Contacts of the helix formed by residues 108 - 120 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106M LYS 3.8 1.6 + - - -
107M PRO* 1.3 74.3 - - - +
109M GLY* 1.3 69.8 + - - +
111M ILE* 3.1 9.8 - - - +
112M ALA* 3.0 19.0 + - - -
203M TRP* 5.1 2.8 - - - +
207M GLU* 4.9 0.7 - - - -
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Residues in contact with GLY 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M GLY* 1.3 78.4 - - - +
110M LYS* 1.3 60.2 + - - -
112M ALA* 3.5 0.7 - - - +
113M ASP* 2.9 29.1 + - - +
207M GLU* 3.4 9.2 - - - -
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Residues in contact with LYS 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M GLY* 1.3 69.4 - - - -
111M ILE* 1.3 66.2 + - - +
113M ASP* 2.8 35.5 + - - +
114M LEU* 2.8 34.1 + - - +
207M GLU* 2.7 12.1 + - - +
210M LEU* 4.0 7.9 - - + -
211M GLN* 2.9 34.5 - - - +
214M LEU* 4.3 15.5 - - + -
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Residues in contact with ILE 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M PRO* 3.8 12.8 - - + -
108M GLY 3.1 12.8 - - - +
110M LYS* 1.3 72.7 - - - +
112M ALA* 1.3 60.1 + - - +
114M LEU* 4.2 0.3 - - - -
115M ILE* 3.0 44.8 + - + +
144M LEU* 4.0 19.7 - - + -
153M LEU* 4.5 5.4 - - + -
172M LEU* 4.8 2.7 - - + -
203M TRP* 3.9 23.3 - - + +
206M VAL* 3.8 30.3 - - + -
207M GLU* 2.6 33.4 + - + +
210M LEU* 3.6 19.9 - - + +
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Residues in contact with ALA 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M PRO* 2.9 40.8 - - + +
108M GLY* 3.0 21.7 + - - +
109M GLY 3.5 1.3 - - - +
111M ILE* 1.3 74.8 - - - +
113M ASP* 1.3 68.1 + - - +
115M ILE* 3.3 3.9 + - - +
116M ASN* 3.0 34.6 + - - +
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Residues in contact with ASP 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M GLY 2.9 22.0 + - - +
110M LYS* 2.8 43.4 + - - +
112M ALA* 1.3 77.3 - - - +
114M LEU* 1.3 64.1 + - + +
116M ASN* 3.1 14.1 + - - +
117M LYS* 3.0 19.4 + - - +
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Residues in contact with LEU 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M LYS* 2.8 37.3 + - - +
111M ILE 4.4 1.3 - - - +
113M ASP* 1.3 72.5 - - + +
115M ILE* 1.3 68.4 + - - +
117M LYS* 3.0 23.6 + - + +
118M PHE* 3.1 40.9 + - + +
146M TYR* 4.5 7.2 - - + -
153M LEU* 3.7 17.5 - - + -
210M LEU* 3.9 24.5 - - + -
214M LEU* 3.9 25.1 - - + -
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Residues in contact with ILE 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M PRO* 4.0 22.0 - - + -
111M ILE* 3.0 45.7 + - + +
112M ALA* 3.7 5.4 - - - +
114M LEU* 1.3 75.1 - - - +
116M ASN* 1.3 65.7 + - - +
119M PHE* 2.9 31.7 + - + +
120M GLY 3.5 0.2 + - - -
121M SER 3.8 10.3 - - - +
122M PHE* 4.1 10.5 - - + -
125M PHE* 3.5 59.2 - - + -
144M LEU* 5.4 0.2 - - + -
153M LEU* 3.8 9.2 - - + +
203M TRP* 4.3 4.3 - - + -
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Residues in contact with ASN 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112M ALA* 3.0 24.0 + - - +
113M ASP* 3.1 13.1 + - - +
115M ILE* 1.3 77.6 - - - +
117M LYS* 1.3 58.5 + - - +
120M GLY* 2.9 36.9 + - - +
121M SER* 3.7 17.5 - - - -
122M PHE* 4.0 6.6 + - - +
12P SER 3.5 5.0 + - - +
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Residues in contact with LYS 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M ASP 3.0 11.9 + - - +
114M LEU* 3.0 20.2 + - + +
116M ASN* 1.3 76.9 - - - +
118M PHE* 1.3 87.5 + - + +
12P SER* 3.2 19.6 + - - +
14P THR* 3.3 32.9 + - - +
16P LYS* 5.1 10.7 - - - +
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Residues in contact with PHE 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M LEU* 3.1 47.0 + - + -
117M LYS* 1.3 102.5 - - + +
119M PHE* 1.3 75.6 + - + +
146M TYR* 5.7 0.2 - + - -
151M GLU 3.9 6.3 - - - -
152M GLN* 3.5 36.6 - - + -
153M LEU* 3.7 30.1 - - + +
13P VAL* 3.6 10.2 - - - +
14P THR* 3.1 26.2 - - - +
15P THR* 4.5 0.9 - - - -
16P LYS* 4.1 13.2 - - + -
65P ARG* 2.9 33.5 + - - +
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Residues in contact with PHE 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M ILE* 2.9 22.9 + - - +
118M PHE* 1.3 89.2 - - + +
120M GLY* 1.3 58.1 + - - +
121M SER 3.2 9.6 + - - +
124M LYS* 3.4 22.2 - - + +
125M PHE* 3.9 46.9 - + + +
128M GLU* 3.9 7.6 - - + -
144M LEU* 4.6 1.8 - - + -
153M LEU* 4.0 31.6 - - + -
155M ILE* 3.7 29.2 - - + -
13P VAL* 3.6 12.6 - - - +
65P ARG* 3.3 45.5 - - + +
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Residues in contact with GLY 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M ILE 3.5 0.4 + - - -
116M ASN* 2.9 29.2 + - - +
118M PHE 3.7 0.8 - - - -
119M PHE* 1.3 77.2 - - - +
121M SER* 1.3 61.7 + - - +
12P SER 3.6 22.1 + - - -
13P VAL* 3.8 8.8 - - - +
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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