Contacts of the strand formed by residues 69 - 73 (chain B) in PDB entry 2GAO
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 MET 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.0 6.7 - - + -
21B LEU* 4.0 40.2 - - + +
24B LYS* 3.4 25.4 - - - +
25B SER 3.9 1.6 - - - -
26B GLY* 3.3 43.7 - - - +
27B LYS 4.2 0.4 - - - +
28B LEU* 3.9 28.0 - - + -
64B LEU 3.8 0.5 - - - +
65B THR* 3.1 5.1 - - - +
66B ILE 2.8 39.3 + - - +
67B ALA 3.3 0.2 - - - -
68B GLY* 1.3 76.9 - - - +
70B THR* 1.3 64.4 + - - +
71B PHE* 3.8 20.1 - - + -
197B ILE* 4.7 5.2 - - + -
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Residues in contact with THR 70 (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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26B GLY 3.1 11.8 + - - +
27B LYS* 3.5 25.0 + - + +
28B LEU 2.9 26.1 + - - -
63B GLU* 3.6 31.0 - - + +
64B LEU 3.3 3.8 - - - +
65B THR* 3.2 26.2 + - - +
68B GLY 5.0 1.7 + - - -
69B MET* 1.3 73.1 - - - +
71B PHE* 1.3 70.0 + - - +
72B THR* 4.1 5.2 - - - +
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Residues in contact with PHE 71 (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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15B VAL* 6.1 0.2 - - + -
16B LEU* 4.0 19.1 - - + -
19B LEU* 4.6 2.5 - - + -
21B LEU* 3.9 13.5 - - + -
28B LEU* 3.3 26.9 - - + -
30B PHE* 3.6 28.0 - + + -
42B LEU* 3.4 22.3 - - + +
45B LEU* 3.9 24.2 - - + -
62B GLU 3.8 0.3 - - - +
63B GLU* 3.2 4.5 - - - +
64B LEU* 2.8 50.5 + - + +
66B ILE* 4.5 12.1 - - + -
69B MET* 3.8 33.0 - - + -
70B THR* 1.3 76.5 - - - +
72B THR* 1.3 62.5 + - - +
190B PHE* 4.6 2.5 - + - -
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Residues in contact with THR 72 (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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28B LEU 2.9 10.7 + - - -
29B VAL* 3.2 9.7 - - - +
30B PHE* 2.7 32.3 + - - +
61B SER* 4.0 3.6 - - - +
62B GLU 3.3 11.9 - - - +
63B GLU* 3.4 23.8 + - + +
70B THR* 4.1 5.0 - - - +
71B PHE* 1.3 76.4 + - - +
73B THR* 1.3 61.9 + - - +
74B PHE* 3.2 38.1 - - + -
89B TYR* 4.5 13.4 - - + -
93B ILE* 6.4 0.7 - - - -
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Residues in contact with THR 73 (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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30B PHE* 3.4 16.6 - - + -
38B LYS* 3.7 39.0 - - + +
39B THR* 4.6 8.2 + - - +
42B LEU* 4.1 20.0 - - + -
60B THR 3.9 2.9 + - - -
61B SER* 2.7 33.5 + - - -
62B GLU* 2.9 34.8 + - - +
72B THR* 1.3 73.5 - - - +
74B PHE* 1.3 66.3 + - - +
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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