Contacts of the helix formed by residues 93 - 104 (chain E) 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 GLY 93 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E THR* 1.3 82.1 - - - +
94E GLU* 1.3 57.4 - - - -
96E ALA* 3.0 19.1 + - - +
97E ALA* 3.0 15.2 + - - +
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Residues in contact with GLU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E THR 3.6 0.6 + - - -
93E GLY* 1.3 67.0 - - - -
95E LEU* 1.3 59.4 + - - +
97E ALA* 3.4 13.5 + - - +
98E ALA* 2.9 30.9 + - - +
194E TYR* 4.2 18.4 + - + -
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Residues in contact with LEU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PRO* 4.2 6.5 - - + -
92E THR 3.7 2.6 + - - +
93E GLY 3.2 0.6 - - - -
94E GLU* 1.3 78.2 - - - +
96E ALA* 1.3 56.7 + - - +
98E ALA* 3.1 5.2 + - + +
99E ILE* 2.9 39.6 + - + +
128E LEU* 5.7 0.9 - - + -
137E LEU* 5.0 4.5 - - + -
156E LEU* 5.5 2.0 - - + -
187E TRP* 4.1 14.6 - - + -
190E VAL* 3.4 21.1 - - + -
191E GLN* 3.1 55.8 - - + +
194E TYR* 3.6 38.8 - - + -
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Residues in contact with ALA 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PRO* 3.6 39.0 - - + +
92E THR* 3.9 4.4 + - - +
93E GLY 3.0 11.5 + - - +
95E LEU* 1.3 75.7 - - - +
97E ALA* 1.3 67.9 + - - +
99E ILE* 3.4 4.9 + - - +
100E ALA* 3.0 25.3 + - - +
106E PHE* 6.1 0.4 - - + +
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Residues in contact with ALA 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY 3.0 12.8 + - - +
94E GLU* 4.0 19.7 - - - +
96E ALA* 1.3 77.6 - - - +
98E ALA* 1.3 64.1 + - - +
100E ALA* 4.1 4.7 - - - +
101E ASP* 3.0 26.0 + - - +
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Residues in contact with ALA 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLU* 2.9 17.0 + - - +
95E LEU* 3.3 9.6 - - + +
97E ALA* 1.3 78.5 - - - +
99E ILE* 1.3 58.6 + - - +
101E ASP* 2.9 8.9 + - - +
102E ALA* 2.8 31.2 + - - +
137E LEU* 4.7 9.4 - - + -
194E TYR* 3.4 33.0 - - + +
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Residues in contact with ILE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PRO* 3.8 25.4 - - + -
95E LEU* 2.9 27.1 + - + +
96E ALA* 3.8 4.9 - - - +
98E ALA* 1.3 77.3 - - - +
100E ALA* 1.3 58.1 + - - +
103E PHE* 2.8 35.0 + - + +
106E PHE* 4.1 21.5 - - + -
109E PHE* 4.0 34.8 - - + -
128E LEU* 5.0 5.6 - - + -
137E LEU* 3.9 24.2 - - + +
187E TRP* 4.1 17.0 - - + -
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Residues in contact with ALA 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ALA 3.0 17.0 + - - +
97E ALA* 4.1 4.9 - - - +
99E ILE* 1.3 77.4 - - - +
101E ASP* 1.3 60.9 + - - +
104E GLY* 2.9 33.3 + - - +
105E SER* 3.9 23.3 - - - +
106E PHE* 4.5 4.3 - - + +
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Residues in contact with ASP 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ALA 3.0 19.3 + - - +
98E ALA* 2.9 7.1 + - - +
100E ALA* 1.3 82.7 - - - +
102E ALA* 1.3 63.5 + - - +
104E GLY* 4.4 2.1 + - - -
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Residues in contact with ALA 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ALA 2.8 14.3 + - - +
101E ASP* 1.3 83.8 - - - +
103E PHE* 1.3 68.8 + - + +
104E GLY 3.5 0.4 - - - -
136E LYS* 6.4 0.2 - - + -
137E LEU* 4.0 34.0 - - + +
48G GLU* 5.6 0.3 - - - +
51G ARG* 3.6 18.2 + - - -
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Residues in contact with PHE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ILE* 2.8 23.3 + - + +
102E ALA* 1.3 80.5 - - + +
104E GLY* 1.3 56.2 + - - +
105E SER 2.9 10.6 + - - +
108E LYS* 3.3 20.1 - - - +
109E PHE* 3.6 40.6 - + + -
112E GLN* 3.8 8.1 - - - -
128E LEU* 3.9 17.5 - - + -
137E LEU* 3.9 34.5 - - + -
138E LEU* 4.2 1.6 - - + -
139E ILE* 3.5 38.8 - - + -
51G ARG* 3.5 39.5 - - - +
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Residues in contact with GLY 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ALA* 2.9 23.3 + - - +
101E ASP 4.3 2.1 + - - -
102E ALA 3.5 1.8 - - - -
103E PHE* 1.3 74.1 - - - +
105E SER* 1.3 62.3 + - - +
108E LYS* 4.8 8.1 - - - -
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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