Contacts of the helix formed by residues 112 - 124 (chain B) 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 ALA 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B ALA 3.4 12.3 - - - +
108B TYR 3.0 6.2 + - - +
109B GLN 3.5 9.2 + - - +
110B GLN 3.7 0.2 - - - -
111B TYR* 1.3 77.4 - - - +
113B HIS* 1.3 61.7 + - - +
114B LEU 3.1 1.8 + - - -
115B THR* 3.2 21.7 + - - -
116B ALA 4.4 0.5 + - - -
177B MET* 3.3 40.6 - - + -
272C LYS* 4.3 5.4 - - - +
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Residues in contact with HIS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLN 5.1 0.6 + - - -
110B GLN 3.2 18.9 + - - -
111B TYR* 3.7 10.8 - - - -
112B ALA* 1.3 76.7 + - - +
114B LEU* 1.3 78.1 + - + +
115B THR 3.1 0.4 - - - -
116B ALA* 3.1 18.2 + - - +
117B LEU* 3.1 17.9 + - + +
208B ASN* 2.9 33.3 + - - +
210B LYS* 3.7 28.1 - - + +
235C THR* 4.8 2.8 + - - +
272C LYS* 5.5 2.7 + - - +
126D GLU* 3.4 27.5 - - - +
130D ALA* 3.8 25.4 - - + +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.2 14.7 - - + +
105B ILE* 4.3 11.0 - - + -
106B ALA* 4.3 1.6 - - + -
111B TYR* 2.9 41.9 + - + +
113B HIS* 1.3 91.8 - - - +
115B THR* 1.3 55.7 + - - +
117B LEU* 3.3 25.5 + - + +
118B ALA* 2.9 28.8 + - - +
135B TYR* 3.1 45.3 - - + +
208B ASN* 4.3 18.8 - - + +
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.6 12.8 - - + +
106B ALA* 3.3 23.5 + - - +
112B ALA 3.2 8.9 + - - -
113B HIS 3.1 0.6 - - - -
114B LEU* 1.3 78.8 - - - +
116B ALA* 1.3 58.2 + - - +
118B ALA* 3.2 7.3 + - + +
119B LYS* 2.9 55.4 + - + +
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 4.4 0.6 + - - -
113B HIS* 3.1 12.7 + - - +
115B THR* 1.3 80.3 - - - +
117B LEU* 1.3 59.0 + - - +
119B LYS* 3.4 7.9 + - - +
120B ALA* 3.0 29.5 + - - +
124D ASN* 4.6 9.8 + - - +
126D GLU* 4.0 23.8 - - + -
127D LEU* 4.4 2.1 - - - +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B HIS* 3.1 23.8 + - + +
114B LEU* 3.6 32.3 - - + +
115B THR 3.2 0.2 - - - -
116B ALA* 1.3 77.5 - - - +
118B ALA* 1.3 57.6 + - - +
120B ALA* 3.4 2.6 + - - +
121B ALA* 3.0 29.3 + - - +
131B LEU* 4.3 22.1 - - + +
135B TYR* 3.9 18.6 + - + +
208B ASN* 5.0 6.7 - - - +
126D GLU* 5.1 1.3 - - + +
127D LEU* 3.2 32.3 - - + -
130D ALA* 4.9 8.7 - - + -
131D LEU* 4.3 19.1 - - + -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.2 21.3 - - + -
114B LEU 2.9 16.6 + - - +
115B THR* 3.2 4.7 + - + +
117B LEU* 1.3 78.3 - - - +
119B LYS* 1.3 57.8 + - + +
121B ALA* 3.2 5.0 + - - +
122B GLU* 3.0 26.7 + - - +
135B TYR* 3.6 18.1 + - + +
136B THR* 5.2 2.7 - - + -
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B THR* 2.9 42.3 + - + +
116B ALA* 4.0 7.4 - - - +
118B ALA* 1.3 73.7 - - + +
120B ALA* 1.3 67.2 + - - +
122B GLU* 3.2 25.5 + - - +
123B GLU* 3.4 21.5 + - - +
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Residues in contact with ALA 120 (chain B).
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 3.0 18.8 + - - +
117B LEU 3.6 5.4 - - - +
119B LYS* 1.3 77.0 - - - +
121B ALA* 1.3 59.1 + - - +
123B GLU* 3.3 8.6 + - - +
124B ASN* 2.8 44.1 + - - +
127B LEU* 4.2 7.4 - - + -
131B LEU* 5.7 0.4 - - + -
124D ASN* 5.2 1.6 - - + +
127D LEU* 3.9 30.3 - - + -
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 6.1 0.5 - - - +
117B LEU 3.0 17.0 + - - +
118B ALA* 3.6 8.1 - - - +
119B LYS 3.2 0.2 - - - -
120B ALA* 1.3 75.6 - - - +
122B GLU* 1.3 64.2 + - - +
123B GLU 3.2 0.7 + - - -
124B ASN 3.2 22.7 + - - +
125B PRO* 3.4 6.8 - - - +
127B LEU* 4.4 5.3 - - - +
128B ALA* 4.3 28.7 - - + +
131B LEU* 4.4 9.0 - - + -
135B TYR* 4.6 5.4 - - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ALA 3.0 13.0 + - - +
119B LYS* 3.2 19.9 + - - +
121B ALA* 1.3 77.2 - - - +
123B GLU* 1.3 58.4 + - + +
125B PRO* 4.4 8.3 - - - +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS* 3.4 17.6 + - - +
120B ALA* 3.3 13.2 + - - +
121B ALA 3.1 0.2 - - - -
122B GLU* 1.3 79.6 - - + +
124B ASN* 1.3 81.9 + - - +
125B PRO* 3.1 13.6 - - - +
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Residues in contact with ASN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA* 2.8 24.7 + - - +
121B ALA 3.3 5.0 - - - +
123B GLU* 1.3 102.6 + - - +
125B PRO* 1.3 71.1 - - - +
127B LEU* 2.9 45.6 + - + +
128B ALA 4.3 0.2 + - - -
120D ALA* 4.5 9.8 - - - +
127D LEU* 5.7 0.2 - - - +
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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