Contacts of the helix formed by residues 117 - 128 (chain D) in PDB entry 4UQJ
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 LEU 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D PRO 3.4 4.5 + - - +
116D ASP* 1.3 72.3 + - - +
118D LYS* 1.3 66.5 + - - +
119D GLY 3.1 2.9 - - - -
120D ALA* 3.0 12.4 + - + +
121D LEU* 2.9 27.1 + - + +
145D THR* 5.3 7.4 - - + -
223D ALA* 3.5 38.6 - - + +
224D ASN* 3.5 14.6 - - - +
225D LEU* 3.8 24.2 - - + +
245D PHE* 3.6 39.0 - - + -
358D ILE* 4.3 4.9 - - + -
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Residues in contact with LYS 118 (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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116D ASP* 3.3 23.1 + - - +
117D LEU* 1.3 77.6 - - - +
119D GLY* 1.3 60.5 + - - +
121D LEU* 3.6 6.3 + - - +
122D LEU* 3.3 30.5 + - + +
144D SER* 5.5 3.8 - - - +
145D THR* 4.5 22.2 - - + +
148D ALA* 4.5 17.9 - - + +
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Residues in contact with GLY 119 (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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116D ASP* 4.2 5.9 + - - -
117D LEU 3.1 1.2 - - - -
118D LYS* 1.3 76.9 - - - +
120D ALA* 1.3 64.9 + - - +
121D LEU 3.3 0.2 + - - -
122D LEU* 3.4 8.2 + - - +
123D SER* 3.1 26.0 + - - -
374D TRP* 3.6 24.0 - - - -
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Residues in contact with ALA 120 (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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117D LEU* 3.0 18.3 + - + +
119D GLY* 1.3 76.1 - - - +
121D LEU* 1.3 62.0 + - - +
123D SER* 3.6 2.4 + - - -
124D LEU* 3.2 17.5 + - - +
245D PHE* 3.4 29.3 - - + -
358D ILE* 4.2 12.6 - - + -
374D TRP* 3.7 37.9 - - + +
380D MET* 4.4 2.9 - - - +
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Residues in contact with LEU 121 (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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117D LEU* 2.9 19.5 + - + +
118D LYS* 3.8 5.6 - - - +
120D ALA* 1.3 74.9 - - - +
122D LEU* 1.3 68.5 + - + +
124D LEU* 3.0 13.7 + - + +
125D ILE* 3.1 36.3 + - + -
135D TYR* 4.5 19.7 - - + +
145D THR* 5.1 12.1 - - + -
149D VAL* 4.7 10.5 - - + -
193D ILE* 4.1 13.5 - - + -
221D ILE* 5.0 5.6 - - + -
223D ALA* 3.9 24.9 - - + -
245D PHE* 3.6 23.7 - - + -
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Residues in contact with LEU 122 (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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118D LYS* 3.3 19.2 + - + +
119D GLY* 3.4 6.0 + - - +
121D LEU* 1.3 80.3 - - + +
123D SER* 1.3 61.3 + - - +
125D ILE* 3.4 9.9 + - + +
126D GLU* 3.4 26.2 + - - +
148D ALA* 4.2 13.0 - - + +
149D VAL* 3.9 35.0 - - + +
152D SER* 3.5 30.5 - - - +
158D TRP* 4.3 12.5 - - + -
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Residues in contact with SER 123 (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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119D GLY 3.1 8.7 + - - -
120D ALA 3.8 1.6 - - - -
121D LEU 3.1 0.6 - - - -
122D LEU* 1.3 74.6 - - - +
124D LEU* 1.3 65.9 + - - +
126D GLU* 3.4 9.6 + - - +
127D TYR* 3.1 21.0 + - - +
374D TRP* 2.8 40.6 + - - -
379D LYS* 4.6 6.6 - - - +
380D MET* 3.9 15.6 - - - +
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Residues in contact with LEU 124 (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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120D ALA 3.2 11.0 + - - +
121D LEU* 3.0 9.0 + - + +
123D SER* 1.3 76.1 - - - +
125D ILE* 1.3 67.4 + - - +
127D TYR* 3.1 17.1 + - + +
128D TYR* 3.2 51.9 + - + -
221D ILE* 3.9 23.8 - - + -
243D SER* 4.4 10.1 - - - -
244D GLY 4.8 5.4 - - - +
245D PHE* 3.6 25.8 - - + -
360D ILE* 3.6 26.7 - - + -
380D MET* 3.6 15.0 - - + +
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Residues in contact with ILE 125 (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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121D LEU* 3.1 34.0 + - + +
122D LEU* 3.6 11.2 - - - +
124D LEU* 1.3 77.5 - - - +
126D GLU* 1.3 56.6 + - - +
128D TYR* 3.4 3.5 + - - +
129D GLN 3.0 20.3 + - - -
130D TRP* 3.1 39.1 + - + +
133D PHE* 3.7 21.3 - - + -
149D VAL* 4.6 7.4 - - + -
158D TRP* 3.7 32.8 - - + -
193D ILE* 3.7 22.0 - - + -
221D ILE* 5.0 6.1 - - + -
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Residues in contact with GLU 126 (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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122D LEU 3.4 12.1 + - - +
123D SER* 3.4 10.7 + - - +
124D LEU 3.3 0.6 - - - -
125D ILE* 1.3 74.3 - - - +
127D TYR* 1.3 67.0 + - - +
129D GLN* 2.9 22.8 + - - +
130D TRP 5.0 0.7 - - - +
156D LYS* 4.8 8.5 - - + +
158D TRP* 4.1 21.6 - - + -
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Residues in contact with TYR 127 (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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123D SER 3.1 13.5 + - - +
124D LEU* 3.1 13.7 + - + +
126D GLU* 1.3 78.2 - - - +
128D TYR* 1.3 98.5 + + - +
129D GLN* 3.3 10.2 + - - +
362D GLU* 4.3 1.7 + - - -
371D ILE* 4.1 17.0 - - + +
380D MET* 3.8 15.3 - - - -
382D LEU* 3.3 44.8 - - + +
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Residues in contact with TYR 128 (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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124D LEU* 3.2 50.5 + - + +
125D ILE* 4.1 0.9 - - - +
127D TYR* 1.3 92.0 - + - +
129D GLN* 1.3 72.9 + - - +
130D TRP* 3.2 27.9 - - + +
191D ARG* 4.5 4.7 + - - -
219D HIS* 3.8 25.8 - + - -
221D ILE* 4.4 8.1 - - + -
241D GLU* 5.2 2.5 - - - -
243D SER* 2.7 27.1 + - - -
361D MET 4.8 0.2 + - - -
362D GLU* 2.6 34.5 + - - +
371D ILE* 4.0 4.7 - - - +
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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