Contacts of the helix formed by residues 113 - 128 (chain E) in PDB entry 1I43
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 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82E VAL* 3.0 22.9 + - - +
84E THR 4.4 7.9 + - - -
87E TYR* 3.3 12.6 + - - -
106E PHE* 3.7 9.9 - - - -
109E GLY* 5.3 2.6 + - - +
112E GLY* 1.3 75.3 + - - +
114E PRO* 1.3 88.7 - - - +
115E THR* 2.7 32.0 + - - +
116E THR* 2.9 28.5 + - - +
117E VAL* 3.0 16.9 + - - +
295E LEU 5.7 1.8 - - - +
297E PRO* 3.3 15.4 - - + +
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Residues in contact with PRO 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ARG 4.9 2.9 - - - +
71E GLY 6.0 0.9 - - - -
72E ILE* 4.2 27.5 - - + +
82E VAL* 3.3 36.1 - - + -
87E TYR* 3.5 17.9 - - + +
106E PHE* 3.5 17.5 - - + -
113E ASN* 1.3 91.1 - - - +
115E THR* 1.3 57.7 + - - +
117E VAL* 2.9 27.4 - - + +
118E VAL* 3.5 11.5 - - - +
74F THR* 5.5 3.4 - - + -
75F ASP* 5.9 1.6 - - - +
76F ALA* 6.1 0.2 - - + -
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Residues in contact with THR 115 (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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72E ILE* 5.6 0.2 - - - +
79E THR* 3.8 16.7 - - - +
80E PRO 3.1 24.6 + - - -
81E VAL* 4.0 3.2 - - - -
82E VAL 3.4 12.6 - - - +
113E ASN* 2.7 24.8 + - - +
114E PRO* 1.3 75.6 - - - +
116E THR* 1.3 58.8 + - - +
118E VAL* 4.2 2.1 - - - +
297E PRO* 3.4 40.0 + - + +
300E ALA* 3.8 4.4 - - - +
301E TYR* 4.5 6.2 - - - +
304E ILE* 3.4 25.8 - - - +
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Residues in contact with THR 116 (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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112E GLY* 5.6 2.7 - - - -
113E ASN* 2.9 28.6 + - + +
115E THR* 1.3 79.1 - - - +
117E VAL* 1.3 68.7 + - + +
118E VAL 3.1 1.6 - - - -
119E LEU* 3.0 15.8 + - - +
120E GLU* 3.1 27.6 + - + +
134E LEU* 4.7 14.1 - - + +
295E LEU* 4.1 20.9 + - + +
297E PRO* 4.5 2.9 - - - +
300E ALA* 3.6 19.1 - - - +
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Residues in contact with VAL 117 (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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70E ARG 4.9 7.6 - - - +
106E PHE* 3.9 25.8 - - + -
112E GLY* 5.9 0.7 - - - -
113E ASN 3.0 16.7 + - - +
114E PRO* 2.9 27.4 - - + +
116E THR* 1.3 73.1 - - + +
118E VAL* 1.3 66.8 + - + +
120E GLU* 2.7 24.3 + - + +
121E GLU* 2.7 37.3 + - + +
285E ARG* 6.1 0.2 - - - +
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Residues in contact with VAL 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ALA 4.4 0.7 - - - +
65E GLY* 3.1 23.2 - - - +
66E GLU* 3.6 18.6 - - + +
70E ARG* 3.5 33.0 - - + +
72E ILE* 5.7 0.4 - - + -
79E THR* 3.7 17.7 - - + +
114E PRO 3.5 16.4 - - - +
115E THR 4.2 2.0 - - - +
116E THR 3.1 0.2 - - - -
117E VAL* 1.3 78.4 - - + +
119E LEU* 1.3 58.1 + - - +
121E GLU* 3.4 7.2 + - - +
122E LYS* 2.9 33.3 + - - +
304E ILE* 4.0 17.3 - - + -
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Residues in contact with LEU 119 (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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115E THR 4.8 0.7 - - - +
116E THR* 3.0 12.3 + - - +
118E VAL* 1.3 79.8 - - - +
120E GLU* 1.3 62.9 + - - +
122E LYS* 3.5 6.5 - - + +
123E ILE* 3.0 30.2 + - + +
134E LEU* 3.4 36.8 - - + -
295E LEU* 4.5 1.3 - - + -
300E ALA* 4.0 14.1 - - + +
303E ILE* 3.4 43.3 - - + -
304E ILE* 3.8 27.7 - - + +
307E MET* 3.7 19.1 - - - -
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Residues in contact with GLU 120 (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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116E THR* 3.1 19.4 + - - +
117E VAL* 2.7 30.0 + - + +
119E LEU* 1.3 78.3 - - - +
121E GLU* 1.3 58.3 + - + +
123E ILE 3.6 0.2 + - - -
124E SER* 2.9 31.1 + - - -
132E THR* 3.2 35.9 - - - +
133E LEU* 4.4 1.0 - - - +
134E LEU* 3.7 33.3 + - + +
285E ARG* 2.9 29.6 + - - -
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Residues in contact with GLU 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 5.2 7.5 - - + -
64E ALA* 4.8 0.2 - - - +
65E GLY* 4.2 21.6 + - - +
69E GLY 5.5 1.6 - - - +
117E VAL* 2.7 29.3 + - + +
118E VAL* 3.9 5.3 - - - +
120E GLU* 1.3 71.3 - - + +
122E LYS* 1.3 59.7 + - - +
124E SER* 3.4 8.7 - - - -
125E ALA* 2.9 29.8 + - - +
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Residues in contact with LYS 122 (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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60E VAL 4.5 0.2 - - - +
61E ALA* 3.0 21.0 + - - +
62E ILE 2.7 27.3 + - - -
64E ALA* 2.9 40.2 + - + +
66E GLU* 2.7 23.7 + - - -
118E VAL* 2.9 20.0 + - - +
119E LEU* 3.5 10.3 - - + +
121E GLU* 1.3 77.7 - - - +
123E ILE* 1.3 62.0 + - - +
125E ALA* 3.2 6.2 + - - +
126E LEU* 3.2 20.1 + - - +
304E ILE* 4.2 15.1 + - + +
307E MET* 4.0 25.8 - - + -
308E LYS* 3.1 11.1 - - - +
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Residues in contact with ILE 123 (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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119E LEU* 3.0 40.8 + - + +
120E GLU 4.0 2.5 - - - +
122E LYS* 1.3 74.2 - - - +
124E SER* 1.3 67.3 + - - +
126E LEU* 3.1 8.8 + - + +
127E GLU* 3.0 28.9 + - + +
132E THR* 3.7 5.6 - - + +
134E LEU* 4.4 7.4 - - + -
242E PRO* 6.0 2.9 - - + -
257E HIS* 5.9 1.6 - - + -
259E ALA* 5.9 1.1 - - + -
263E LEU* 4.5 15.3 - - + -
273E CYS* 3.5 30.5 - - - -
275E SER* 3.6 22.9 - - - +
303E ILE* 5.3 1.6 - - + -
307E MET* 3.9 22.9 - - + -
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Residues in contact with SER 124 (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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120E GLU 2.9 15.7 + - - -
121E GLU* 3.4 11.6 - - - -
123E ILE* 1.3 78.3 - - - +
125E ALA* 1.3 55.9 + - - +
127E GLU 3.6 0.2 + - - -
128E GLY* 2.9 7.8 + - - -
129E ALA* 2.8 42.6 + - - +
130E GLU 5.1 1.1 - - - -
131E SER* 3.3 10.6 + - - -
132E THR* 3.0 36.9 + - - -
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Residues in contact with ALA 125 (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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50E TYR* 4.5 20.0 - - + +
60E VAL* 3.8 11.0 - - + +
64E ALA* 3.8 20.4 - - + -
121E GLU 2.9 12.8 + - - +
122E LYS 3.4 9.4 - - - +
123E ILE 3.1 0.2 - - - -
124E SER* 1.3 74.7 - - - +
126E LEU* 1.3 65.7 + - - +
128E GLY* 3.2 11.5 + - - +
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Residues in contact with LEU 126 (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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57E ASP* 3.7 33.6 - - + +
60E VAL* 3.9 13.0 - - + -
61E ALA* 4.0 7.4 - - + +
122E LYS 3.2 8.4 + - - +
123E ILE* 3.1 10.4 + - + +
125E ALA* 1.3 81.6 - - - +
127E GLU* 1.3 60.5 + - - +
128E GLY* 3.4 0.3 + - - -
242E PRO* 4.1 21.5 - - + +
243E LEU* 4.0 17.3 - - + -
246E LYS* 2.9 28.8 + - - +
307E MET* 3.6 30.5 - - + -
310E LEU* 3.9 20.9 - - + -
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Residues in contact with GLU 127 (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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123E ILE* 3.0 20.3 + - + +
124E SER 4.3 0.2 - - - +
126E LEU* 1.3 74.8 - - - +
128E GLY* 1.3 63.2 + - - +
129E ALA 3.4 4.9 + - - +
242E PRO* 3.3 25.4 - - + +
245E GLN 4.3 7.8 - - - +
246E LYS* 4.5 18.3 - - - +
247E ALA 4.7 1.2 + - - -
248E LEU* 3.8 22.8 + - + +
249E ALA* 5.2 1.0 + - - +
255E VAL* 3.7 17.8 - - - +
257E HIS* 2.5 37.6 + - + -
275E SER* 4.0 24.2 - - - +
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Residues in contact with GLY 128 (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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124E SER 2.9 7.9 + - - -
125E ALA* 3.2 9.1 + - - -
126E LEU 3.1 4.6 - - - -
127E GLU* 1.3 79.9 - - - +
129E ALA* 1.3 63.1 + - - +
248E LEU* 4.4 4.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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