Contacts of the helix formed by residues 108 - 120 (chain N) in PDB entry 1P7G
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 108 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106N LYS 4.1 0.2 + - - -
107N PRO* 1.3 74.7 - - - +
109N GLY* 1.3 71.2 + - - +
111N ILE* 3.0 11.3 - - - +
112N ALA* 2.9 20.5 + - - -
203N TRP* 5.2 2.4 - - - +
207N GLU* 4.8 1.6 - - - -
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Residues in contact with GLY 109 (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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108N GLY* 1.3 78.8 - - - +
110N LYS* 1.3 61.6 - - - -
112N ALA* 3.2 6.6 + - - +
113N ASP* 3.2 20.3 + - - +
207N GLU* 3.2 11.7 - - - -
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Residues in contact with LYS 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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31I GLU* 4.8 16.5 + - - +
32I PRO* 6.6 0.2 - - - -
109N GLY* 1.3 70.3 - - - -
111N ILE* 1.3 63.8 + - - +
113N ASP* 2.6 33.7 + - - +
114N LEU* 2.9 37.4 + - + +
207N GLU* 2.8 19.7 + - - +
210N LEU* 3.8 10.5 - - + -
211N GLN* 4.2 19.3 - - - +
214N LEU* 4.5 13.9 - - + -
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Residues in contact with ILE 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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107N PRO* 4.0 13.7 - - + -
108N GLY 3.0 18.4 - - - +
110N LYS* 1.3 72.0 - - - +
112N ALA* 1.3 56.7 + - - +
114N LEU 3.9 0.6 - - - +
115N ILE* 2.9 50.8 + - + +
144N LEU* 4.2 9.9 - - + -
153N LEU* 4.1 19.1 - - + -
172N LEU* 4.5 6.1 - - + -
203N TRP* 4.5 8.7 - - + +
206N VAL* 3.9 26.2 - - + -
207N GLU* 2.8 39.3 + - + +
210N LEU* 3.3 22.1 - - + +
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Residues in contact with ALA 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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107N PRO* 3.3 34.5 - - + +
108N GLY* 2.9 26.9 + - - +
109N GLY 3.5 1.1 - - - +
111N ILE* 1.3 80.0 - - - +
113N ASP* 1.3 65.4 + - - +
115N ILE* 3.4 3.4 + - - +
116N ASN* 3.1 34.2 + - - +
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Residues in contact with ASP 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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109N GLY 3.4 15.3 - - - +
110N LYS* 2.6 41.8 + - - +
112N ALA* 1.3 79.8 - - - +
114N LEU* 1.3 59.9 + - + +
116N ASN* 3.3 11.4 + - - +
117N LYS* 2.9 26.6 + - - +
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Residues in contact with LEU 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 LYS* 2.9 26.2 + - + +
111N ILE 4.0 1.3 - - - +
113N ASP* 1.3 77.3 - - + +
115N ILE* 1.3 66.7 + - - +
117N LYS* 4.0 22.4 - - + +
118N PHE* 2.9 38.3 + - + +
146N TYR* 4.7 5.4 - - + -
153N LEU* 3.7 21.8 - - + -
210N LEU* 3.4 37.7 - - + -
214N LEU* 4.4 17.9 - - + -
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Residues in contact with ILE 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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107N PRO* 3.9 23.3 - - + -
111N ILE* 2.9 45.6 + - + +
112N ALA* 3.6 5.2 - - - +
113N ASP 3.3 0.2 - - - -
114N LEU* 1.3 76.4 - - - +
116N ASN* 1.3 60.7 + - - +
119N PHE* 2.9 36.9 + - - +
121N SER 4.0 1.7 - - - +
122N PHE* 4.0 20.2 - - + -
125N PHE* 3.6 55.0 - - + -
144N LEU* 5.0 0.2 - - + -
153N LEU* 4.2 7.2 - - + -
203N TRP* 4.3 5.2 - - + -
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Residues in contact with ASN 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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112N ALA* 3.1 24.7 + - - +
113N ASP* 3.6 11.0 + - - +
115N ILE* 1.3 79.1 - - - +
117N LYS* 1.3 58.5 + - - +
120N GLY* 2.8 38.3 + - - +
121N SER* 3.3 21.0 - - - -
122N PHE* 3.6 8.7 + - - +
12O SER 3.5 4.9 - - - +
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Residues in contact with LYS 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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113N ASP 2.9 14.4 + - - +
114N LEU* 3.1 20.5 + - + +
116N ASN* 1.3 80.2 - - - +
118N PHE* 1.3 97.7 + - + +
151N GLU 4.9 2.0 + - - -
12O SER 3.6 8.3 - - - +
14O THR* 3.1 40.0 + - + +
16O LYS* 4.7 13.9 - - - +
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Residues in contact with PHE 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 LEU* 2.9 41.6 + - + +
117N LYS* 1.3 114.4 - - + +
119N PHE* 1.3 73.3 + - + +
146N TYR* 5.7 0.9 - + - -
151N GLU 3.9 4.9 - - - -
152N GLN* 3.5 35.0 - - + -
153N LEU* 3.6 31.4 - - + +
13O VAL* 3.3 10.4 - - - +
14O THR 3.0 28.7 - - - -
15O THR* 4.6 1.0 - - - +
16O LYS* 3.8 11.2 - - + -
65O ARG* 2.8 34.4 + - - +
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Residues in contact with PHE 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 ILE* 2.9 24.6 + - - +
118N PHE* 1.3 89.8 - - + +
120N GLY* 1.3 58.3 + - - +
121N SER 3.3 6.6 + - - +
124N LYS* 3.3 23.0 - - + +
125N PHE* 3.9 40.8 - + + +
128N GLU* 3.5 15.9 - - + -
144N LEU* 4.5 4.5 - - + -
153N LEU* 4.1 29.6 - - + -
155N ILE* 3.6 26.2 - - + -
13O VAL* 3.8 12.8 - - - +
65O ARG* 3.4 45.1 - - + +
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Residues in contact with GLY 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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116N ASN* 2.8 32.8 + - - +
118N PHE 3.8 0.6 - - - -
119N PHE* 1.3 76.9 - - - +
121N SER* 1.3 60.1 + - - +
12O SER* 3.6 17.9 + - - -
13O VAL* 4.1 6.7 - - - +
65O ARG 5.6 0.2 - - - -
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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