Contacts of the strand formed by residues 108 - 113 (chain D) in PDB entry 5WBY
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 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D THR* 3.4 5.0 + - - +
103D GLY 3.8 0.2 - - - -
104D GLY* 3.1 22.3 + - - -
106D ASP* 2.5 33.0 + - - +
107D CYS* 1.3 84.5 - - - +
109D ALA* 1.3 58.5 + - - +
110D ARG* 2.7 37.0 + - - +
124D ILE* 3.9 19.5 - - + -
125D PHE 3.5 3.6 - - - -
126D GLN* 4.1 15.9 - - + +
131D ILE* 3.5 6.1 - - - +
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Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR 3.3 9.0 - - - +
103D GLY* 4.5 0.4 - - - -
108D THR* 1.3 71.4 - - - +
110D ARG* 1.3 59.3 + - - +
124D ILE* 3.7 0.9 - - - -
125D PHE* 2.8 47.8 + - + +
131D ILE* 3.4 9.3 - - + +
134D VAL* 4.5 3.1 - - + -
143D LEU* 4.2 6.5 - - + -
145D VAL* 3.8 27.8 - - + -
155D TRP* 3.7 18.6 - - + -
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLY 5.4 3.2 + - - -
84D VAL* 3.4 24.3 - - - +
100D MET 3.7 1.2 - - - +
101D TYR* 3.4 5.8 - - - +
102D THR* 2.9 43.5 + - - +
106D ASP* 2.5 31.3 + - - -
108D THR* 2.7 35.4 + - - +
109D ALA* 1.3 78.0 - - - +
111D ILE* 1.3 61.9 + - - +
112D TRP* 3.7 24.1 - - - +
121D CYS* 3.5 25.9 - - - -
123D ARG 3.4 3.4 - - - -
124D ILE* 4.0 23.9 - - + +
143D LEU* 5.7 0.5 - - - +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D TRP* 3.8 29.4 - - + -
100D MET 3.4 5.2 - - - +
101D TYR* 3.8 28.9 - - + +
110D ARG* 1.3 73.2 - - - +
112D TRP* 1.3 62.8 + - - +
121D CYS* 3.6 1.8 - - - +
122D GLN* 2.9 31.2 + - - +
123D ARG* 3.0 37.7 + - + +
155D TRP* 3.4 35.7 - - + -
157D LEU* 3.8 20.2 - - + -
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Residues in contact with TRP 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ILE* 4.1 15.5 - - + -
81D TYR* 3.3 50.7 - + + +
82D ASP 4.6 2.0 - - - -
84D VAL* 3.9 24.5 - - + -
88D ILE* 5.5 1.1 - - + -
99D TRP* 3.5 11.3 - - - -
100D MET* 2.7 61.7 + - + +
102D THR* 3.0 38.7 + - + +
110D ARG* 3.7 28.7 - - + +
111D ILE* 1.3 72.4 - - - +
113D ASP* 1.3 62.0 + - - +
114D LEU* 3.5 1.5 + - + -
119D LEU 3.5 17.3 - - - -
120D GLN* 4.3 2.2 - - - -
121D CYS* 3.6 30.3 - - + -
122D GLN 4.5 1.3 - - - +
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D TYR* 3.5 9.7 + - - -
98D ARG* 3.4 36.1 + - - +
99D TRP* 3.6 22.9 - - + -
111D ILE 4.1 1.6 + - - -
112D TRP* 1.3 69.3 - - - +
114D LEU* 1.3 63.9 + - - +
115D ARG 3.4 14.5 + - - +
116D SER* 3.3 39.8 + - - +
118D ASN* 5.3 1.6 - - + +
120D GLN 5.9 0.4 + - - -
121D CYS* 5.4 0.4 - - - +
122D GLN* 4.5 13.8 - - + +
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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