Contacts of the helix formed by residues 72 - 81 (chain E) in PDB entry 1AXC
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 LEU 72 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16E LEU* 3.9 13.5 - - + +
19E LEU* 4.2 13.0 - - + -
20E LYS* 4.0 9.1 - - - +
23E ILE* 3.4 54.7 - - + +
24E ASN 2.8 10.0 + - - +
26E ALA* 3.8 17.7 - - + +
28E TRP* 3.1 39.5 - - + +
37E LEU* 4.3 4.5 - - + -
70E VAL* 3.6 10.5 + - + -
71E ASN* 1.3 68.7 - - - +
73E THR* 1.3 64.5 + - - +
75E MET* 3.9 2.6 - - - -
76E SER* 3.0 24.1 + - - -
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Residues in contact with THR 73 (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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20E LYS* 4.6 9.9 + - + +
24E ASN* 3.6 24.2 + - - +
71E ASN* 2.8 15.4 + - - -
72E LEU* 1.3 77.5 - - - +
74E SER* 1.3 60.7 + - - +
76E SER* 3.2 9.1 + - - -
77E LYS* 3.2 37.8 + - + +
80E LYS* 5.2 0.2 + - - -
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Residues in contact with SER 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.1 35.2 - - - +
71E ASN* 2.9 31.7 + - - +
73E THR* 1.3 78.4 - - - +
75E MET* 1.3 61.1 + - - +
77E LYS* 3.1 10.6 + - - +
78E ILE* 3.0 27.1 + - - +
116E MET* 4.6 8.5 - - - -
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Residues in contact with MET 75 (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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12E LEU* 5.1 5.4 - - + -
16E LEU* 3.6 36.3 - - + -
28E TRP* 4.0 25.4 - - + -
70E VAL* 3.8 21.1 - - + -
71E ASN 2.9 14.2 + - - +
72E LEU 4.0 0.7 - - - +
74E SER* 1.3 76.1 - - - +
76E SER* 1.3 56.4 + - - +
78E ILE* 3.9 3.4 - - - +
79E LEU* 2.9 37.2 + - + +
90E LEU* 5.1 9.9 - - + -
99E LEU* 4.3 19.1 - - + -
101E LEU* 4.6 12.1 - - + -
116E MET* 3.5 27.3 - - - -
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Residues in contact with SER 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 4.4 11.7 - - - -
17E GLU* 3.2 12.3 + - - -
20E LYS* 3.2 32.9 - - - +
72E LEU 3.0 19.6 + - - -
73E THR* 3.3 7.2 - - - -
74E SER 3.1 0.2 - - - -
75E MET* 1.3 76.9 - - - +
77E LYS* 1.3 66.6 + - - +
79E LEU* 3.2 4.3 + - - +
80E LYS* 2.9 37.6 + - - +
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Residues in contact with LYS 77 (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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153A HIS* 3.8 35.8 + - + +
154A ILE* 5.1 0.9 - - + -
175A LEU* 3.9 19.2 - - + +
73E THR* 3.2 27.5 + - + +
74E SER* 3.1 10.1 + - - +
76E SER* 1.3 78.3 - - - +
78E ILE* 1.3 62.1 + - + +
80E LYS* 3.1 38.0 + - - +
81E CYS* 3.4 12.6 - - - -
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Residues in contact with ILE 78 (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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154A ILE* 4.0 10.3 - - + -
175A LEU* 3.4 28.7 - - + -
177A ASN 5.7 0.9 - - - +
74E SER 3.0 13.8 + - - +
75E MET* 3.9 4.9 - - - +
77E LYS* 1.3 80.1 - - - +
79E LEU* 1.3 62.7 + - - +
81E CYS* 3.1 25.4 + - - +
101E LEU* 3.6 26.0 - - + -
103E PHE* 3.4 9.7 - - + -
114E TYR* 3.8 27.6 - - + -
115E GLU 4.9 0.9 - - - -
116E MET* 3.4 41.5 - - + +
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Residues in contact with LEU 79 (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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12E LEU* 3.4 23.6 - - + +
13E LYS* 3.2 26.6 + - + +
16E LEU* 3.3 38.4 - - + -
75E MET* 2.9 28.1 + - + +
76E SER* 3.2 5.3 + - - +
78E ILE* 1.3 71.6 - - - +
80E LYS* 1.3 61.3 + - - +
81E CYS 3.0 5.6 - - - -
82E ALA* 3.1 15.2 + - - +
88E ILE* 3.7 31.4 - - + -
101E LEU* 4.3 12.8 - - + -
103E PHE* 3.9 14.6 - - + -
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Residues in contact with LYS 80 (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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146A ARG* 3.2 19.6 + - - -
149A ARG* 4.0 6.2 + - - +
150A ASP* 5.0 0.7 - - - -
153A HIS* 4.1 26.5 - - + +
13E LYS* 4.3 6.7 + - - +
17E GLU* 4.7 15.7 - - + +
20E LYS* 4.7 8.3 - - - +
73E THR 5.2 0.2 + - - -
76E SER* 2.9 31.8 + - - +
77E LYS* 3.1 38.6 + - - +
79E LEU* 1.3 77.5 - - - +
81E CYS* 1.3 55.7 + - - +
82E ALA 3.1 5.6 + - - +
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Residues in contact with CYS 81 (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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146A ARG* 4.3 0.8 + - - -
150A ASP* 3.4 51.1 - - + +
153A HIS* 4.4 4.3 - - - -
154A ILE* 4.5 4.7 - - - -
77E LYS 3.4 17.5 - - - -
78E ILE* 3.3 14.8 - - - +
79E LEU 3.0 0.6 - - - -
80E LYS* 1.3 78.7 - - - +
82E ALA* 1.3 57.3 + - - +
83E GLY 4.2 0.2 + - - -
86E ASP* 4.7 1.7 - - - +
103E PHE* 3.8 10.9 - - + -
110E LYS* 5.5 3.6 + - - -
112E SER* 5.0 3.8 + - - -
114E TYR* 3.5 32.8 + - + +
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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