Contacts of the helix formed by residues 108 - 120 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106J LYS 4.1 0.4 + - - -
107J PRO* 1.3 74.8 - - - +
109J GLY* 1.3 71.6 + - - +
111J ILE* 2.9 11.9 - - - +
112J ALA* 2.8 19.4 + - - -
203J TRP* 5.0 3.6 + - - +
207J GLU* 4.6 1.1 - - - -
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Residues in contact with GLY 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J GLY* 1.3 76.8 - - - +
110J LYS* 1.3 61.7 + - - -
112J ALA* 3.7 0.9 - - - +
113J ASP* 3.0 24.8 + - - +
207J GLU* 3.8 11.7 - - - -
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Residues in contact with LYS 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G GLU* 4.3 24.2 + - - +
32G PRO* 3.7 24.4 - - - +
109J GLY* 1.3 71.4 - - - -
111J ILE* 1.3 55.7 + - - +
113J ASP* 3.0 12.3 + - + +
114J LEU* 2.6 43.8 + - + +
207J GLU* 3.1 14.1 + - - +
210J LEU* 3.9 11.0 - - + -
211J GLN* 4.1 16.0 + - - +
214J LEU* 3.4 30.0 - - + +
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Residues in contact with ILE 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J PRO* 3.9 12.8 - - + -
108J GLY 2.9 21.3 - - - +
110J LYS* 1.3 76.0 - - - +
112J ALA* 1.3 56.9 - - - +
114J LEU* 4.4 0.4 - - - +
115J ILE* 2.9 51.6 + - + +
144J LEU* 4.1 25.1 - - + -
153J LEU* 4.4 8.3 - - + -
172J LEU* 4.5 5.4 - - + -
203J TRP* 4.1 13.5 - - + +
206J VAL* 3.9 20.0 - - + -
207J GLU* 2.9 36.8 + - + +
210J LEU* 3.4 22.1 - - + +
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Residues in contact with ALA 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J PRO* 3.1 40.3 - - + +
108J GLY* 2.8 25.1 + - - +
109J GLY 3.7 1.6 - - - +
111J ILE* 1.3 77.6 - - - +
113J ASP* 1.3 63.1 + - - +
115J ILE* 3.7 3.0 - - - +
116J ASN* 2.9 33.8 + - - +
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Residues in contact with ASP 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J GLY 3.0 20.0 + - - +
110J LYS* 3.0 14.9 + - + +
112J ALA* 1.3 77.5 - - - +
114J LEU* 1.3 61.3 + - + +
116J ASN* 3.2 13.2 + - - +
117J LYS* 3.0 26.4 + - - +
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Residues in contact with LEU 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J LYS* 2.6 24.6 + - + +
111J ILE 4.1 1.8 - - - +
113J ASP* 1.3 72.2 - - + +
115J ILE* 1.3 64.9 + - - +
117J LYS* 3.3 29.6 + - + +
118J PHE* 3.0 39.4 + - + +
146J TYR* 5.3 5.2 - - + -
153J LEU* 3.5 23.8 - - + +
210J LEU* 3.9 33.4 - - + -
214J LEU* 4.3 16.8 - - + -
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Residues in contact with ILE 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J PRO* 4.0 12.3 - - + -
111J ILE* 2.9 46.4 + - + +
112J ALA* 3.7 6.1 - - - +
114J LEU* 1.3 75.7 - - - +
116J ASN* 1.3 59.9 + - - +
119J PHE* 2.8 36.2 + - - +
120J GLY 3.6 0.3 + - - -
121J SER 3.8 8.9 - - - +
122J PHE* 3.8 13.7 - - + +
125J PHE* 3.5 45.8 - - + -
144J LEU* 5.1 0.4 - - + -
153J LEU* 4.0 7.6 - - + -
203J TRP* 4.0 22.7 - - + -
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Residues in contact with ASN 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ALA* 2.9 25.2 + - - +
113J ASP* 3.2 14.9 + - - +
115J ILE* 1.3 78.2 - - - +
117J LYS* 1.3 58.3 + - - +
120J GLY* 2.9 33.7 + - - +
121J SER* 3.4 21.0 - - - +
122J PHE* 3.7 7.6 + - - +
12K SER 3.1 10.7 - - - +
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Residues in contact with LYS 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J ASP 3.0 13.4 + - - +
114J LEU* 3.5 29.9 - - + +
115J ILE 3.2 0.2 - - - -
116J ASN* 1.3 79.9 - - - +
118J PHE* 1.3 76.6 + - + +
151J GLU 5.3 1.6 + - - -
12K SER 3.5 7.3 - - - +
14K THR* 3.1 40.7 + - + +
16K LYS* 3.5 34.5 - - - +
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Residues in contact with PHE 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J LEU* 3.0 37.7 + - + +
117J LYS* 1.3 100.5 - - + +
119J PHE* 1.3 74.2 + - + +
120J GLY 3.5 0.2 - - - -
151J GLU 3.7 8.3 - - - -
152J GLN* 3.4 33.0 - - + -
153J LEU* 3.7 31.6 - - + +
13K VAL* 3.2 10.3 - - - +
14K THR* 3.0 31.1 - - + +
15K THR* 4.0 7.0 - - - -
16K LYS* 3.9 20.9 - - + -
65K ARG* 3.1 31.7 + - - +
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Residues in contact with PHE 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J ILE* 2.8 25.4 + - - +
118J PHE* 1.3 87.6 - - + +
120J GLY* 1.3 56.6 + - - +
121J SER 2.9 10.0 + - - +
124J LYS* 2.8 30.7 - - + +
125J PHE* 3.7 50.5 - + + +
128J GLU* 3.6 9.2 - - + -
144J LEU* 4.3 4.0 - - + -
153J LEU* 4.0 25.6 - - + -
155J ILE* 3.4 33.9 - - + -
13K VAL* 4.0 6.3 - - - +
65K ARG* 3.5 41.0 - - + +
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Residues in contact with GLY 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J ILE 3.6 0.2 + - - -
116J ASN* 2.9 31.0 + - - +
118J PHE 3.5 1.8 - - - -
119J PHE* 1.3 76.1 - - - +
121J SER* 1.3 58.7 + - - -
124J LYS* 5.2 0.2 - - - -
12K SER 3.2 27.0 + - - +
13K VAL* 3.6 11.5 - - - +
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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