Contacts of the helix formed by residues 90 - 101 (chain B) in PDB entry 2GOJ
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 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B HIS* 1.3 76.0 - - - +
91B GLU* 1.3 67.9 + - - -
93B LYS* 3.2 14.4 + - - +
94B GLU* 3.4 12.2 + - - +
188B ASN* 4.0 6.1 - - - -
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLY* 1.3 71.8 - - - -
92B ILE* 1.3 57.5 + - - +
94B GLU* 3.2 27.5 + - - +
95B LYS* 2.9 28.8 + - - +
188B ASN* 3.4 10.3 + - - +
191B LEU* 3.9 16.8 - - + +
192B LYS* 3.8 30.7 - - + +
195B MET* 5.9 2.6 - - - +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PRO* 4.3 3.1 - - + -
89B HIS 3.4 11.7 - - - +
91B GLU* 1.3 70.4 - - - +
93B LYS* 1.3 64.3 + - - +
95B LYS* 4.3 0.2 - - - -
96B ILE* 2.9 48.7 + - + +
125B LEU* 4.1 5.2 - - + -
133B LEU* 4.0 24.5 - - + -
153B ILE* 4.1 20.9 - - + -
184B TRP* 3.7 30.7 - - + +
187B ALA* 4.1 13.0 - - + +
188B ASN* 2.8 28.0 + - - +
191B LEU* 4.1 21.7 - - + +
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLU* 6.1 2.7 - - - -
88B PRO* 3.5 49.1 - - + +
89B HIS* 3.8 5.4 - - - +
90B GLY 3.2 11.7 + - - +
92B ILE* 1.3 83.4 - - - +
94B GLU* 1.3 61.7 + - - +
96B ILE* 3.8 2.9 - - - +
97B GLN* 3.1 50.8 + - + +
103B PHE* 6.4 0.2 - - + -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLY 3.4 7.4 + - - +
91B GLU* 3.2 31.2 + - - +
93B LYS* 1.3 80.2 - - - +
95B LYS* 1.3 57.3 + - - +
97B GLN* 3.4 14.6 + - - +
98B GLU* 3.0 28.4 + - + +
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Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLU 2.9 17.7 + - - +
92B ILE* 3.8 2.9 - - - +
93B LYS 3.3 0.2 - - - -
94B GLU* 1.3 74.2 - - - +
96B ILE* 1.3 60.7 + - - +
98B GLU* 3.3 27.8 + - - +
99B ASP* 2.6 56.0 + - - +
127B LEU* 4.1 7.2 - - - -
131B ASN 2.7 28.7 + - - -
132B LYS* 4.1 0.2 - - - +
133B LEU* 3.4 24.9 - - + -
191B LEU* 4.1 12.6 - - + -
195B MET* 3.5 33.9 - - + -
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PRO* 4.7 6.5 - - + -
92B ILE* 2.9 28.2 + - + +
93B LYS* 3.8 4.3 - - - +
95B LYS* 1.3 74.7 - - - +
97B GLN* 1.3 57.6 + - + +
100B PHE* 2.8 41.7 + - + +
101B GLY 3.5 0.7 + - - -
102B SER 3.9 0.9 - - - +
103B PHE* 3.8 22.9 - - + -
106B PHE* 3.7 41.7 - - + -
125B LEU* 4.7 4.0 - - + -
133B LEU* 3.9 15.7 - - + -
184B TRP* 3.8 31.9 - - + -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LYS* 3.1 51.9 + - + +
94B GLU* 3.5 15.6 - - - +
96B ILE* 1.3 74.7 - - - +
98B GLU* 1.3 58.4 + - - +
101B GLY* 2.9 43.7 + - - +
102B SER* 4.3 9.4 - - - +
103B PHE* 4.8 4.9 - - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLU* 3.0 16.2 + - + +
95B LYS* 3.3 34.9 + - - +
96B ILE 3.2 0.2 - - - -
97B GLN* 1.3 79.0 - - - +
99B ASP* 1.3 70.9 + - - +
101B GLY* 4.4 1.7 + - - -
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LYS* 2.6 48.3 + - - +
98B GLU* 1.3 90.2 - - - +
100B PHE* 1.3 76.8 + - + +
132B LYS* 3.9 27.4 + - + +
133B LEU* 2.9 35.6 + - + +
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 2.8 21.1 + - + +
99B ASP* 1.3 85.7 - - + +
101B GLY* 1.3 56.6 + - - +
102B SER 3.1 10.6 + - - +
105B ASN* 3.1 22.7 + - + +
106B PHE* 3.7 46.2 - + + +
109B GLN* 3.6 26.5 - - - -
125B LEU* 4.2 6.3 - - + -
133B LEU* 3.7 46.7 - - + -
134B VAL* 4.4 0.9 - - - -
135B ILE* 4.0 24.5 - - + -
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE 3.5 0.4 + - - -
97B GLN* 2.9 30.7 + - - +
98B GLU 4.3 1.4 + - - -
99B ASP 3.7 0.8 - - - -
100B PHE* 1.3 74.9 - - - +
102B SER* 1.3 60.7 + - - +
105B ASN* 4.3 5.8 - - - -
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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