Contacts of the helix formed by residues 105 - 119 (chain F) in PDB entry 1GN2
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 SER 105 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F ILE* 4.7 0.4 - - - -
100F ALA* 3.6 15.1 + - - +
103F PHE* 2.9 4.4 + - - +
104F GLY* 1.3 79.7 - - - +
106F PHE* 1.3 65.3 + - - +
107F ASP* 3.2 8.2 + - - +
108F LYS* 2.8 38.2 + - - +
109F PHE* 3.0 13.1 + - - +
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Residues in contact with PHE 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ASP 4.4 7.4 - - - -
90F LYS* 3.9 37.7 - - + +
91F PRO* 3.1 40.8 - - + -
96F ALA 6.1 0.2 - - - +
99F ILE* 4.1 17.5 - - + +
100F ALA* 4.5 5.2 - - + +
105F SER* 1.3 72.4 - - - +
107F ASP* 1.3 65.5 + - - +
109F PHE* 3.6 15.4 - + - +
110F ARG* 3.1 58.5 + - - +
182F TRP* 4.6 2.5 - + - -
187F TRP* 3.5 24.9 - + - -
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Residues in contact with ASP 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LYS* 4.4 12.3 + - - -
105F SER* 3.0 8.2 + - - +
106F PHE* 1.3 87.6 - - - +
108F LYS* 1.3 58.1 + - + +
110F ARG* 3.5 28.5 + - - +
111F ALA* 3.1 24.6 + - - +
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Residues in contact with LYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F PHE 3.3 22.4 - - - +
104F GLY* 4.8 4.9 - - - -
105F SER* 2.8 23.1 + - - +
107F ASP* 1.3 76.1 - - + +
109F PHE* 1.3 63.9 + - - +
111F ALA* 3.2 8.1 + - + +
112F GLN* 3.2 21.3 + - - +
51H ARG* 4.1 37.3 + - + +
52H ALA* 4.4 15.8 + - - +
54H GLU* 5.5 6.7 - - + -
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Residues in contact with PHE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ILE* 4.0 14.4 - - + -
103F PHE* 3.6 47.2 - + + +
105F SER 3.0 8.6 + - - +
106F PHE* 3.6 28.0 - + - +
108F LYS* 1.3 75.5 - - - +
110F ARG* 1.3 75.0 + - + +
112F GLN* 3.1 5.3 + - - +
113F PHE* 2.9 46.9 + + - +
128F LEU* 3.8 29.6 - - + -
139F ILE* 3.8 13.6 - - + +
157F LEU* 4.4 12.3 - - + -
182F TRP* 3.6 28.9 - + - -
187F TRP* 4.3 5.4 - + - -
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Residues in contact with ARG 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LYS* 5.4 7.3 - - - +
106F PHE* 3.1 41.1 + - - +
107F ASP* 3.7 21.6 + - - +
109F PHE* 1.3 94.5 - - + +
111F ALA* 1.3 61.2 + - - +
113F PHE* 4.1 1.3 - - - +
114F HIS* 3.3 21.7 + - + +
179F LYS 5.3 0.4 + - - -
182F TRP* 3.3 63.8 - - + +
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ASP 3.1 13.7 + - - +
108F LYS* 3.6 11.0 - - + +
109F PHE 3.1 0.8 - - - -
110F ARG* 1.3 75.2 - - - +
112F GLN* 1.3 66.6 + - - +
114F HIS* 3.5 6.9 + - - +
115F ALA* 3.1 21.8 + - - +
56H HIS* 4.0 12.1 - - + +
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Residues in contact with GLN 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F PHE* 3.8 5.6 - - - -
108F LYS 3.2 7.2 + - - +
109F PHE 3.1 7.7 + - - +
111F ALA* 1.3 79.1 - - - +
113F PHE* 1.3 66.9 + - - +
115F ALA* 2.9 5.9 + - - +
116F ALA* 2.9 20.6 + - - +
139F ILE* 3.5 27.1 + - + +
47H LEU* 4.1 17.5 - - - +
51H ARG* 2.7 40.4 + - - +
56H HIS* 3.6 26.4 + - + +
59H ILE* 4.1 9.1 - - + +
63H GLU* 3.5 19.4 + - - +
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Residues in contact with PHE 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F PHE* 2.9 33.4 + + + +
110F ARG* 4.1 4.5 - - - +
112F GLN* 1.3 76.3 - - - +
114F HIS* 1.3 63.0 + - - +
116F ALA* 3.4 7.7 + - - +
117F ALA* 3.0 20.4 + - - +
126F ALA* 3.6 25.7 - - + +
127F ALA 4.0 2.9 - - - -
128F LEU* 3.9 27.6 - - + -
139F ILE* 3.9 19.2 - - + +
157F LEU* 4.2 20.9 - - + -
159F LEU* 3.8 34.5 - - + -
181F PHE* 4.2 8.1 - + - -
182F TRP* 3.7 22.9 - + + -
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Residues in contact with HIS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ARG 3.3 17.0 + - - +
111F ALA* 3.7 6.8 + - - +
112F GLN 3.1 0.2 - - - -
113F PHE* 1.3 82.1 - - - +
115F ALA* 1.3 57.7 + - - +
117F ALA* 3.4 3.2 + - - +
118F THR* 2.7 51.1 + - + +
159F LEU* 6.1 1.1 - - - -
175F VAL* 3.8 27.2 + - + -
178F ALA* 3.7 30.7 - - + -
179F LYS* 4.0 29.7 + - + -
182F TRP* 5.0 8.5 - - - +
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F ALA 3.1 13.7 + - - +
112F GLN 2.9 10.0 + - - +
114F HIS* 1.3 80.5 + - - +
116F ALA* 1.3 60.3 + - - +
118F THR* 3.4 5.5 + - - -
119F THR* 3.1 33.9 + - + +
56H HIS* 3.9 31.6 - - + -
59H ILE* 4.2 11.4 - - + -
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Residues in contact with ALA 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F GLN 2.9 11.7 + - - +
113F PHE 3.6 7.4 - - - +
115F ALA* 1.3 76.6 - - - +
117F ALA* 1.3 61.2 + - - +
119F THR* 3.8 0.2 + - - -
120F VAL* 3.6 2.9 - - - +
126F ALA* 4.3 8.8 - - + +
139F ILE* 4.1 22.9 - - + -
140F PHE 4.8 0.2 - - - +
141F GLN* 3.0 46.0 + - + +
59H ILE* 4.1 8.0 - - + +
63H GLU* 4.2 11.0 - - - +
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Residues in contact with ALA 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F PHE 3.0 12.7 + - - +
114F HIS* 4.1 3.4 - - - +
115F ALA 3.3 0.2 - - - -
116F ALA* 1.3 78.8 - - - +
118F THR* 1.3 63.7 + - + +
119F THR 3.6 0.9 + - - -
120F VAL* 3.7 10.5 + - - +
126F ALA* 3.4 24.0 - - + +
159F LEU* 4.1 13.0 - - + -
161F MET* 3.2 45.0 - - + +
174F LYS* 4.9 1.6 - - - -
178F ALA* 5.1 1.1 - - + -
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Residues in contact with THR 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F HIS* 2.7 37.7 + - - +
115F ALA* 3.5 7.4 + - - -
117F ALA* 1.3 77.1 - - - +
119F THR* 1.3 61.3 + - - +
120F VAL 3.6 0.7 - - - -
161F MET* 4.8 1.1 - - + -
174F LYS* 3.0 33.9 + - + +
175F VAL* 4.1 26.7 - - + +
178F ALA* 3.8 26.5 - - + -
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Residues in contact with THR 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ALA* 3.1 19.7 + - + +
117F ALA 3.4 0.6 - - - -
118F THR* 1.3 82.8 - - - +
120F VAL* 1.3 67.1 + - - +
121F GLN* 3.3 6.6 + - - +
141F GLN* 2.7 25.6 + - - -
174F LYS* 5.2 0.2 - - - -
59H ILE* 3.5 25.5 - - + +
60H LEU* 3.7 18.3 + - - +
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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