Contacts of the helix formed by residues 113 - 123 (chain K) in PDB entry 1O1F
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 LYS 113 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111K SER 3.9 1.5 + - - +
112K ILE* 1.3 74.9 - - + +
114K LYS* 1.3 65.9 + - - +
115K SER* 3.3 20.8 + - - +
116K PHE* 3.1 27.2 + - + +
117K LEU* 3.2 4.7 + - - +
146K GLY 2.9 4.5 - - - -
147K ASN* 3.0 11.6 - - - +
148K VAL* 4.4 6.5 - - + -
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Residues in contact with LYS 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K LYS* 1.3 67.5 - - - +
115K SER* 1.3 64.3 + - - +
118K GLU* 3.0 36.5 + - - +
137K TRP* 3.3 29.6 - - + +
146K GLY* 1.8 30.9 + - - +
147K ASN* 2.4 19.8 + - - -
148K VAL* 4.3 6.1 - - + +
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Residues in contact with SER 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K LYS* 3.3 22.1 + - - +
114K LYS* 1.3 79.7 - - - +
116K PHE* 1.3 58.9 + - - +
118K GLU* 3.2 14.8 + - - +
119K GLU* 3.0 49.7 + - - +
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Residues in contact with PHE 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K LEU* 5.0 6.1 - - + -
112K ILE* 3.5 30.7 - - + -
113K LYS* 3.1 25.1 + - + +
115K SER* 1.3 79.8 + - - +
117K LEU* 1.3 59.9 + - + +
119K GLU* 3.3 12.8 + - - +
120K LEU* 2.9 60.1 + - + +
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Residues in contact with LEU 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K PHE* 5.2 11.4 - - + -
104K LEU* 4.2 20.0 - - + -
112K ILE* 3.5 31.9 - - + -
113K LYS 3.2 1.6 + - - +
114K LYS 3.3 0.2 + - - -
116K PHE* 1.3 81.3 - - + +
118K GLU* 1.3 55.0 + - - +
120K LEU* 4.2 6.5 - - + +
121K LEU* 3.0 34.1 + - - +
133K ILE* 5.8 0.2 - - - -
144K VAL 5.0 0.7 - - - +
147K ASN* 1.7 87.3 - - + +
150K TYR* 5.7 1.3 - - + -
153K ILE* 6.5 0.2 - - + -
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Residues in contact with GLU 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K LYS* 3.0 31.9 - - - +
115K SER* 3.2 23.2 - - - +
116K PHE 3.3 0.2 - - - -
117K LEU* 1.3 78.3 - - - +
119K GLU* 1.3 61.4 + - + +
122K THR* 3.0 30.5 + - - -
133K ILE* 3.5 32.9 - - + +
137K TRP* 3.1 24.9 + - - +
147K ASN* 4.1 4.5 - - - +
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Residues in contact with GLU 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K SER* 3.0 33.4 + - - +
116K PHE* 3.7 11.7 - - - +
118K GLU* 1.3 80.0 - - + +
120K LEU* 1.3 57.1 + - - +
122K THR* 3.8 2.1 - - - -
123K THR* 2.8 44.3 + - + +
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Residues in contact with LEU 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809J ARG* 5.1 22.0 - - - +
813J ILE* 6.0 1.9 - - + +
104K LEU* 3.7 31.2 - - + -
116K PHE* 2.9 39.4 + - + +
117K LEU* 4.2 6.7 - - + +
119K GLU* 1.3 73.9 - - - +
121K LEU* 1.3 65.2 + - - +
123K THR* 3.7 8.5 - - - +
124K GLY* 3.6 18.9 + - - +
128K PHE* 4.5 2.3 - - - -
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Residues in contact with LEU 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K LEU 3.0 19.8 + - - +
118K GLU 3.9 2.2 - - - +
120K LEU* 1.3 74.2 - - - +
122K THR* 1.3 61.5 + - - +
125K GLY 2.9 12.5 + - - +
127K ARG 4.3 4.7 - - - +
128K PHE* 0.6 158.7 - - + +
132K GLU* 5.9 1.1 - - + -
133K ILE* 4.0 16.8 - - + +
136K MET* 5.2 14.6 - - + -
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Residues in contact with THR 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K GLU 3.0 16.1 + - - -
119K GLU* 3.8 3.4 - - - -
121K LEU* 1.3 77.9 - - - +
123K THR* 1.3 63.5 + - + +
124K GLY 3.0 3.7 + - - -
125K GLY 2.6 21.1 + - - +
128K PHE 2.9 19.1 + - - -
129K THR* 4.2 3.1 - - - +
130K PRO* 3.9 23.0 - - + +
133K ILE* 3.3 8.1 - - - +
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Residues in contact with THR 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119K GLU* 2.8 38.6 + - + +
120K LEU* 3.7 11.8 + - - +
121K LEU 3.5 0.2 - - - -
122K THR* 1.3 76.1 - - + +
124K GLY* 1.2 58.5 + - - +
19L ARG* 5.8 1.6 + - - -
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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