Contacts of the helix formed by residues 119 - 132 (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 LYS 119 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112Z ASN 4.7 4.0 - - - +
113Z MET* 4.7 17.3 - - + +
115Z PRO* 3.5 26.8 - - + +
117Z GLU 2.6 5.1 + - - +
118Z ASN* 1.3 75.1 - - - +
120Z ARG* 1.3 64.4 + - - +
122Z ALA* 3.8 7.8 + - - +
123Z ALA* 3.2 20.8 + - - +
145Z VAL* 4.1 13.0 - - + +
147Z SER* 5.6 3.1 - - - -
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Residues in contact with ARG 120 (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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117Z GLU* 2.4 35.4 + - + +
118Z ASN* 3.0 3.1 - - - -
119Z LYS* 1.3 65.6 - - - +
121Z PHE* 1.3 58.6 + - - +
123Z ALA* 2.8 21.5 + - - +
124Z ASP 2.8 11.3 + - - -
147Z SER 4.4 3.8 - - - +
148Z GLN* 3.0 52.5 - - + +
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Residues in contact with PHE 121 (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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118Z ASN 4.2 5.5 + - - +
119Z LYS 3.7 0.2 - - - -
120Z ARG* 1.3 78.4 - - - +
122Z ALA* 1.3 51.9 + - - +
124Z ASP* 3.0 9.0 + - - +
125Z ILE* 2.7 37.5 + - - +
149Z GLU 5.6 0.7 - - - -
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Residues in contact with ALA 122 (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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106Z LEU 5.7 3.8 - - - +
109Z ILE* 6.1 3.8 - - + +
110Z TYR* 5.4 14.4 - - + +
118Z ASN 4.9 3.7 + - - +
119Z LYS* 3.8 9.5 + - - +
120Z ARG 3.2 0.6 - - - -
121Z PHE* 1.3 76.7 - - - +
123Z ALA* 1.3 58.6 + - - +
125Z ILE* 4.4 4.7 - - - +
126Z ILE* 3.0 37.1 + - + +
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Residues in contact with ALA 123 (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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119Z LYS 3.2 9.7 + - - +
120Z ARG 2.8 5.6 + - - +
122Z ALA* 1.3 77.9 - - - +
124Z ASP* 1.3 57.2 + - - +
126Z ILE* 5.5 0.4 - - - -
127Z SER* 2.9 24.2 - - - -
142Z TYR* 3.3 29.5 - - + +
145Z VAL* 3.0 31.6 - - + +
146Z GLY* 3.7 3.8 - - - -
149Z GLU* 4.6 6.9 - - - +
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Residues in contact with ASP 124 (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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120Z ARG 2.8 7.6 + - - +
121Z PHE* 3.5 11.4 - - - +
123Z ALA* 1.3 78.4 - - - +
125Z ILE* 1.3 58.9 + - - +
127Z SER* 4.0 0.6 - - - -
128Z VAL* 2.8 32.8 + - - +
149Z GLU* 3.1 42.4 - - + +
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Residues in contact with ILE 125 (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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121Z PHE 2.7 20.3 + - - +
122Z ALA* 4.1 3.8 - - - +
124Z ASP* 1.3 69.6 - - - +
126Z ILE* 1.3 55.5 + - - +
128Z VAL* 3.0 5.8 + - - +
129Z LEU* 2.3 40.5 + - - +
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Residues in contact with ILE 126 (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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106Z LEU* 5.6 11.7 - - + +
122Z ALA* 3.0 16.0 + - + +
123Z ALA* 5.5 0.7 - - - -
125Z ILE* 1.3 77.1 - - - +
127Z SER* 1.3 52.1 + - - +
129Z LEU* 3.1 10.8 - - - +
130Z ALA* 2.4 34.9 + - - +
142Z TYR* 5.5 2.2 - - + -
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Residues in contact with SER 127 (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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122Z ALA 4.1 0.4 + - - -
123Z ALA 2.9 25.6 + - - -
124Z ASP* 3.6 2.4 + - - -
125Z ILE 3.1 0.6 - - - -
126Z ILE* 1.3 76.9 - - - +
128Z VAL* 1.3 53.7 + - - +
130Z ALA* 2.9 10.5 + - - +
131Z MET* 2.3 35.2 + - - +
138Z GLU 5.4 0.2 - - - -
139Z CYS* 4.1 16.9 - - - +
142Z TYR* 3.5 19.8 - - - +
149Z GLU* 6.3 0.7 - - - -
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Residues in contact with VAL 128 (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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124Z ASP 2.8 23.6 + - - +
125Z ILE* 3.6 4.0 - - - +
127Z SER* 1.3 69.3 - - - +
129Z LEU* 1.3 59.1 + - - +
131Z MET* 2.8 11.3 + - + -
132Z THR* 2.7 36.0 + - - -
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Residues in contact with LEU 129 (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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125Z ILE 2.3 32.5 + - - +
126Z ILE* 3.1 15.5 - - - +
128Z VAL* 1.3 68.9 - - - +
130Z ALA* 1.3 54.8 + - - +
132Z THR* 5.2 2.4 - - - -
133Z MET* 2.9 22.9 + - - +
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Residues in contact with ALA 130 (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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126Z ILE 2.4 28.0 + - - +
127Z SER* 2.9 12.3 + - - +
129Z LEU* 1.3 71.3 - - - +
131Z MET* 1.3 60.5 + - - +
133Z MET* 3.5 8.2 - - - +
134Z SER 3.4 3.6 + - - -
135Z GLY* 3.3 28.0 + - - +
138Z GLU* 4.5 11.7 - - + -
139Z CYS* 4.1 22.2 - - + +
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Residues in contact with MET 131 (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 2.3 25.7 + - - +
128Z VAL* 2.8 14.9 + - + +
130Z ALA* 1.3 68.4 - - - +
132Z THR* 1.3 61.4 + - - +
133Z MET 3.0 4.3 - - - -
134Z SER* 3.1 13.7 + - - -
135Z GLY 4.5 5.1 + - - -
139Z CYS* 5.4 3.1 - - + -
156Z HIS* 5.3 9.2 - - + -
158Z TYR* 4.9 17.5 - - + +
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Residues in contact with THR 132 (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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128Z VAL 2.7 16.2 + - - -
129Z LEU* 5.2 1.6 - - - -
131Z MET* 1.3 73.4 - - - +
133Z MET* 1.3 60.8 + - - +
134Z SER* 3.1 3.7 + - - -
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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