Contacts of the strand formed by residues 73 - 79 (chain B) in PDB entry 5GOW
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 ASP 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B HIS* 5.1 4.0 - - - -
69B LEU* 2.8 59.3 + - + +
71B ALA* 3.3 6.9 - - + +
72B GLY* 1.3 81.6 - - - +
74B THR* 1.3 82.3 + - - +
75B THR* 4.0 8.7 + - - -
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Residues in contact with THR 74 (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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395A GLU* 4.5 10.0 + - - +
18B LYS* 5.4 1.9 + - - +
54B LYS* 5.2 0.4 - - - +
66B GLN* 3.6 16.4 + - - +
67B LEU 3.0 5.6 - - - -
68B VAL* 3.5 28.5 - - + -
72B GLY 5.8 0.7 - - - -
73B ASP* 1.3 93.2 + - - +
75B THR* 1.3 63.2 + - - +
76B ASN* 3.8 16.7 + - - +
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Residues in contact with THR 75 (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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17B GLN* 3.5 21.1 - - - +
43B ILE* 4.2 3.6 - - + -
45B HIS* 3.4 38.3 + - + +
66B GLN* 3.2 2.6 - - - -
67B LEU* 2.6 51.5 + - - +
69B LEU* 4.2 3.5 - - - +
73B ASP* 4.0 7.1 + - - -
74B THR* 1.3 73.9 - - - +
76B ASN* 1.3 59.7 + - - +
77B PHE* 3.6 25.6 - - + -
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Residues in contact with ASN 76 (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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395A GLU* 3.1 25.7 + - - +
397A ASP* 3.6 12.1 - - + +
400A ASP* 2.7 43.0 + - - +
403A PHE* 3.1 13.1 - - + -
17B GLN* 3.4 22.3 - - - +
18B LYS* 3.4 11.3 + - - +
64B GLN* 6.0 0.2 - - - -
65B LEU 3.5 4.3 - - - +
66B GLN* 3.0 27.8 + - - +
74B THR* 3.8 12.4 + - - -
75B THR* 1.3 73.9 - - - +
77B PHE* 1.3 60.6 + - - +
78B HIS 4.1 0.4 - - - -
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Residues in contact with PHE 77 (chain B).
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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15B VAL* 3.6 24.9 - - + -
16B ARG 3.7 0.9 - - - -
17B GLN* 3.5 21.8 - - + -
24B LEU* 3.5 24.7 - - + -
31B ILE* 3.6 23.3 - - + -
33B TRP* 3.7 12.1 - + + -
43B ILE* 3.5 24.7 - - + -
64B GLN* 3.3 6.1 - - - -
65B LEU* 2.6 54.7 + - + +
67B LEU* 3.6 17.0 - - + -
75B THR* 3.6 20.6 - - + -
76B ASN* 1.3 72.2 - - - +
78B HIS* 1.3 62.4 + - - +
79B PHE* 3.4 9.1 + - + -
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Residues in contact with HIS 78 (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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397A ASP* 4.2 11.2 + - - +
398A GLU* 3.2 29.2 + - - +
15B VAL* 3.3 2.2 - - - -
16B ARG* 2.6 82.5 + - + +
62B LYS* 3.2 38.3 - - + +
64B GLN* 3.9 15.4 + - - +
76B ASN* 4.1 1.2 - - - +
77B PHE* 1.3 68.5 - - - +
79B PHE* 1.3 60.0 + - - +
80B SER* 3.0 29.9 + - - -
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Residues in contact with PHE 79 (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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12B VAL* 3.2 26.2 - - + -
13B LYS 5.0 0.2 - - - -
14B LYS 4.0 3.4 - - - -
15B VAL* 3.8 14.8 - - + -
24B LEU* 4.7 3.8 - - + -
62B LYS* 4.3 2.3 - - - +
63B ILE* 2.7 35.0 + - - +
64B GLN* 4.1 2.0 - - - -
65B LEU* 3.4 30.3 - - + -
77B PHE* 3.6 17.0 - - + -
78B HIS* 1.3 72.8 - - - +
80B SER* 1.3 58.9 + - - +
81B ASN 3.4 2.0 - - - +
85B ALA* 3.5 28.4 - - + +
88B GLU* 3.4 28.0 - - + -
89B ARG* 3.5 15.7 - - + -
92B VAL* 3.4 26.0 - - + -
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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