Contacts of the helix formed by residues 137 - 145 (chain Z) in PDB entry 5GJQ
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 ARG 137 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135Z GLY* 3.6 2.0 - - - -
136Z GLU* 1.3 77.7 - - - +
138Z GLU* 1.3 68.5 + - - +
139Z CYS 3.0 2.1 + - - -
140Z LEU* 3.1 14.0 + - - +
141Z LYS* 3.4 9.0 + - - +
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Residues in contact with GLU 138 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Z SER* 5.4 0.3 - - - -
130Z ALA* 4.5 14.1 - - + -
135Z GLY 5.5 0.4 - - - -
137Z ARG* 1.3 79.3 - - - +
139Z CYS* 1.3 61.3 + - - +
141Z LYS* 3.3 10.6 + - - +
142Z TYR* 3.2 21.7 + - - +
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Residues in contact with CYS 139 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Z SER* 4.1 16.9 - - - +
130Z ALA* 4.1 19.3 - - + +
131Z MET* 5.1 2.7 - - + +
135Z GLY 3.6 25.3 + - - +
136Z GLU* 4.5 4.7 - - - -
137Z ARG 3.0 0.6 + - - +
138Z GLU* 1.3 80.0 - - - +
140Z LEU* 1.3 61.9 + - - +
142Z TYR* 3.3 7.1 + - - +
143Z ARG* 3.1 18.1 + - - +
158Z TYR* 6.3 2.9 - - + -
162Z LEU* 5.1 2.0 - - - +
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Residues in contact with LEU 140 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Z GLU 4.3 11.0 + - - +
137Z ARG 3.1 8.8 + - - +
139Z CYS* 1.3 75.6 - - - +
141Z LYS* 1.3 60.4 + - - +
143Z ARG* 2.5 29.8 + - + +
144Z LEU* 3.0 14.0 + - - +
162Z LEU* 4.5 14.1 - - + +
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Residues in contact with LYS 141 (chain Z).
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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137Z ARG 3.4 7.5 + - - +
138Z GLU* 3.3 14.6 + - - +
140Z LEU* 1.3 77.6 - - - +
142Z TYR* 1.3 59.3 + - - +
144Z LEU* 4.1 6.3 - - - +
145Z VAL* 3.5 19.6 + - - +
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Residues in contact with TYR 142 (chain Z).
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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123Z ALA* 3.3 33.0 - - + +
126Z ILE* 5.5 1.8 - - + -
127Z SER* 3.5 20.2 - - - +
138Z GLU 3.2 10.8 + - - +
139Z CYS 3.6 2.5 - - - +
140Z LEU 3.0 0.6 - - - -
141Z LYS* 1.3 75.2 - - - +
143Z ARG* 1.3 52.8 + - - +
145Z VAL* 2.9 8.4 - - - -
146Z GLY* 2.4 33.8 + - - -
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Residues in contact with ARG 143 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Z SER* 6.1 0.4 - - - -
139Z CYS 3.1 9.4 + - - +
140Z LEU* 2.5 16.8 + - + +
142Z TYR* 1.3 68.7 - - - +
144Z LEU* 1.3 66.1 + - - +
145Z VAL 3.1 0.7 - - - -
146Z GLY* 3.1 11.8 + - - +
162Z LEU* 3.6 40.2 - - + +
163Z ALA* 4.7 3.0 - - - +
187Z LEU* 3.2 18.5 - - - +
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Residues in contact with LEU 144 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Z LEU 3.0 7.9 + - - +
141Z LYS* 4.1 9.6 - - - +
143Z ARG* 1.3 74.3 - - - +
145Z VAL* 1.3 58.1 + - + +
146Z GLY 3.4 0.9 + - - -
162Z LEU 5.6 0.2 + - - -
166Z VAL* 5.7 7.2 - - + +
183Z PRO* 2.7 44.4 - - + +
184Z LEU* 5.5 0.2 - - - -
186Z THR* 3.4 4.3 - - - -
187Z LEU* 2.7 28.3 + - - +
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Residues in contact with VAL 145 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Z TYR 6.0 0.4 - - - +
113Z MET* 4.0 29.4 - - + +
119Z LYS* 3.7 16.0 - - + +
123Z ALA* 3.0 14.8 - - + +
141Z LYS 3.5 16.6 + - - +
142Z TYR* 2.9 11.2 + - - +
143Z ARG 3.1 0.4 - - - -
144Z LEU* 1.3 76.7 - - + +
146Z GLY* 1.3 59.9 + - - +
147Z SER 3.5 3.8 + - - -
183Z PRO* 5.5 1.6 - - + -
186Z THR* 5.0 5.4 - - - -
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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