Contacts of the helix formed by residues 107 - 123 (chain N) in PDB entry 5G04
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 CYS 107 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102N ALA* 3.3 39.1 + - - +
108N LEU* 1.3 65.4 + - - +
109N LEU* 3.3 6.0 - - - +
110N LEU* 3.3 22.3 + - - +
111N LEU 3.1 18.0 + - - -
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Residues in contact with LEU 108 (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 ALA* 4.2 10.4 - - + +
107N CYS* 1.3 76.2 - - - +
109N LEU* 1.3 64.8 + - - +
111N LEU* 3.4 6.3 + - - +
112N LEU* 3.3 22.7 + - - +
220N LEU* 6.0 0.7 - - + -
232N TRP* 4.1 32.8 - - + +
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Residues in contact with LEU 109 (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 CYS 4.0 4.9 - - - +
108N LEU* 1.3 79.8 - - - +
110N LEU* 1.3 55.9 + - - +
112N LEU 3.5 0.3 + - - -
113N ASP* 2.9 28.8 + - - +
232N TRP 5.2 3.9 - - - +
235N GLN* 3.5 29.6 - - - +
239N GLN* 3.0 19.2 + - - +
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Residues in contact with LEU 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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101N SER* 5.5 1.1 - - - -
102N ALA 5.8 0.4 - - - +
107N CYS* 3.3 21.7 + - - +
108N LEU 3.3 0.6 - - - -
109N LEU* 1.3 76.6 - - - +
111N LEU* 1.3 58.4 + - - +
113N ASP* 3.8 6.7 - - - +
114N ALA* 3.0 30.3 + - - +
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Residues in contact with LEU 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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101N SER* 3.9 27.7 - - - -
102N ALA* 4.0 9.9 - - + +
107N CYS 3.1 12.7 + - - +
108N LEU* 3.6 10.3 - - - +
109N LEU 3.3 0.2 - - - -
110N LEU* 1.3 74.4 - - - +
112N LEU* 1.3 61.4 + - - +
114N ALA* 3.4 5.2 + - - +
115N PHE* 3.1 25.1 + - - +
172N MET* 6.1 0.9 - - - +
176N LEU* 5.6 6.2 - - + +
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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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108N LEU 3.3 11.6 + - - +
111N LEU* 1.3 78.5 - - - +
113N ASP* 1.3 57.2 + - - +
115N PHE* 3.7 5.4 + - - +
116N GLY* 3.1 26.3 + - - -
176N LEU* 5.3 11.6 - - + +
236N ALA* 6.3 1.1 - - - -
239N GLN* 3.7 28.9 - - + +
240N PHE* 5.4 15.3 - - + -
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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 LEU 2.9 21.9 + - - +
110N LEU* 3.8 7.0 - - - +
112N LEU* 1.3 73.9 - - - +
114N ALA* 1.3 59.9 + - - +
116N GLY* 5.3 0.2 - - - -
117N LEU* 2.9 34.3 + - - +
239N GLN* 3.6 10.0 - - - +
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Residues in contact with ALA 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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97N GLN* 4.1 31.4 - - + +
110N LEU 3.0 18.7 + - - +
111N LEU* 3.4 5.6 + - - +
113N ASP* 1.3 73.3 - - - +
115N PHE* 1.3 58.4 + - - +
117N LEU* 3.9 4.4 - - - +
118N LEU* 3.0 30.0 + - - +
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Residues in contact with PHE 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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97N GLN* 6.1 0.7 - - - -
111N LEU 3.1 17.0 + - - +
112N LEU 3.9 2.2 - - - +
114N ALA* 1.3 73.6 - - - +
116N GLY* 1.3 64.0 + - - +
118N LEU* 3.4 6.7 + - - +
119N GLU* 3.2 23.2 + - - +
172N MET* 5.4 10.3 - - + -
176N LEU* 3.8 29.8 - - + -
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Residues in contact with GLY 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 LEU 3.1 16.4 + - - -
113N ASP* 4.0 0.4 - - - -
115N PHE* 1.3 76.2 - - - +
117N LEU* 1.3 56.6 + - - +
119N GLU* 3.6 4.3 + - - +
120N SER* 2.9 33.7 + - - -
176N LEU* 5.6 0.4 - - - +
243N LEU* 5.5 16.6 - - - -
246N VAL* 5.1 2.6 - - - +
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Residues in contact with LEU 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 21.3 + - - +
114N ALA* 3.9 4.7 - - - +
116N GLY* 1.3 73.5 - - - +
118N LEU* 1.3 57.1 + - - +
120N SER* 4.0 4.9 - - - -
121N ARG* 2.8 36.4 + - - +
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Residues in contact with LEU 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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91N PHE* 5.0 9.6 - - + -
93N ASN* 5.1 8.1 - - + +
94N ALA* 4.8 21.1 - - + +
97N GLN* 5.6 3.1 - - + -
114N ALA 3.0 18.1 + - - +
115N PHE* 3.5 8.1 - - - +
117N LEU* 1.3 70.8 - - - +
119N GLU* 1.3 55.9 + - - +
121N ARG* 3.0 6.4 + - - +
122N LEU* 2.7 37.5 + - - +
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Residues in contact with GLU 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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91N PHE* 5.0 9.8 - - + -
115N PHE 3.2 13.3 + - - +
116N GLY* 4.1 4.7 - - - +
118N LEU* 1.3 77.1 - - - +
120N SER* 1.3 51.6 + - - +
122N LEU* 3.1 10.9 - - - +
123N ASP* 2.8 33.1 + - - +
243N LEU* 5.5 8.1 - - + -
246N VAL* 4.3 14.6 - - + +
247N LEU* 5.6 6.3 - - + -
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Residues in contact with SER 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 GLY 2.9 22.2 + - - -
117N LEU* 4.0 5.4 - - - -
119N GLU* 1.3 74.9 - - - +
121N ARG* 1.3 53.5 + - - +
123N ASP* 3.4 7.5 + - - +
124N PRO* 2.7 33.6 - - - +
246N VAL* 4.0 22.8 - - - +
249N ARG* 4.6 6.6 + - - +
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Residues in contact with ARG 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 LEU 2.8 21.6 + - - +
118N LEU* 3.8 2.9 - - - +
120N SER* 1.3 71.1 - - - +
122N LEU* 1.3 56.6 + - - +
123N ASP 3.4 0.5 + - - -
124N PRO* 3.4 11.3 - - - +
125N TYR* 2.8 35.5 + - + -
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Residues in contact with LEU 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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87N ILE* 4.8 4.8 - - + +
91N PHE* 4.3 33.4 - - + -
118N LEU 2.7 13.8 + - - +
119N GLU* 3.1 18.2 - - - +
121N ARG* 1.3 77.2 - - - +
123N ASP* 1.3 58.6 + - - +
125N TYR* 3.3 15.5 + - - +
126N LEU* 3.2 19.8 - - - +
161N LEU* 6.2 1.6 - - + -
250N LEU* 5.4 0.2 - - - +
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Residues in contact with ASP 123 (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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119N GLU 2.8 12.2 + - - +
120N SER* 3.5 7.9 - - - +
121N ARG 3.2 0.4 - - - -
122N LEU* 1.3 72.2 - - - +
124N PRO* 1.4 66.4 - - + +
125N TYR 3.1 5.2 + - - -
126N LEU* 3.1 6.4 - - - +
127N ARG* 2.7 25.3 + - - +
246N VAL* 4.7 7.6 - - + -
249N ARG* 4.0 13.9 - - - +
250N LEU* 3.7 36.4 - - + +
251N SER* 5.6 1.6 - - - +
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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