Contacts of the helix formed by residues 121 - 143 (chain A) in PDB entry 5TJB
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 THR 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ALA* 4.7 0.7 - - - +
120A TYR* 1.3 86.9 + - + +
122A ARG* 1.3 65.6 + - - +
123A GLU* 3.6 8.1 + - - +
124A GLN* 3.1 41.2 + - - +
125A LEU* 3.0 23.7 + - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A THR* 1.3 74.4 - - - +
123A GLU* 1.3 58.4 + - - +
125A LEU* 3.2 3.2 + - - +
126A TYR* 2.8 37.9 + - + -
225A PHE* 3.2 63.0 - - + +
226A HIS* 3.4 35.0 + - - -
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 3.3 7.1 - - - +
122A ARG* 1.3 79.3 - - - +
124A GLN* 1.3 56.3 + - - +
126A TYR* 3.2 8.1 + - - +
127A GLN* 2.8 59.7 + - + +
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Residues in contact with GLN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 5.6 0.5 - - - +
118A ALA 4.5 1.9 - - - +
119A ALA* 3.7 11.9 - - + -
120A TYR* 2.8 39.4 + - - +
121A THR* 3.1 37.5 + - - +
123A GLU* 1.3 76.9 - - - +
125A LEU* 1.3 59.7 + - - +
127A GLN* 3.4 13.8 + - - +
128A ALA* 2.9 31.6 + - - +
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ALA* 4.3 15.5 - - + +
121A THR 3.0 16.9 + - - +
122A ARG* 3.7 6.5 - - - +
124A GLN* 1.3 77.7 - - - +
126A TYR* 1.3 61.5 + - - +
128A ALA* 3.8 1.5 - - + +
129A ILE* 3.2 38.2 + - + +
223A LEU* 4.1 13.2 - - + -
225A PHE* 4.1 19.5 - - + -
228A LEU* 4.1 13.0 - - + -
231A VAL* 5.2 1.8 - - + -
262A PHE* 3.4 41.3 - - + -
271A ILE* 3.8 28.3 - - + -
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 2.8 28.1 + - + +
123A GLU* 3.2 7.8 + - - +
125A LEU* 1.3 75.0 - - - +
127A GLN* 1.3 65.2 + - + +
129A ILE* 3.3 4.6 + - + +
130A PHE* 3.0 56.3 + + + -
221A LEU* 3.5 27.0 + - + -
222A THR* 3.3 9.9 - - - +
223A LEU* 2.7 48.9 + - + +
225A PHE* 3.6 23.7 - + - -
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.9 20.8 - - + +
123A GLU* 2.8 62.2 + - + +
124A GLN* 3.7 14.6 - - - +
126A TYR* 1.3 73.4 - - + +
128A ALA* 1.3 57.4 - - - +
130A PHE* 4.0 6.8 - - - +
131A HIS* 2.8 33.6 + - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE 4.5 2.9 - - - +
107A LEU* 4.3 15.2 - - + +
117A PHE* 6.6 0.2 - - + -
124A GLN 2.9 19.1 + - - +
125A LEU* 3.8 5.2 - - - +
126A TYR 3.2 0.2 - - - -
127A GLN* 1.3 77.9 - - - +
129A ILE* 1.3 63.6 + - - +
131A HIS* 3.7 4.9 - - - +
132A ALA* 3.1 23.4 + - - +
262A PHE* 3.9 21.8 - - + -
273A ILE* 4.3 13.9 - - + -
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 3.2 34.2 + - + +
126A TYR* 3.7 4.5 - - - +
128A ALA* 1.3 78.1 - - - +
130A PHE* 1.3 68.7 + - + +
132A ALA* 3.3 2.4 + - - +
133A VAL* 3.2 23.4 + - + +
165A LEU* 3.7 35.0 - - + -
221A LEU* 4.2 11.7 - - + -
223A LEU* 4.1 20.9 - - + -
231A VAL* 4.0 21.5 - - + -
233A ILE* 4.1 8.1 - - + -
262A PHE* 4.0 20.6 - - + -
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Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 3.0 58.7 + + + +
127A GLN* 4.0 5.2 - - - +
129A ILE* 1.3 75.0 - - + +
131A HIS* 1.3 62.1 + - - +
133A VAL 3.2 1.4 + - - -
134A ASP* 2.8 36.5 + - - +
218A TYR* 3.6 27.5 + + - -
219A LYS* 3.5 65.5 - - + +
221A LEU* 4.4 16.2 - - + -
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Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A HIS 5.2 2.2 + - - -
104A LEU 3.5 15.4 + - - -
105A PHE 3.6 19.1 - - - -
106A LEU 4.5 1.2 + - - -
107A LEU* 3.6 46.2 + - + +
127A GLN 2.8 23.6 + - - +
128A ALA 3.7 3.8 - - - +
130A PHE* 1.3 73.5 - - - +
132A ALA* 1.3 62.0 + - - +
134A ASP* 3.7 8.0 + - - +
135A GLN* 2.9 52.0 + - + +
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.5 29.2 + - + +
128A ALA 3.1 12.0 + - - +
129A ILE 3.6 8.5 - - - +
131A HIS* 1.3 78.5 - - - +
133A VAL* 1.3 58.0 + - - +
135A GLN* 3.3 4.1 + - - +
136A TYR* 2.9 27.4 + - - +
163A LEU* 5.5 1.1 - - - -
233A ILE* 3.8 20.0 - - + -
235A PHE* 5.6 1.5 - - + -
260A ILE* 4.2 16.8 - - + -
262A PHE* 5.4 2.9 - - + -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ILE 3.3 14.4 - - - +
130A PHE 3.2 2.3 + - - +
132A ALA* 1.3 73.1 - - - +
134A ASP* 1.3 67.2 + - - +
136A TYR* 3.0 10.1 + - - +
137A LEU* 3.0 22.5 + - + +
163A LEU* 4.4 20.0 - - + -
165A LEU* 4.6 8.3 - - + -
195A VAL* 4.2 24.9 - - + -
218A TYR* 3.4 46.0 - - + +
233A ILE* 4.1 15.3 - - + -
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Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 2.8 24.9 + - - +
131A HIS* 3.7 7.7 + - - +
133A VAL* 1.3 70.5 - - - +
135A GLN* 1.3 60.7 + - + +
137A LEU* 3.1 12.6 + - - +
138A ALA* 2.9 30.0 + - - +
218A TYR* 2.6 27.3 + - - -
219A LYS* 3.3 23.8 + - - -
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Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A HIS 5.4 0.4 + - - -
104A LEU* 3.0 46.5 + - + +
105A PHE* 3.6 13.3 - - + -
131A HIS* 2.9 48.7 + - + +
132A ALA 3.4 4.9 - - - +
134A ASP* 1.3 77.1 - - + +
136A TYR* 1.3 65.6 + - - +
138A ALA* 3.7 10.4 - - - +
139A LEU* 2.9 27.4 + - + +
142A VAL* 4.8 12.6 - - - +
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.6 12.5 - + + -
132A ALA 2.9 14.0 + - - +
133A VAL 3.0 8.0 + - - +
135A GLN* 1.3 78.0 - - - +
137A LEU* 1.3 67.4 + - + +
139A LEU* 3.4 9.9 - - + +
149A TYR* 2.7 62.7 + + - +
150A VAL 5.2 1.0 + - - -
162A GLY* 3.5 15.8 + - - -
163A LEU* 3.5 33.7 - - + -
195A VAL* 4.6 3.4 - - + -
197A PRO* 3.4 31.5 - - + +
235A PHE* 3.6 44.0 - + + -
236A ARG 5.0 2.2 + - - -
237A LEU* 4.5 7.0 - - + -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 3.0 24.0 + - + +
134A ASP* 3.5 11.0 - - - +
136A TYR* 1.3 85.7 - - + +
138A ALA* 1.3 58.1 + - - +
140A PRO* 3.9 4.0 - - - +
141A ASP* 5.5 0.3 - - - +
149A TYR* 3.2 13.1 + - - -
195A VAL* 3.8 26.5 - - + -
197A PRO* 3.9 13.6 - - + +
198A PRO* 5.6 1.6 - - - +
199A GLU* 3.5 62.7 - - + +
216A SER* 4.3 19.1 - - - +
218A TYR* 4.7 4.9 - - + -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASP 2.9 16.3 + - - +
135A GLN* 3.7 11.2 - - - +
137A LEU* 1.3 75.1 - - - +
139A LEU* 1.3 66.2 + - - +
140A PRO* 3.3 4.0 - - - -
141A ASP* 2.8 26.9 + - + +
142A VAL* 3.4 22.1 + - + -
199A GLU* 4.9 5.4 - - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 4.2 12.8 - - + -
105A PHE* 4.0 22.7 - - + -
135A GLN 2.9 11.0 + - - +
136A TYR* 3.4 15.3 - - - +
137A LEU 3.3 0.2 - - - -
138A ALA* 1.3 75.5 - - - +
140A PRO* 1.3 66.6 - - + +
142A VAL* 3.9 7.0 - - + -
143A SER* 3.0 56.6 + - - +
147A TYR* 4.0 18.8 - - + +
149A TYR* 4.1 5.6 - - + +
237A LEU* 3.6 41.7 - - + -
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Residues in contact with PRO 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU 3.9 3.4 - - - +
138A ALA 3.3 5.6 - - - -
139A LEU* 1.3 96.3 - - + +
141A ASP* 1.3 69.0 + - - +
142A VAL 3.7 0.5 + - - -
143A SER 4.9 4.3 + - - +
147A TYR 5.4 7.9 - - - +
149A TYR* 3.4 29.2 - - + +
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Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU 5.5 0.3 - - - +
138A ALA* 2.8 22.1 + - + +
140A PRO* 1.3 82.0 - - - +
142A VAL* 1.3 66.4 + - + +
199A GLU* 5.1 5.2 - - - +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 4.6 15.1 - - + +
135A GLN* 4.8 15.5 - - - +
138A ALA* 3.7 28.5 - - + +
139A LEU* 3.3 12.1 + - + +
140A PRO 3.4 0.4 - - - -
141A ASP* 1.3 88.8 - - + +
143A SER* 1.3 73.9 + - - +
144A LEU* 3.7 7.8 + - - +
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.1 16.6 - - - +
139A LEU* 3.0 39.9 + - - +
140A PRO 5.0 4.0 - - - +
142A VAL* 1.3 84.4 + - - +
144A LEU* 1.3 63.4 + - - +
145A GLY 2.9 23.2 + - - +
147A TYR* 3.4 17.7 - - - -
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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