Contacts of the helix formed by residues 109 - 122 (chain N) in PDB entry 5GAH
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 PRO 109 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107N GLY 4.6 1.6 - - - +
108N VAL* 1.3 90.9 - - + +
110N GLU* 1.3 66.9 + - - +
111N GLU* 3.4 3.4 - - + +
112N LEU* 3.3 24.8 + - + +
113N ALA* 3.1 17.2 + - - +
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Residues in contact with GLU 110 (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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31N PHE* 3.9 29.0 - - + -
108N VAL 3.7 2.4 + - - -
109N PRO* 1.3 68.7 - - - +
111N GLU* 1.3 68.8 - - - +
113N ALA* 2.8 13.9 + - - +
114N ARG* 2.9 48.9 + - + +
130N PHE* 3.4 12.7 - - + -
132N THR* 4.1 7.2 + - - -
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Residues in contact with GLU 111 (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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109N PRO* 3.4 3.1 - - + -
110N GLU* 1.3 79.6 - - - +
112N LEU* 1.3 64.7 + - - +
114N ARG* 3.2 14.9 + - - +
115N GLU* 3.0 23.9 + - + +
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Residues in contact with LEU 112 (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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56N ALA* 3.6 21.8 - - + +
57N VAL* 4.4 28.3 - - + +
108N VAL* 4.5 17.3 - - + -
109N PRO* 3.3 24.0 + - + +
110N GLU 3.2 0.2 - - - -
111N GLU* 1.3 79.3 - - - +
113N ALA* 1.3 58.1 + - - +
115N GLU* 3.2 12.0 + - + +
116N ALA* 2.9 27.3 + - + +
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Residues in contact with ALA 113 (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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31N PHE* 3.9 28.3 - - + -
57N VAL* 6.1 0.2 - - - -
105N MET* 4.2 10.5 - - - -
108N VAL* 4.1 9.6 - - + -
109N PRO 3.1 11.6 + - - +
110N GLU 2.8 15.2 + - - +
112N LEU* 1.3 69.0 - - - +
114N ARG* 1.3 65.6 + - - +
115N GLU 3.0 1.3 - - - -
116N ALA* 3.4 7.2 + - - +
117N PHE* 2.9 29.2 + - + +
130N PHE* 4.2 10.1 - - + -
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Residues in contact with ARG 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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110N GLU* 2.9 50.9 + - + +
111N GLU* 3.6 12.3 - - - +
113N ALA* 1.3 76.1 - - - +
115N GLU* 1.3 64.3 + - - +
117N PHE* 3.3 2.1 + - - +
118N LYS* 3.0 22.5 + - - +
130N PHE* 3.3 48.9 + - + +
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Residues in contact with GLU 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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111N GLU* 3.0 13.9 + - + +
112N LEU* 3.2 17.7 - - + +
114N ARG* 1.3 77.0 - - - +
116N ALA* 1.3 59.7 + - - +
118N LYS* 2.8 40.7 + - - +
119N LEU* 3.0 35.9 + - + +
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Residues in contact with ALA 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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53N MET* 3.7 15.6 - - + +
56N ALA* 3.5 32.7 - - + +
57N VAL* 4.5 13.7 - - + -
105N MET* 4.6 5.6 - - + -
112N LEU* 2.9 18.3 + - - +
113N ALA* 3.4 7.8 + - - +
115N GLU* 1.3 73.5 - - - +
117N PHE* 1.3 59.1 + - - +
119N LEU* 3.4 5.1 + - - +
120N ALA* 2.9 27.5 + - - +
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Residues in contact with PHE 117 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31N PHE* 4.4 2.7 - - + -
32N GLY* 3.2 13.7 - - - -
33N LEU* 3.2 51.9 - - + +
53N MET* 3.7 18.6 - - + -
103N TYR* 3.9 17.0 - - + -
105N MET* 3.4 41.3 - - + -
113N ALA 2.9 15.2 + - - +
114N ARG 3.8 4.0 - - - +
116N ALA* 1.3 77.6 - - - +
118N LYS* 1.3 65.7 + - - +
120N ALA* 3.7 5.9 - - + +
121N ALA* 2.9 25.3 + - - +
130N PHE* 3.5 31.4 - + + -
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Residues in contact with LYS 118 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1031A G 4.4 17.2 + - - -
2468A A 5.8 4.4 + - - +
114N ARG 3.0 12.5 + - - +
115N GLU* 2.8 27.5 + - - +
117N PHE* 1.3 76.1 - - - +
119N LEU* 1.3 67.5 + - + +
121N ALA* 3.1 7.2 + - - +
122N ALA* 3.0 22.2 + - - +
8f LYS* 4.8 13.7 - - - +
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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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2467A C 4.7 5.0 + - - +
2468A A 3.9 33.7 - - - +
2469A A 5.1 9.6 - - - +
52N ALA* 3.7 21.3 - - + +
56N ALA* 4.2 23.8 - - + -
115N GLU* 3.0 33.4 + - + +
116N ALA* 3.7 7.2 - - - +
118N LYS* 1.3 84.0 - - + +
120N ALA* 1.3 59.5 + - - +
122N ALA* 3.7 16.2 - - - +
123N LYS* 3.9 6.4 - - - +
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Residues in contact with ALA 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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33N LEU* 4.8 6.5 - - + -
49N ALA* 3.7 12.0 - - + +
52N ALA* 4.1 9.8 - - - +
53N MET* 3.5 35.2 - - + -
116N ALA 2.9 18.2 + - - +
117N PHE* 3.7 10.5 - - + +
118N LYS 3.2 0.2 - - - -
119N LEU* 1.3 76.7 - - - +
121N ALA* 1.3 62.1 + - - +
123N LYS* 3.2 21.8 + - - +
124N LEU* 4.1 4.2 + - - +
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Residues in contact with ALA 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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33N LEU* 4.5 6.5 - - + -
117N PHE 2.9 18.0 + - - +
118N LYS* 3.1 6.3 + - - +
120N ALA* 1.3 72.8 - - - +
122N ALA* 1.3 62.1 + - - +
123N LYS 3.0 6.7 + - - -
124N LEU* 3.1 29.1 + - - +
126N ILE 5.3 1.4 - - - +
128N THR* 3.3 29.4 - - + +
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Residues in contact with ALA 122 (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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2466A C 4.8 1.0 - - - +
2467A C 3.3 43.2 - - - +
2484A G 3.5 19.8 + - - -
2485A G 4.4 4.0 + - - +
118N LYS 3.0 12.2 + - - +
119N LEU* 3.7 12.6 - - - +
120N ALA 3.2 0.2 - - - -
121N ALA* 1.3 76.0 - - - +
123N LYS* 1.3 61.5 + - + +
124N LEU 3.3 3.2 + - - +
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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