Contacts of the helix formed by residues 82 - 89 (chain B) in PDB entry 2GOO
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 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASN* 3.1 23.3 + - - -
62A ILE* 3.8 12.0 - - - +
80B TYR 3.2 1.2 + - - -
81B GLU* 1.3 73.6 + - - +
83B SER* 1.3 62.6 + - - +
84B ASP* 3.3 3.8 - - - -
85B PHE* 3.2 25.4 + - - +
86B GLN* 3.2 19.0 + - - +
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Residues in contact with SER 83 (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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58B HIS* 3.1 40.0 + - - -
78B MET* 3.7 15.7 - - - -
79B LYS 3.5 10.5 + - - -
80B TYR* 2.7 26.5 + - - -
81B GLU 3.3 1.4 + - - -
82B GLY* 1.3 75.7 - - - +
84B ASP* 1.3 65.7 + - - +
87B CYS* 2.8 36.6 + - - +
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Residues in contact with ASP 84 (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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80B TYR* 5.1 9.6 + - - -
82B GLY* 4.9 1.3 - - - -
83B SER* 1.3 83.1 + - - +
85B PHE* 1.3 72.4 + - + +
87B CYS* 4.6 1.8 - - - +
88B LYS* 3.2 23.2 + - - +
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Residues in contact with PHE 85 (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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59A ASN* 4.1 22.2 - - + -
62A ILE* 3.9 15.3 - - + -
63A VAL* 4.2 26.5 - - + -
66A LEU* 3.8 15.7 - - + +
82B GLY* 3.2 20.3 + - - +
83B SER 3.2 0.4 - - - -
84B ASP* 1.3 84.0 - - + +
86B GLN* 1.3 59.6 + - - +
88B LYS* 3.4 5.4 + - - +
89B ASP* 2.8 27.4 + - - -
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Residues in contact with GLN 86 (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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49A PHE* 3.4 36.5 - - + -
50A PRO* 3.4 9.6 - - + +
51A LEU* 2.8 49.5 + - - +
62A ILE* 3.5 36.7 - - + +
65A THR* 5.6 0.7 - - - +
78B MET* 3.7 34.7 - - + +
81B GLU 5.5 0.4 + - - -
82B GLY 3.2 15.1 + - - +
85B PHE* 1.3 72.7 - - - +
87B CYS* 1.3 66.2 + - - +
89B ASP 3.4 4.0 + - - -
99B ILE* 3.4 8.7 - - - +
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Residues in contact with CYS 87 (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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58B HIS* 4.3 13.0 - - - -
78B MET* 3.5 13.2 - - - -
83B SER* 2.8 24.2 + - - +
84B ASP* 4.6 1.8 - - - +
86B GLN* 1.3 74.3 - - - +
88B LYS* 1.3 63.5 + - - +
99B ILE* 3.9 17.3 - - - +
101B CYS* 2.1 53.6 - - + +
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Residues in contact with LYS 88 (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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84B ASP 3.2 20.2 + - - +
85B PHE* 3.5 5.4 - - - +
86B GLN 3.2 0.2 - - - -
87B CYS* 1.3 80.1 - - - +
89B ASP* 1.3 79.4 + - - +
91B PRO* 5.6 0.9 - - - +
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Residues in contact with ASP 89 (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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49A PHE* 3.8 9.2 - - - -
66A LEU* 3.3 12.9 - - - +
85B PHE 2.8 19.3 + - - -
86B GLN 3.4 4.1 + - - +
88B LYS* 1.3 90.8 - - - +
90B SER* 1.3 83.4 + - - +
91B PRO* 3.9 5.9 - - - +
97B ARG* 2.8 57.5 + - - +
98B THR* 5.3 0.2 - - - -
99B ILE* 3.9 19.3 + - + +
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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