Contacts of the strand formed by residues 78 - 86 (chain A) in PDB entry 5WUX
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 THR 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER* 3.8 12.3 - - - -
22A CYS 3.2 13.0 - - - +
23A ALA* 3.4 17.8 - - + +
29A PHE* 4.1 5.4 - - - -
72A LEU* 3.6 2.4 - - - -
73A ASP* 3.0 34.4 + - - +
76A LYS* 3.3 16.6 + - - +
77A SER* 1.3 76.4 - - - +
79A ALA* 1.3 66.6 + - - +
80A TYR* 3.5 37.6 - - + +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU 3.7 0.2 - - - +
21A SER* 3.5 3.1 - - - -
22A CYS* 2.7 42.1 + - + +
29A PHE* 4.2 7.4 - - + -
34A MET* 4.0 27.1 - - + -
36A TRP* 3.8 11.7 - - + +
51A ILE* 5.2 1.8 - - + -
71A SER 3.5 4.9 - - - +
72A LEU* 3.7 17.5 - - + -
78A THR* 1.3 74.3 - - - +
80A TYR* 1.3 63.1 + - - +
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 3.9 48.2 + - + -
20A LEU 3.2 11.9 - - - +
21A SER* 3.5 22.4 - - - -
36A TRP* 3.8 7.0 + - - -
70A PHE* 3.1 11.6 - - - +
71A SER* 2.6 58.9 + - - +
72A LEU 4.2 2.0 - - - -
73A ASP* 3.9 30.0 + - + +
78A THR* 3.5 18.0 - - + +
79A ALA* 1.3 78.3 - - - +
81A LEU* 1.3 61.2 + - - +
82A GLN* 4.0 1.6 - - + +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU 3.6 0.7 - - - +
19A ARG* 3.2 4.2 - - - -
20A LEU* 2.6 56.8 + - + +
36A TRP* 3.6 33.4 - - + -
48A MET* 4.0 9.4 - - + -
68A PHE* 3.9 22.9 - - + -
69A THR 3.7 0.7 - - - +
70A PHE* 3.5 29.8 - - + -
80A TYR* 1.3 72.5 - - - +
82A GLN* 1.3 63.1 + - - +
83A MET* 3.7 13.4 + - + +
94A TYR* 4.0 26.5 - - + -
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Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 4.9 4.0 + - - -
18A LEU 3.5 6.5 + - - +
19A ARG* 3.3 39.9 - - + +
68A PHE* 3.2 9.7 - - - +
69A THR* 2.7 49.5 + - - +
71A SER* 5.8 3.8 - - - +
80A TYR* 4.0 1.7 - - + +
81A LEU* 1.3 72.0 - - - +
83A MET* 1.3 62.5 + - - +
84A ASN* 2.7 34.3 + - - +
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Residues in contact with MET 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.0 3.3 - - - -
18A LEU* 2.4 67.7 + - - +
20A LEU* 3.7 25.8 - - - -
68A PHE* 3.5 24.5 - - + -
81A LEU* 3.7 16.8 - - + +
82A GLN* 1.3 72.7 + - - +
84A ASN* 1.3 63.8 + - - +
86A LEU* 3.7 16.2 - - + -
94A TYR* 3.3 48.9 - - + +
114A VAL* 4.1 13.0 - - + -
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Residues in contact with ASN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY 3.3 2.2 - - - -
17A SER* 3.2 21.1 + - - +
66A GLY 4.8 1.9 - - - +
67A ARG* 2.7 46.4 + - - +
68A PHE* 4.3 0.7 - - - -
69A THR* 4.7 5.1 + - - -
82A GLN* 2.7 34.8 + - - +
83A MET* 1.3 74.7 - - - +
85A SER* 1.3 78.6 + - - +
86A LEU* 3.3 5.6 + - - +
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY* 3.5 20.8 + - - -
16A GLY 2.8 9.3 + - - -
17A SER* 4.2 0.4 + - - -
67A ARG* 3.2 22.5 + - - -
84A ASN* 1.3 78.8 - - - +
86A LEU* 1.3 60.9 + - - +
87A ARG* 3.3 31.2 + - - -
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.0 21.1 - - + -
14A PRO* 3.2 5.4 - - - +
15A GLY 2.5 31.4 + - - -
16A GLY 3.2 25.2 + - - +
18A LEU* 4.1 24.5 - - + +
68A PHE* 3.8 13.7 - - + -
83A MET* 3.7 28.9 - - + -
84A ASN 3.8 11.7 - - - +
85A SER* 1.3 75.7 - - - +
87A ARG* 1.3 60.7 + - - +
90A ASP* 3.5 12.8 - - + +
114A VAL* 4.8 7.0 - - + -
116A VAL* 3.7 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