Contacts of the helix formed by residues 135 - 158 (chain A) in PDB entry 4TXQ
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 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLU 4.7 4.9 - - - +
134A LEU* 1.3 78.6 - - - +
136A ASP* 1.3 65.2 + - - +
137A GLU* 3.5 9.8 + - - +
138A ASN* 2.8 40.6 + - - +
139A VAL* 3.0 22.8 + - - +
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Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 1.3 74.7 - - - +
137A GLU* 1.3 59.8 + - + +
139A VAL* 3.3 11.7 + - - +
140A LYS* 3.0 62.0 + - - +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 3.2 8.6 + - - +
136A ASP* 1.3 78.1 - - + +
138A ASN* 1.3 66.0 + - - +
140A LYS* 3.3 8.0 + - + +
141A HIS* 2.7 46.1 + - + +
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 5.0 11.9 + - - +
125A ILE* 3.8 30.5 - - + +
128A ILE* 4.5 15.1 - - - +
133A GLU 4.7 0.7 - - - +
134A LEU* 3.6 18.3 - - + +
135A THR* 2.8 51.7 + - - +
137A GLU* 1.3 76.8 - - - +
139A VAL* 1.3 58.5 + - - +
141A HIS* 3.8 1.5 - - - -
142A ARG* 2.9 31.7 + - - +
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.9 25.8 - - + +
135A THR 3.0 14.5 + - - +
136A ASP* 3.5 16.2 - - - +
138A ASN* 1.3 79.8 - - - +
140A LYS* 1.3 60.6 + - + +
142A ARG* 3.5 7.5 + - - +
143A LYS* 3.1 30.4 + - + +
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Residues in contact with LYS 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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136A ASP* 3.0 50.2 + - - +
137A GLU* 3.9 7.9 - - + +
139A VAL* 1.3 77.4 - - + +
141A HIS* 1.3 63.7 + - + +
143A LYS* 3.5 5.2 + - - +
144A TYR* 2.9 32.4 + - - +
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Residues in contact with HIS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 5.1 12.8 - - + +
98A PHE* 3.7 42.0 - + + -
125A ILE* 3.9 13.9 - - + -
137A GLU* 2.7 45.6 + - + +
138A ASN* 3.8 3.4 - - - +
140A LYS* 1.3 76.9 - - + +
142A ARG* 1.3 60.7 + - - +
144A TYR* 3.7 5.0 - - - +
145A ALA* 2.9 33.1 + - - +
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER* 3.7 17.8 + - - +
125A ILE* 3.5 24.8 - - + +
126A ASP* 2.7 30.1 + - - -
134A LEU* 4.9 9.4 - - - -
138A ASN 2.9 18.1 + - - +
139A VAL* 3.7 7.0 - - - +
141A HIS* 1.3 77.4 - - - +
143A LYS* 1.3 60.8 + - - +
146A ARG* 2.9 60.2 + - - +
160B GLU* 5.8 0.6 - - - +
161B THR* 3.1 38.2 + - - +
162B PRO* 3.3 25.1 + - - -
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Residues in contact with LYS 143 (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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139A VAL* 3.1 19.8 + - + +
140A LYS* 3.9 5.8 - - - +
142A ARG* 1.3 79.0 - - - +
144A TYR* 1.3 64.9 + - - +
146A ARG* 3.9 1.4 - - - +
147A TRP* 2.9 27.2 + - + +
105B ASP* 2.7 51.8 + - - -
106B ARG* 4.4 4.6 + - - +
108B GLY* 4.9 1.8 - - - +
110B PHE* 3.9 16.7 - - + -
148B LYS* 5.1 6.3 - - - +
162B PRO* 3.9 29.6 - - - +
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Residues in contact with TYR 144 (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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98A PHE* 3.5 29.6 - + + -
102A ASP* 3.9 15.6 + - - -
105A ASP* 4.1 5.0 + - - -
118A PHE* 4.2 9.2 - + - -
140A LYS 2.9 19.1 + - - +
141A HIS* 3.7 6.1 - - - +
143A LYS* 1.3 75.7 - - - +
145A ALA* 1.3 57.4 + - - +
147A TRP* 3.3 8.3 + + - +
148A LYS* 3.0 71.4 + - + +
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Residues in contact with ALA 145 (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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98A PHE* 4.0 11.2 - - + -
118A PHE* 3.3 46.3 - - + +
121A ALA* 4.7 0.7 - - + -
122A SER* 4.1 9.4 - - - +
125A ILE* 5.9 0.4 - - + -
141A HIS 2.9 19.4 + - - +
142A ARG 3.9 2.7 - - - +
144A TYR* 1.3 75.8 - - - +
146A ARG* 1.3 65.6 + - - +
148A LYS* 3.5 0.7 + - - -
149A ALA* 3.0 26.2 + - - +
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 4.2 27.3 + - + -
122A SER* 3.3 22.7 + - - +
123A LEU* 5.3 2.6 - - - +
126A ASP* 4.8 7.3 + - - -
142A ARG* 2.9 54.2 + - - +
143A LYS 3.9 0.7 - - - +
145A ALA* 1.3 75.2 - - - +
147A TRP* 1.3 64.2 + - - +
149A ALA* 3.8 3.9 - - - +
150A THR* 3.0 31.3 + - + +
151B TYR* 2.9 37.1 + - + +
155B CYS* 3.9 8.3 - - - -
160B GLU* 3.2 29.1 + - - +
161B THR 3.2 17.6 + - - -
162B PRO 2.9 11.5 + - - +
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Residues in contact with TRP 147 (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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143A LYS* 2.9 21.2 + - + +
144A TYR* 3.5 7.4 - + - +
145A ALA 3.2 0.2 - - - -
146A ARG* 1.3 78.0 - - - +
148A LYS* 1.3 81.7 + - + +
150A THR* 3.5 2.1 + - - -
151A TYR* 2.8 57.3 + + + +
144B TYR* 3.7 35.6 - + - -
147B TRP* 3.3 33.2 - + - -
148B LYS* 3.2 58.1 - - + +
151B TYR* 4.2 20.6 + + + -
162B PRO 5.2 0.4 + - - -
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Residues in contact with LYS 148 (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 ASP* 3.2 38.5 + - - -
118A PHE* 3.7 23.3 - - + -
144A TYR* 3.0 54.2 + - + +
145A ALA 4.1 1.6 - - - +
147A TRP* 1.3 92.1 - - + +
149A ALA* 1.3 55.6 + - - +
151A TYR* 4.5 7.6 - - + -
152A ILE* 2.8 48.2 + - + +
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Residues in contact with ALA 149 (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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115A ILE* 3.6 35.9 - - + +
118A PHE* 3.9 5.3 - - + +
119A TYR* 3.8 22.9 - - + -
145A ALA 3.0 18.9 + - - +
146A ARG 3.8 3.4 - - - +
147A TRP 3.2 0.2 - - - -
148A LYS* 1.3 77.6 - - - +
150A THR* 1.3 64.4 + - + +
152A ILE* 5.0 0.2 - - - -
153A HIS* 3.0 26.9 + - - +
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Residues in contact with THR 150 (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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119A TYR* 5.2 13.0 - - + -
146A ARG* 3.0 18.8 + - + +
147A TRP* 3.5 4.5 + - - -
149A ALA* 1.3 78.7 - - + +
151A TYR* 1.3 59.9 + - - +
153A HIS* 3.6 6.1 - - - +
154A ASN* 2.9 32.2 + - - +
147B TRP* 3.3 24.9 + - + -
151B TYR* 3.6 31.4 - - + +
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Residues in contact with TYR 151 (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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147A TRP* 2.8 56.3 + + + +
148A LYS* 3.9 8.3 - - + +
150A THR* 1.3 77.3 + - - +
152A ILE* 1.3 68.9 + - + +
154A ASN* 3.3 2.3 + - - +
155A CYS* 2.9 45.3 + - - -
162A PRO* 2.8 41.3 + - + +
140B LYS* 4.9 4.7 + - - +
143B LYS* 3.9 36.8 - - + +
144B TYR* 4.3 10.6 + + + +
147B TRP* 3.6 18.2 - + + -
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Residues in contact with ILE 152 (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 ASP* 3.9 11.9 - - - +
110A PHE* 3.9 37.2 - - + -
114A MET* 3.7 29.4 - - + -
115A ILE* 3.9 22.0 - - + -
118A PHE* 4.3 2.0 - - + -
148A LYS* 2.8 42.2 + - + +
151A TYR* 1.3 79.5 - - + +
153A HIS* 1.3 63.4 + - - +
155A CYS* 3.3 6.2 + - - +
156A LEU* 3.0 27.8 + - + +
162A PRO* 4.2 13.9 - - + -
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Residues in contact with HIS 153 (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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115A ILE* 3.7 29.0 - - + +
149A ALA 3.0 20.7 + - - +
150A THR* 3.6 7.0 - - - +
152A ILE* 1.3 79.6 - - - +
154A ASN* 1.3 62.0 + - + +
156A LEU* 3.3 2.8 + - - +
157A LYS* 2.9 48.7 + - + +
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Residues in contact with ASN 154 (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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150A THR 2.9 21.2 + - - +
151A TYR 4.0 2.5 - - - +
153A HIS* 1.3 74.2 - - + +
155A CYS* 1.3 69.0 + - - +
157A LYS* 3.5 13.3 + - - +
158A ASN* 2.9 38.1 + - - +
160A GLU* 5.7 0.7 - - - +
147B TRP* 2.9 51.0 - - + +
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Residues in contact with CYS 155 (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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151A TYR* 2.9 53.7 + - - -
152A ILE 3.3 8.7 + - - +
154A ASN* 1.3 76.8 + - - +
156A LEU* 1.3 58.1 + - - +
158A ASN* 2.9 19.5 + - - +
160A GLU* 2.9 42.3 + - - +
161A THR 4.2 3.8 - - - -
162A PRO* 3.7 20.6 - - + -
143B LYS* 4.7 9.6 - - - -
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Residues in contact with LEU 156 (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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110A PHE* 4.0 27.6 - - + +
111A HIS* 4.2 4.3 - - - +
115A ILE* 3.9 25.1 - - + -
152A ILE* 3.0 24.6 + - + +
153A HIS* 3.8 3.4 - - - +
155A CYS* 1.3 75.7 - - - +
157A LYS* 1.3 63.6 + - - +
159A GLY* 3.2 12.3 + - - +
160A GLU 3.9 14.1 - - - +
161A THR* 5.3 0.7 - - - -
162A PRO* 4.3 15.3 - - + -
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Residues in contact with LYS 157 (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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153A HIS* 2.9 38.8 + - + +
154A ASN* 3.6 14.3 - - - +
156A LEU* 1.3 78.2 - - - +
158A ASN* 1.3 71.7 + - - +
159A GLY 3.7 1.2 + - - -
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Residues in contact with ASN 158 (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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154A ASN* 2.9 46.0 + - - +
155A CYS* 2.9 5.7 + - - +
157A LYS* 1.3 92.3 + - - +
159A GLY* 1.3 59.9 + - - +
160A GLU* 3.0 22.1 + - + +
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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
------------------------------------------------------------
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