Contacts of the helix formed by residues 113 - 121 (chain N) in PDB entry 3HOU
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 TYR 113 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110N HIS* 5.5 3.3 - + - +
111N ALA* 2.9 23.3 - - + -
112N LEU* 1.3 91.7 - - - +
114N PRO* 1.3 84.5 - - + +
115N GLN* 4.8 3.1 - - + +
116N GLU* 3.2 14.3 + - + +
117N ALA* 3.0 17.8 + - - +
124N TYR* 3.9 6.7 - - - -
180N TYR* 3.3 47.9 - + + +
181N LEU* 5.8 1.1 - - + -
192N LEU* 3.1 40.1 - - + +
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Residues in contact with PRO 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N TYR* 1.3 92.4 - - + +
115N GLN* 1.3 74.5 + - + +
116N GLU 2.6 2.6 + - - -
117N ALA* 2.7 16.1 + - + +
118N ARG* 3.1 16.5 + - - +
124N TYR* 3.6 23.4 - - + +
174N LEU* 3.8 14.6 - - + -
180N TYR* 5.3 0.2 - - + -
181N LEU* 3.2 37.7 - - + -
192N LEU* 6.2 1.6 - - + -
194N GLU* 3.6 21.5 - - + +
204N ILE* 4.3 6.3 - - + -
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Residues in contact with GLN 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N TYR* 3.6 3.1 - - + -
114N PRO* 1.3 80.8 - - + +
116N GLU* 1.3 60.2 + - - +
118N ARG* 3.3 30.1 + - - +
119N LEU* 3.3 47.5 + - + +
192N LEU 3.5 16.4 - - - +
193N LYS* 3.3 40.9 - - + +
194N GLU* 4.2 7.1 - - + +
784N ASN* 3.7 13.8 + - - -
787N VAL* 3.6 18.7 + - - +
788N ARG* 4.6 6.7 - - - +
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Residues in contact with GLU 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N HIS* 3.4 24.9 + - - -
112N LEU* 4.2 15.2 - - + +
113N TYR* 3.2 15.4 + - + +
114N PRO 2.6 5.1 + - - -
115N GLN* 1.3 73.3 - - - +
117N ALA* 1.3 56.9 + - - +
118N ARG 3.1 1.8 - - - -
119N LEU* 3.4 6.7 + - - +
120N ARG* 2.8 62.4 + - + +
122N LEU* 4.5 0.3 - - - +
53X HIS* 4.0 16.6 + - + +
54X ARG* 2.9 32.6 + - - +
55X ILE* 4.8 12.8 - - + -
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Residues in contact with ALA 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N LEU* 4.0 16.5 - - + +
113N TYR 3.0 10.7 + - - +
114N PRO 2.7 13.4 + - - +
116N GLU* 1.3 73.7 - - - +
118N ARG* 1.3 56.3 + - - +
121N ASN* 2.9 7.8 + - - -
122N LEU* 2.8 40.0 + - + +
124N TYR* 4.0 31.4 - - + +
204N ILE* 4.3 7.2 - - + -
207N GLY* 3.8 1.9 - - - -
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Residues in contact with ARG 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114N PRO* 3.1 6.5 + - - +
115N GLN* 3.3 34.5 + - - +
117N ALA* 1.3 73.5 - - - +
119N LEU* 1.3 68.0 + - + +
121N ASN* 3.0 24.1 + - - -
174N LEU* 3.5 5.9 - - - +
194N GLU* 2.7 44.6 + - - +
202N TYR* 3.5 7.0 + - - -
204N ILE* 3.1 44.0 - - + +
207N GLY* 3.7 13.9 - - - +
209N GLU* 3.4 28.7 - - - -
784N ASN* 4.4 2.2 - - - +
788N ARG* 3.4 24.9 - - - +
965N LYS* 3.7 4.4 + - - -
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Residues in contact with LEU 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N GLN* 3.3 46.7 + - + +
116N GLU* 3.8 5.6 - - - +
118N ARG* 1.3 79.3 - - + +
120N ARG* 1.3 64.6 + - + +
193N LYS* 5.5 5.4 - - + +
787N VAL* 4.2 15.0 - - + +
789N MET* 3.4 34.5 - - + +
951N GLN* 5.5 1.8 - - - +
953N LEU* 3.6 25.2 - - + +
963N PHE* 3.5 9.9 - - - -
965N LYS* 3.4 22.0 + - - +
55X ILE* 5.3 13.0 - - + -
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Residues in contact with ARG 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N VAL* 4.7 1.2 - - - +
104N GLU* 3.4 10.7 + - - -
116N GLU* 2.8 45.5 + - + +
119N LEU* 1.3 76.0 - - + +
121N ASN* 1.3 69.0 + - - +
122N LEU* 3.8 28.2 - - + +
955N THR* 3.1 31.9 - - + +
956N THR* 2.9 29.4 + - - +
957N ASN* 3.4 15.9 - - - +
958N GLN* 3.5 10.5 - - - +
963N PHE* 3.3 18.2 - - - -
54X ARG* 2.5 51.9 - - - +
55X ILE* 4.9 6.5 - - + -
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Residues in contact with ASN 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N ALA 2.9 7.7 + - - -
118N ARG 3.0 15.2 + - - -
120N ARG* 1.3 80.9 - - - +
122N LEU* 1.3 65.8 + - - +
206N ASN* 3.8 18.8 + - - +
207N GLY* 3.1 25.2 - - - -
208N SER 4.5 0.4 - - - +
860N MET* 3.6 18.4 - - - +
862N GLN* 5.5 2.0 - - - +
963N PHE* 3.1 27.4 - - + -
965N LYS* 3.6 15.4 - - - +
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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