SER* 3.5 14.6 + - - -
88C LEU* 4.6 7.1 - - - +
94C LEU* 3.2 41.9 - - + +
139C PHE* 6.2 0.2 - - - -
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 2.6 36.6 + - + +
81C ALA* 2.8 16.9 + - - +
83C ILE* 1.3 83.6 - - + +
85C ALA* 1.3 58.1 + - - +
86C ASN* 3.1 8.8 + - - -
87C SER* 4.6 3.6 + - - -
88C LEU* 4.6 6.9 - - - +
94C LEU* 5.2 6.1 - - + -
109C HIS 5.3 1.1 - - - +
110C LEU* 6.4 1.3 - - + -
113C ALA* 4.3 5.4 - - + -
119C MET* 4.1 8.5 - - + -
136C LEU* 3.5 32.8 - - + -
137C PRO* 3.4 23.9 - - - +
139C PHE* 3.2 43.3 - - + -
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B LYS* 4.0 36.2 - - + +
187B LEU* 4.4 13.2 - - + +
81C ALA 2.4 32.9 + - - +
82C ALA* 3.7 8.8 + - - +
84C LEU* 1.3 63.9 - - - +
86C ASN* 1.3 74.6 + - - +
134C LEU* 4.9 10.3 - - + -
136C LEU* 5.4 4.5 - - + +
137C PRO* 5.3 1.1 - - - -
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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