Contacts of the helix formed by residues 108 - 121 (chain D) in PDB entry 3TQS
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 PRO 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D ASN 4.0 5.2 - - - +
107D LEU* 1.3 88.7 - - + +
109D TYR* 1.3 60.1 + - - +
110D ASN* 3.3 20.5 + - - +
111D ILE* 3.4 14.7 + - + +
112D SER* 2.7 27.9 + - - -
134D GLN* 5.6 1.3 - - + +
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Residues in contact with TYR 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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107D LEU 3.9 0.6 + - - -
108D PRO* 1.3 71.8 - - - +
110D ASN* 1.3 64.8 + - + +
111D ILE 3.1 1.2 + - - -
112D SER* 3.1 20.3 + - - -
113D THR 4.5 1.9 + - - -
134D GLN* 3.1 41.8 - - + +
136D GLU* 3.3 32.4 - - + +
137D VAL* 3.4 23.1 - - + -
140D ARG* 3.0 34.1 + - - -
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Residues in contact with ASN 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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108D PRO* 3.3 19.4 - - - +
109D TYR* 1.3 81.5 - - - +
111D ILE* 1.3 83.0 + - - +
112D SER 3.5 0.2 - - - -
114D PRO* 3.8 13.4 - - - +
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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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170A SER* 5.8 3.8 - - - +
172A GLN* 5.5 2.2 - - - +
88D LEU* 3.7 32.1 - - + -
107D LEU* 4.4 9.6 - - + -
108D PRO* 3.4 23.9 + - + +
109D TYR 3.1 0.2 - - - -
110D ASN* 1.3 102.2 + - - +
112D SER* 1.3 60.3 + - - +
114D PRO* 3.3 8.8 - - + +
115D LEU* 2.9 44.0 + - + +
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Residues in contact with SER 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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107D LEU* 4.0 9.2 + - - +
108D PRO 2.7 22.2 + - - -
109D TYR* 3.1 15.4 + - - -
110D ASN 3.5 0.2 - - - -
111D ILE* 1.3 79.4 - - - +
113D THR* 1.3 63.1 + - - +
115D LEU* 4.0 0.9 - - - +
116D LEU* 3.0 33.4 + - - +
133D LEU* 3.7 22.9 - - - +
134D GLN 5.5 0.2 + - - -
137D VAL* 4.1 25.6 - - - +
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Residues in contact with THR 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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109D TYR 4.5 1.4 + - - -
112D SER* 1.3 77.9 - - - +
114D PRO* 1.3 68.1 - - + +
116D LEU* 3.3 4.5 + - - +
117D PHE* 2.9 62.2 + - + +
137D VAL* 5.5 0.2 - - - +
140D ARG* 4.2 12.2 + - - +
152D ARG* 5.7 3.6 - - - +
153D LEU* 3.7 29.7 - - + +
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Residues in contact with PRO 114 (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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172A GLN* 6.5 0.4 - - + -
88D LEU* 3.6 18.8 - - + +
110D ASN 3.8 10.3 - - - +
111D ILE* 3.3 30.3 - - + +
113D THR* 1.3 96.5 - - + +
115D LEU* 1.3 55.6 + - - +
117D PHE* 3.5 6.5 + - + +
118D HIS* 3.0 27.9 + - - +
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Residues in contact with LEU 115 (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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39D ILE* 3.9 19.5 - - + -
87D ALA* 3.5 35.4 - - + +
88D LEU* 3.4 12.9 - - + +
92D PHE* 5.1 2.7 - - + -
107D LEU* 3.5 41.1 - - + -
111D ILE* 2.9 27.9 + - + +
112D SER 4.1 2.0 - - - +
114D PRO* 1.3 73.0 - - - +
116D LEU* 1.3 65.8 + - - +
118D HIS* 3.2 5.3 + - + +
119D LEU* 3.0 41.1 + - + +
131D PHE* 5.0 0.7 - - + -
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Residues in contact with LEU 116 (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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107D LEU* 5.2 4.7 - - + -
112D SER* 3.0 26.5 + - - +
113D THR* 3.7 3.6 - - - +
115D LEU* 1.3 76.2 - - - +
117D PHE* 1.3 57.9 + - + +
119D LEU* 3.1 8.5 + - + +
120D PHE* 2.8 48.3 + - + -
129D MSE 4.7 3.4 - - - -
131D PHE* 3.8 34.5 - - + -
133D LEU* 4.8 6.5 - - + -
137D VAL* 5.2 1.8 - - + -
141D ILE* 3.7 30.5 - - + -
153D LEU* 4.2 14.8 - - + -
157D ALA* 5.7 0.2 - - + -
187D LEU* 4.2 21.3 - - + -
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Residues in contact with PHE 117 (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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113D THR* 2.9 37.4 + - + +
114D PRO* 3.9 6.5 - - + +
116D LEU* 1.3 78.0 - - + +
118D HIS* 1.3 63.3 + - - +
120D PHE* 3.3 21.6 + + - +
121D SER* 3.0 21.7 + - - -
152D ARG* 3.7 46.4 - - + -
153D LEU* 4.0 23.1 - - + -
156D MSE 3.7 36.3 - - + -
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Residues in contact with HIS 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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87D ALA 3.3 22.4 - - - -
88D LEU* 3.4 24.2 + - - +
89D GLN* 4.1 7.2 - - - -
90D PHE 2.8 26.2 + - - -
92D PHE* 4.1 10.1 - + - -
114D PRO 3.0 18.8 + - - +
115D LEU* 3.4 8.7 - - + +
117D PHE* 1.3 74.9 - - - +
119D LEU* 1.3 63.4 + - - +
121D SER* 2.5 29.9 + - - -
122D GLN* 3.3 29.5 + - - +
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Residues in contact with LEU 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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39D ILE* 6.0 0.4 - - + -
92D PHE* 3.6 42.6 - - + -
103D VAL* 4.5 8.1 - - + -
115D LEU* 3.0 32.0 + - + +
116D LEU* 3.1 8.7 + - - +
118D HIS* 1.3 75.6 - - - +
120D PHE* 1.3 60.5 + - - +
122D GLN* 2.9 21.3 + - - -
123D ILE* 3.2 9.9 + - - -
126D ILE* 3.5 29.3 - - + +
129D MSE 3.9 16.2 - - - -
131D PHE* 3.6 36.8 - - + -
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Residues in contact with PHE 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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116D LEU* 2.8 30.0 + - + -
117D PHE* 3.4 31.6 - + - +
119D LEU* 1.3 80.3 - - + +
121D SER* 1.3 61.2 + - - +
122D GLN 3.1 1.0 + - - -
123D ILE* 3.2 31.2 + - + +
129D MSE 4.3 13.7 - - + -
156D MSE 4.1 1.8 - - + -
157D ALA* 3.5 41.7 - - + -
160D PHE* 3.5 48.0 - + + -
161D CYS* 3.9 20.0 - - - -
187D LEU* 4.2 14.4 - - + -
200D LEU* 5.9 0.3 - - - +
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Residues in contact with SER 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 PHE 3.0 12.8 + - - -
118D HIS* 2.5 30.3 + - - -
120D PHE* 1.3 75.7 - - - +
122D GLN* 1.3 66.8 + - - +
123D ILE 3.6 0.6 + - - -
124D HIS* 5.0 4.0 + - - -
160D PHE* 5.6 1.8 - - - -
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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