Contacts of the strand formed by residues 58 - 65 (chain E) 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 HIS 58 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E LEU* 3.8 2.5 - - - -
38E CYS* 3.9 6.2 - - - -
55E THR* 3.9 2.2 - - - +
57E GLY* 1.3 81.7 - - - +
59E CYS* 1.3 66.8 + - - +
77E CYS* 3.4 3.8 - - - -
78E MET* 2.8 42.4 + - + +
79E LYS 4.4 0.2 - - - -
80E TYR* 3.9 14.6 - + - -
83E SER* 2.9 38.9 + - - -
87E CYS* 4.4 8.3 - - - -
101E CYS* 4.2 17.8 - - + +
102E CYS* 3.6 8.9 + - - +
103E ARG* 3.4 32.5 - - + +
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Residues in contact with CYS 59 (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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36E LEU* 3.9 10.3 - - - -
37E LYS 3.5 12.1 - - - -
38E CYS* 2.0 47.1 - - - -
58E HIS* 1.3 75.1 - - - +
60E PHE* 1.3 60.9 + - - +
76E GLY 3.4 2.0 - - - -
101E CYS* 3.2 5.4 - - - +
102E CYS* 2.9 31.6 + - - -
104E THR 4.1 1.8 - - - -
106E LEU 4.6 1.1 - - - -
107E CYS* 3.9 23.6 - - - -
108E ASN* 3.5 22.9 - - + +
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Residues in contact with PHE 60 (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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50D PRO* 3.6 25.6 - - + -
52D ALA* 4.6 5.8 - - + -
43E HIS* 3.6 33.0 - + - -
59E CYS* 1.3 75.5 - - - +
61E ALA* 1.3 66.9 + - - +
62E ILE* 4.0 7.0 - - + -
75E SER* 3.3 5.9 - - - -
76E GLY* 2.9 67.6 + - - -
77E CYS 3.5 20.0 - - - -
78E MET* 4.0 20.9 - - + -
99E ILE* 4.0 23.6 - - + -
100E GLU 3.1 11.9 - - - +
101E CYS* 4.3 2.7 - - - -
108E ASN* 2.5 21.4 + - - +
111E LEU* 4.3 0.4 - - - -
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E PHE* 1.3 75.6 - - - +
62E ILE* 1.3 62.0 + - - +
73E LEU* 4.7 5.8 - - + -
74E ALA 3.4 9.2 - - - +
75E SER* 4.3 3.8 - - - +
98E THR 3.9 0.9 - - - +
99E ILE* 3.4 3.1 - - - +
100E GLU 2.9 30.4 + - - -
108E ASN* 4.3 7.2 - - - +
111E LEU* 3.8 31.4 - - + +
113E PRO* 4.0 15.6 - - + +
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Residues in contact with ILE 62 (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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49D PHE* 3.8 38.6 - - + +
50D PRO* 3.9 9.6 - - + -
43E HIS* 4.4 4.0 - - - +
60E PHE* 4.0 13.9 - - + -
61E ALA* 1.3 75.3 - - - +
63E ILE* 1.3 70.2 + - - +
64E GLU* 3.9 17.4 - - - +
72E THR 3.8 0.5 - - - +
73E LEU* 3.3 8.9 - - - +
74E ALA* 2.8 57.8 + - + +
97E ARG* 4.3 11.7 - - + -
98E THR 3.3 15.3 - - - +
99E ILE* 4.1 10.1 - - + -
113E PRO* 4.3 0.2 - - - -
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Residues in contact with ILE 63 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E ILE* 1.3 73.6 - - - +
64E GLU* 1.3 61.4 + - - +
71E THR* 4.8 11.7 - - - +
72E THR 3.3 13.5 - - - +
73E LEU* 4.2 18.8 - - + -
97E ARG* 3.1 5.2 - - - +
98E THR* 2.9 64.0 + - - +
113E PRO* 3.0 29.6 - - + +
114E THR* 3.3 21.5 - - - -
115E LEU* 3.3 19.7 - - + +
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Residues in contact with GLU 64 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D LYS* 4.9 6.2 + - - -
49D PHE 4.3 13.5 - - - +
43E HIS* 4.8 3.3 + - - -
62E ILE* 3.9 29.6 - - + +
63E ILE* 1.3 79.7 - - - +
65E GLU* 1.3 62.7 + - - +
66E ASP 4.1 0.2 + - - -
70E GLU 3.7 1.4 - - - +
71E THR* 3.2 3.5 - - - -
72E THR* 2.9 46.9 + - - +
74E ALA* 4.4 9.4 - - + +
95E LEU* 6.3 0.9 - - + -
96E ARG 3.6 4.9 - - - +
97E ARG* 3.8 18.6 + - + -
115E LEU* 4.0 4.3 - - - -
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Residues in contact with GLU 65 (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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64E GLU* 1.3 75.9 - - - +
66E ASP* 1.3 65.3 + - - +
69E GLY* 3.8 26.8 - - - +
70E GLU 3.4 2.2 - - - -
71E THR* 3.8 20.8 - - + +
95E LEU* 3.5 24.8 - - + +
96E ARG* 2.8 66.8 + - + +
115E LEU* 4.0 6.2 - - + +
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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