Contacts of the helix formed by residues 122 - 134 (chain E) in PDB entry 3IFS
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 SER 122 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120E ASN* 3.0 13.2 + - - +
121E ILE* 1.3 73.6 - - - +
123E SER* 1.3 63.8 + - - +
124E THR* 3.5 2.6 + - - -
125E TYR* 3.1 27.3 + - - +
126E MSE 3.1 27.6 + - - +
274F TYR 4.6 2.5 - - - -
275F GLU* 2.6 33.4 + - - -
276F PRO* 3.8 14.1 - - - +
360F ASP* 6.2 0.2 - - - -
363F ASN* 4.8 0.9 - - - +
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Residues in contact with SER 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE 3.7 4.9 + - - -
122E SER* 1.3 68.9 - - - +
124E THR* 1.3 58.9 + - - +
126E MSE 3.9 0.4 - - - +
127E LYS* 2.8 34.6 + - - +
275F GLU* 5.1 1.0 + - - -
335F SER* 3.4 8.1 + - - -
337F HIS* 2.9 25.2 + - - -
338F GLU* 4.0 2.9 - - - -
339F LEU* 4.0 24.9 - - - +
359F VAL* 3.8 26.0 - - - +
360F ASP* 4.1 15.4 + - - +
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Residues in contact with THR 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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122E SER* 3.2 6.9 - - - -
123E SER* 1.3 79.9 + - - +
125E TYR* 1.3 56.5 + - - +
127E LYS 3.6 0.3 + - - -
128E ASP* 2.9 49.1 + - - +
99F SER* 4.0 6.3 - - - +
275F GLU* 4.5 7.9 + - - -
277F ALA* 6.1 4.7 - - + -
335F SER* 3.2 10.8 + - - -
336F THR* 3.3 20.8 + - + +
337F HIS* 3.1 37.9 + - + -
389F LEU* 6.5 0.2 - - + -
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Residues in contact with TYR 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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90E ARG* 5.1 4.6 + - - -
115E LEU* 5.6 0.2 - - - +
116E PHE* 2.7 33.8 + - - +
117E VAL* 4.4 8.7 - - + -
119E GLN* 3.3 22.0 + - - -
120E ASN* 3.6 17.7 - - - +
122E SER* 3.1 24.9 + - - +
124E THR* 1.3 78.1 - - - +
126E MSE 1.3 64.8 + - + +
128E ASP* 3.3 2.1 + - - +
129E LEU* 2.9 32.2 + - + +
99F SER* 3.8 18.2 - - - +
100F PHE* 3.4 36.1 - + - -
276F PRO* 4.1 20.2 - - + -
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Residues in contact with MSE 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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117E VAL* 3.7 23.6 - - + -
118E GLY 5.5 0.4 - - - +
120E ASN* 4.3 7.9 - - - +
121E ILE* 3.8 7.9 - - + -
122E SER 3.1 39.2 + - - +
123E SER* 4.0 0.4 - - - +
125E TYR* 1.3 79.8 - - + +
127E LYS* 1.3 66.2 + - - +
129E LEU* 3.2 8.7 + - - +
130E MSE 3.1 28.0 + - - +
154E LEU* 5.6 3.4 - - + -
155E ALA* 4.5 15.3 - - - -
158E ILE* 4.1 24.0 - - - -
159E PHE* 3.7 14.1 - - + -
339F LEU* 3.7 13.2 - - + -
359F VAL* 3.4 29.6 - - + -
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Residues in contact with LYS 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 SER 2.8 22.9 + - - +
124E THR 4.0 0.7 - - - +
126E MSE 1.3 72.7 - - - +
128E ASP* 1.3 63.9 + - - +
130E MSE 3.2 36.0 + - + +
131E ASP* 3.4 33.8 + - - +
337F HIS* 3.8 38.3 - - + +
338F GLU 5.5 1.8 - - - +
339F LEU* 4.2 14.9 - - + +
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Residues in contact with ASP 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 THR* 2.9 27.2 + - - +
125E TYR 3.7 0.4 - - - +
127E LYS* 1.3 78.4 - - - +
129E LEU* 1.3 61.3 + - - +
131E ASP* 3.2 14.9 + - - +
132E VAL* 3.6 2.8 + - - +
97F ASN 4.9 0.5 - - - +
98F HIS* 3.3 50.8 + - + -
99F SER* 2.7 43.4 + - - -
100F PHE* 3.8 3.4 - - + -
337F HIS* 3.2 25.0 + - - -
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Residues in contact with LEU 129 (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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78E LEU* 3.5 26.0 - - + -
115E LEU* 3.3 39.0 - - + -
116E PHE 4.3 5.4 - - - +
117E VAL* 3.5 28.9 - - + -
125E TYR* 2.9 17.9 + - + +
126E MSE 3.2 8.7 + - - +
128E ASP* 1.3 74.5 - - - +
130E MSE 1.3 65.0 + - - +
132E VAL* 3.0 17.1 + - + +
133E LEU* 3.1 16.1 + - + +
159E PHE* 3.9 13.0 - - + -
100F PHE* 3.6 21.7 - - + -
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Residues in contact with MSE 130 (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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126E MSE 3.1 10.5 + - - +
127E LYS* 3.2 28.0 + - + +
129E LEU* 1.3 75.6 - - - +
131E ASP* 1.3 62.7 + - - +
133E LEU* 3.3 11.5 + - - +
134E GLU* 3.2 22.5 + - - +
158E ILE* 3.5 32.8 - - + -
159E PHE* 3.9 12.3 - - + -
162E LEU* 3.6 33.7 - - + -
339F LEU* 3.9 28.9 - - + -
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Residues in contact with ASP 131 (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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127E LYS* 3.4 28.0 + - - +
128E ASP* 3.3 14.1 - - - +
129E LEU 3.1 0.6 - - - -
130E MSE 1.3 80.0 - - - +
132E VAL* 1.3 59.3 + - - +
134E GLU* 3.4 15.0 - - - +
98F HIS* 2.8 32.1 + - + +
104F LEU* 4.4 8.1 - - + -
108F GLN* 3.3 24.3 + - - +
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Residues in contact with VAL 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ILE* 3.6 8.3 - - + +
113E GLN* 4.1 9.4 - - - +
115E LEU* 3.9 24.7 - - + -
128E ASP 3.6 6.7 + - - +
129E LEU* 3.0 8.7 + - - +
131E ASP* 1.3 76.7 - - - +
133E LEU* 1.3 61.9 + - - +
134E GLU 3.3 1.4 + - - +
136E LYS* 3.5 21.8 - - - +
100F PHE* 3.6 39.7 - - + -
103F THR* 4.3 16.8 - - + -
104F LEU* 4.5 12.8 - - + +
108F GLN* 5.3 0.9 - - - +
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Residues in contact with LEU 133 (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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76E ILE* 3.7 32.8 - - + -
78E LEU* 4.5 7.6 - - + -
129E LEU* 3.1 21.7 + - + +
130E MSE 3.6 11.2 - - - +
131E ASP 3.3 0.4 - - - -
132E VAL* 1.3 75.2 - - - +
134E GLU* 1.3 66.0 + - - +
135E GLY 3.2 0.7 + - - -
136E LYS* 2.9 25.2 + - - +
138E PHE* 3.9 43.0 - - + -
159E PHE* 3.6 36.3 - - + -
162E LEU* 4.6 5.8 - - + -
166E LYS* 5.2 1.2 + - - +
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Residues in contact with GLU 134 (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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130E MSE 3.2 12.0 + - - +
131E ASP* 3.4 19.0 - - - +
132E VAL 3.3 2.6 - - - +
133E LEU* 1.3 76.5 - - - +
135E GLY* 1.3 69.2 + - - +
136E LYS* 3.3 11.6 + - - +
108F GLN* 4.9 8.8 + - - +
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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