Contacts of the helix formed by residues 132 - 139 (chain B) in PDB entry 1F0K
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 GLY 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B GLU* 2.9 19.4 + - - -
128B ASN* 6.1 0.2 - - - -
130B ILE 3.5 2.9 + - - -
131B ALA* 1.3 77.2 - - - +
133B LEU* 1.3 67.8 + - - -
134B THR 3.3 3.1 - - - -
135B ASN* 4.1 3.4 - - - -
136B LYS* 3.1 20.6 + - - +
288B GLN* 6.0 4.3 - - - -
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Residues in contact with LEU 133 (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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68B GLY 3.4 29.8 - - - +
69B LYS 3.6 5.8 - - - +
70B GLY* 3.6 29.8 - - - +
106B TYR* 3.9 21.1 - - + +
131B ALA 3.8 0.8 + - - -
132B GLY* 1.3 73.5 - - - +
134B THR* 1.3 63.0 + - - +
136B LYS* 3.7 13.8 + - + +
137B TRP* 3.2 16.4 - - + +
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Residues in contact with THR 134 (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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69B LYS 5.0 1.4 + - - -
105B GLY 3.6 15.4 - - - +
106B TYR* 3.2 34.3 - - - +
108B SER* 3.4 24.2 - - - +
109B GLY* 3.6 24.2 - - - +
132B GLY 3.3 0.4 - - - -
133B LEU* 1.3 74.6 - - - +
135B ASN* 1.3 65.3 + - - +
136B LYS 3.3 0.5 + - - -
137B TRP* 3.3 20.6 + - + +
138B LEU* 2.9 28.5 + - + +
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Residues in contact with ASN 135 (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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102B GLY 4.4 0.2 + - - -
103B MET 4.3 0.2 - - - +
104B GLY* 3.6 29.6 - - - +
105B GLY 5.6 0.2 - - - +
108B SER* 4.6 1.4 + - - -
124B LEU* 4.0 31.9 - - - +
125B HIS 3.2 21.2 - - - +
126B GLU* 3.1 31.8 - - - +
132B GLY* 3.5 5.2 + - - +
134B THR* 1.3 78.1 - - - +
136B LYS* 1.3 64.9 + - - +
138B LEU* 4.3 7.8 - - - +
139B ALA* 2.9 27.5 + - - +
153B PHE* 3.7 12.1 - - + -
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Residues in contact with LYS 136 (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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131B ALA* 4.2 19.0 - - + +
132B GLY 3.1 17.8 + - - +
133B LEU* 3.7 9.6 - - + +
134B THR 3.2 0.2 - - - -
135B ASN* 1.3 79.0 - - - +
137B TRP* 1.3 58.9 + - - +
139B ALA* 3.9 9.4 - - - +
140B LYS* 4.6 11.4 - - - +
152B ALA 6.2 0.2 - - - -
153B PHE* 3.9 15.4 - - + -
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Residues in contact with TRP 137 (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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69B LYS 4.7 1.0 + - - -
70B GLY* 4.2 6.2 - - - -
71B ILE* 3.6 59.5 - - + +
74B LEU* 3.6 21.9 - - + +
109B GLY* 3.6 37.9 - - - -
113B LEU* 3.8 26.5 - - + -
133B LEU* 3.2 23.3 - - + -
134B THR* 3.3 20.3 + - + +
136B LYS* 1.3 74.7 - - - +
138B LEU* 1.3 98.6 + - + +
139B ALA 3.1 2.0 - - - -
140B LYS* 3.1 30.3 + - + +
141B ILE* 4.5 5.2 + - + +
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Residues in contact with LEU 138 (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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12B MET* 4.9 0.7 - - + -
108B SER* 3.4 38.6 - - - +
112B GLY* 3.8 20.4 - - - -
122B VAL* 4.9 2.9 - - + -
124B LEU* 3.7 33.7 - - + -
134B THR* 2.9 21.6 + - + +
135B ASN* 4.0 4.0 - - - +
137B TRP* 1.3 98.2 - - + +
139B ALA* 1.3 62.5 + - - +
140B LYS 2.9 1.8 + - - -
141B ILE* 3.0 49.4 + - + +
142B ALA* 3.3 5.4 + - - +
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Residues in contact with ALA 139 (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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124B LEU* 3.6 12.7 - - + +
135B ASN 2.9 17.8 + - - +
136B LYS 3.9 5.4 - - - +
137B TRP 3.1 0.2 - - - -
138B LEU* 1.3 77.5 - - - +
140B LYS* 1.3 61.1 + - + +
141B ILE 3.3 0.9 + - - -
142B ALA* 3.3 16.4 + - - +
145B VAL* 3.9 20.5 - - + +
153B PHE* 3.7 25.1 - - + -
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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