Contacts of the helix formed by residues 113 - 124 (chain D) in PDB entry 1FIU
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 HIS 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A THR* 4.8 2.4 + - - +
126B GLU* 5.4 9.2 - - + +
130B ALA* 3.5 28.8 - - + +
109D GLN 5.2 0.6 + - - -
110D GLN 3.3 17.8 + - - -
111D TYR* 3.8 9.8 - - - -
112D ALA* 1.3 75.1 + - - +
114D LEU* 1.3 79.3 + - + +
115D THR 3.1 2.5 - - - -
116D ALA* 3.1 14.3 + - + +
117D LEU* 3.1 25.6 + - + +
208D ASN* 2.9 34.5 + - - +
210D LYS* 3.6 36.6 - - + +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 3.9 17.6 - - + +
105D ILE* 3.9 22.7 - - + -
111D TYR* 3.0 28.1 + - + +
113D HIS* 1.3 95.5 - - - +
115D THR* 1.3 58.0 + - - +
117D LEU* 3.3 21.1 + - + +
118D ALA* 2.9 29.5 + - - +
135D TYR* 3.6 44.7 - - + +
208D ASN* 4.3 16.6 - - + +
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 4.6 8.3 - - + +
106D ALA* 3.5 23.2 + - - +
112D ALA 3.3 10.6 + - - -
113D HIS 3.1 0.6 - - - -
114D LEU* 1.3 79.0 - - - +
116D ALA* 1.3 57.4 + - - +
118D ALA* 3.2 6.9 + - - +
119D LYS* 2.9 57.8 + - + +
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Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLU* 4.3 24.0 - - + +
127B LEU* 4.1 17.1 - - + +
112D ALA 4.5 0.2 + - - -
113D HIS* 3.1 15.0 + - + +
115D THR* 1.3 77.7 - - - +
117D LEU* 1.3 59.8 + - - +
119D LYS* 3.3 8.6 + - - +
120D ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 3.4 27.4 - - + -
130B ALA* 4.6 10.1 - - + -
131B LEU* 4.3 26.2 - - + -
113D HIS* 3.1 21.7 + - + +
114D LEU* 3.8 31.0 - - + +
115D THR 3.3 0.4 - - - -
116D ALA* 1.3 75.8 - - - +
118D ALA* 1.3 58.4 + - - +
120D ALA* 3.2 5.2 + - + +
121D ALA* 2.9 29.3 + - - +
131D LEU* 4.1 22.8 - - + +
135D TYR* 3.8 15.7 - - + +
208D ASN* 5.3 5.2 - - - +
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 4.0 20.6 - - + -
114D LEU 2.9 17.2 + - - +
115D THR 3.6 4.0 - - - +
117D LEU* 1.3 77.4 - - - +
119D LYS* 1.3 57.8 + - + +
121D ALA* 3.3 5.3 + - - +
122D GLU* 3.0 29.6 + - - +
135D TYR* 3.4 16.7 + - + +
136D THR* 5.4 2.7 - - + -
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D THR* 2.9 47.4 + - + +
116D ALA* 3.7 8.1 - - - +
117D LEU 3.2 0.2 - - - -
118D ALA* 1.3 77.6 - - + +
120D ALA* 1.3 62.9 + - - +
122D GLU* 3.1 38.0 + - - +
123D GLU* 3.4 17.9 + - - +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ASN* 4.5 9.4 - - - +
127B LEU* 4.0 22.9 - - + -
116D ALA 2.9 17.0 + - - +
117D LEU* 3.5 7.0 - - + +
119D LYS* 1.3 76.8 - - - +
121D ALA* 1.3 57.9 + - - +
123D GLU* 3.1 6.7 + - - +
124D ASN* 2.9 23.4 + - - +
127D LEU* 3.3 24.8 - - + +
131D LEU* 5.6 0.9 - - + -
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C ILE* 5.8 1.2 - - - +
117D LEU 2.9 16.1 + - - +
118D ALA* 3.7 8.1 - - - +
120D ALA* 1.3 76.3 - - - +
122D GLU* 1.3 61.3 + - - +
124D ASN 3.0 25.9 + - - +
125D PRO* 4.0 3.5 - - - +
127D LEU* 3.9 7.8 - - + +
128D ALA* 3.9 31.3 - - + +
131D LEU* 4.4 4.9 - - + -
132D GLY 5.8 1.1 - - - +
135D TYR* 4.8 3.6 - - - +
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Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ALA 3.0 12.7 + - - +
119D LYS* 3.1 38.2 + - - +
121D ALA* 1.3 77.9 - - - +
123D GLU* 1.3 65.4 + - + +
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LYS* 3.4 13.8 + - - +
120D ALA* 3.1 8.1 + - - +
122D GLU* 1.3 89.4 - - + +
124D ASN* 1.3 61.2 + - - +
125D PRO* 4.2 5.6 - - - +
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Residues in contact with ASN 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 4.6 10.1 + - - +
120B ALA* 5.2 1.4 - - + +
120D ALA 2.9 5.5 + - - +
121D ALA* 3.0 12.6 - - - +
123D GLU* 1.3 79.4 - - + +
125D PRO* 1.3 83.9 - - - +
126D GLU* 3.7 12.0 + - - +
127D LEU* 2.7 64.3 + - + +
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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