Contacts of the strand formed by residues 117 - 123 (chain C) in PDB entry 4GUP
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 GLN 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C ALA* 3.2 4.9 - - - -
114C TYR* 3.1 29.5 + - - +
115C ASP 3.3 7.5 - - - +
116C GLY* 1.4 90.3 - - - +
118C ASP* 1.4 69.6 + - - +
119C PHE* 4.0 1.4 - - - +
1D ILE* 3.5 53.3 - - + +
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Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLN* 5.2 4.4 - - + +
112C TYR 3.9 6.3 - - - -
113C ALA* 4.3 2.6 - - - +
116C GLY 5.1 0.2 - - - +
117C GLN* 1.4 72.2 - - - +
119C PHE* 1.3 59.2 + - - +
121C ILE* 4.4 21.0 - - + +
132C VAL* 3.4 26.9 - - + +
60D TRP* 3.7 23.8 + - - +
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Residues in contact with PHE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 3.2 35.0 - - + -
84C TYR* 3.4 25.1 - + - -
92C TYR* 4.8 15.5 - + - -
112C TYR* 2.9 17.7 + - + +
113C ALA* 4.1 7.0 - - - +
114C TYR* 4.1 12.8 - - + +
117C GLN 4.0 7.0 - - - +
118C ASP* 1.3 74.8 - - - +
120C LEU* 1.4 93.7 + - + +
121C ILE* 4.4 2.9 - - - -
130C LEU 3.9 0.5 - - - +
132C VAL* 3.1 43.4 + - + +
133C ASP* 3.5 11.2 - - - -
135C VAL* 4.1 2.7 - - + -
136C ALA* 3.4 22.4 - - + +
139C ILE* 4.3 8.1 - - + -
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C TYR* 5.5 2.2 - - - +
111C GLN* 3.4 4.0 - - - +
112C TYR* 2.9 41.7 + - + +
119C PHE* 1.4 105.0 - - + +
121C ILE* 1.3 64.9 + - - +
129C TRP* 3.7 41.3 - - + -
130C LEU 3.6 2.7 - - - +
131C ALA* 3.8 25.6 - - + -
136C ALA* 4.0 14.6 - - + +
139C ILE* 3.8 22.9 - - + -
140C LYS* 4.0 4.7 - - + +
143C TRP* 5.2 8.7 - - + -
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LEU 3.7 2.9 - - - -
111C GLN* 3.8 30.7 - - + +
112C TYR 5.5 0.2 - - - +
118C ASP* 4.4 24.0 - - + +
119C PHE 4.4 2.2 - - - +
120C LEU* 1.3 86.7 - - - +
122C PHE* 1.3 66.8 + - - +
123C ASN 3.9 0.7 + - - -
129C TRP* 3.4 7.1 - - - -
130C LEU* 2.8 70.4 + - + +
132C VAL* 5.8 2.9 - - + -
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Residues in contact with PHE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C PHE* 5.7 1.2 - - - -
110C LEU* 2.9 46.7 + - + +
121C ILE* 1.3 80.4 - - - +
123C ASN* 1.4 65.9 + - - +
124C LYS* 3.6 32.7 + - + +
127C LEU* 4.0 23.3 - - + -
128C SER 3.4 13.2 - - - -
129C TRP* 3.5 32.6 - + + -
130C LEU* 5.4 0.2 - - - -
150C LEU* 3.8 31.9 - - + -
153C GLN* 4.3 6.3 - - + -
154C LYS* 4.1 8.7 - - - -
157C LEU* 4.1 15.5 - - + -
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Residues in contact with ASN 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE 3.9 1.6 + - - -
122C PHE* 1.4 71.4 - - - +
124C LYS* 1.3 57.8 + - - +
125C ASP* 3.4 22.1 + - - +
126C THR* 2.7 39.6 + - - +
127C LEU* 3.0 23.6 + - - -
128C SER* 2.9 24.4 + - - +
129C TRP* 5.0 0.2 - - - +
130C LEU* 5.0 15.7 - - + +
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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