Contacts of the helix formed by residues 132 - 139 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A HIS* 6.4 1.3 - - - -
126A GLU* 3.0 18.9 + - - -
128A ASN* 6.0 0.4 - - - -
130A ILE 3.5 2.7 + - - -
131A ALA* 1.3 77.4 - - - +
133A LEU* 1.3 65.0 + - - -
134A THR* 3.3 2.9 - - - -
135A ASN* 3.4 4.1 + - - -
136A LYS* 3.0 19.5 + - - +
288A GLN* 6.2 2.0 - - - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 3.1 30.1 - - + -
72A LYS* 4.7 12.8 - - + +
131A ALA 3.8 0.8 + - - -
132A GLY* 1.3 72.6 - - - -
134A THR* 1.3 62.0 + - - +
136A LYS* 3.3 14.1 + - + +
137A TRP* 3.2 72.7 + - + +
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Residues in contact with THR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 3.3 23.5 - - + +
105A GLY 3.3 17.0 - - - +
106A TYR* 3.3 21.8 + - - +
108A SER* 3.2 26.2 - - - +
109A GLY* 3.5 23.6 - - - +
132A GLY* 3.3 0.8 - - - -
133A LEU* 1.3 78.8 - - - +
135A ASN* 1.3 57.9 + - - +
137A TRP* 3.3 2.7 + - - +
138A LEU* 2.9 33.6 + - + +
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Residues in contact with ASN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLY 4.4 0.8 + - - -
104A GLY* 3.6 28.7 - - - +
124A LEU* 3.9 31.8 - - - +
125A HIS 3.4 20.1 - - - +
126A GLU* 2.8 34.6 - - - +
132A GLY* 3.4 6.5 + - - +
133A LEU 3.3 0.4 - - - -
134A THR* 1.3 78.8 - - - +
136A LYS* 1.3 58.7 + - - +
138A LEU* 3.7 7.9 - - - +
139A ALA* 2.9 31.9 + - - +
153A PHE* 3.7 12.7 - - + -
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Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ALA* 4.5 11.2 - - + +
132A GLY 3.0 16.8 + - - +
133A LEU* 3.6 19.1 - - + +
134A THR 3.3 0.4 - - - -
135A ASN* 1.3 78.9 - - - +
137A TRP* 1.3 69.6 + - + +
139A ALA* 3.6 12.0 - - - +
140A LYS* 4.0 10.2 - - - +
153A PHE* 3.9 16.9 - - + -
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Residues in contact with TRP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.1 18.2 - - + -
72A LYS* 4.2 9.9 - - + -
75A ILE* 3.7 39.3 - - + -
133A LEU* 3.2 54.6 + - + +
134A THR* 4.0 2.9 - - - +
136A LYS* 1.3 86.9 - - + +
138A LEU* 1.3 65.7 + - - +
140A LYS* 3.0 28.2 + - + +
141A ILE* 4.4 1.9 + - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 5.2 1.6 - - + -
108A SER* 3.5 38.6 - - - +
109A GLY* 4.0 11.2 - - - +
112A GLY* 3.7 26.7 - - - -
122A VAL* 4.8 2.9 - - + -
124A LEU* 3.5 31.6 - - + -
134A THR* 2.9 21.2 + - + +
135A ASN* 3.7 8.1 - - - +
137A TRP* 1.3 71.4 - - - +
139A ALA* 1.3 64.1 + - - +
140A LYS 2.9 5.4 - - - -
141A ILE* 2.8 38.2 + - + +
142A ALA* 3.1 10.0 + - - +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.5 10.9 - - + +
135A ASN 2.9 18.7 + - - +
136A LYS 3.6 6.1 - - - +
137A TRP 3.2 0.2 - - - -
138A LEU* 1.3 76.4 - - - +
140A LYS* 1.3 63.2 + - + +
141A ILE 3.1 1.3 + - - -
142A ALA* 3.5 15.1 + - - +
145A VAL* 4.0 18.2 - - + +
153A PHE* 3.6 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