Contacts of the helix formed by residues 117 - 138 (chain B) in PDB entry 4NAW
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 SER 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B CYS* 3.3 6.6 + - - -
116B PRO* 1.3 85.2 - - - +
118B LYS* 1.3 63.5 + - - +
119B ASP* 3.3 12.3 + - - +
120B ALA* 3.2 31.0 + - - +
121B ILE* 3.7 9.8 + - - +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.1 17.5 - - + -
117B SER* 1.3 73.2 - - - +
119B ASP* 1.3 56.2 - - - +
121B ILE* 2.9 28.4 + - + +
122B GLU* 3.1 12.1 + - - +
154B TRP* 4.0 18.8 - - + +
155B MET* 6.0 0.2 - - - +
158B GLN* 2.7 37.2 + - - +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 3.1 11.8 + - - +
118B LYS* 1.3 79.8 - - - +
120B ALA* 1.3 57.3 + - - +
122B GLU* 3.2 19.8 + - - +
123B ALA* 2.8 33.9 + - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TRP* 3.9 13.9 - - + -
115B CYS* 4.9 1.1 - - - -
116B PRO* 4.1 23.6 - - + -
117B SER* 3.2 22.5 + - - +
118B LYS 3.2 0.2 - - - -
119B ASP* 1.3 77.8 + - - +
121B ILE* 1.3 57.3 + - - +
123B ALA* 3.8 6.4 - - - +
124B HIS* 3.0 28.1 + - - +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR* 4.4 18.4 - - + -
46B THR* 3.5 37.7 - - - +
47B LEU* 4.0 23.1 - - + +
79B TRP* 3.9 17.0 - - + -
115B CYS* 3.5 23.8 - - - -
117B SER 3.8 2.2 - - - +
118B LYS* 2.9 20.3 + - + +
120B ALA* 1.3 74.7 - - - +
122B GLU* 1.3 59.0 + - - +
124B HIS* 3.3 3.5 + - + +
125B PHE* 2.9 28.4 + - - +
154B TRP* 3.8 18.4 - - + -
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LYS 3.1 8.3 + - - +
119B ASP* 3.6 21.6 - - - +
121B ILE* 1.3 75.5 - - - +
123B ALA* 1.3 61.0 + - - +
125B PHE* 3.2 0.7 + - - +
126B MET* 2.8 43.5 + - + +
150B HIS 5.6 0.5 - - - +
151B LYS* 5.2 8.5 - - - +
154B TRP* 3.7 57.5 + - + +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLN* 5.9 2.7 - - - +
140A GLY 5.3 1.3 - - - +
119B ASP* 2.8 28.8 + - - +
120B ALA* 3.8 7.6 - - - +
122B GLU* 1.3 73.4 - - - +
124B HIS* 1.3 63.8 + - - +
126B MET* 4.0 4.6 - - - +
127B SER* 3.0 25.5 + - - -
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Residues in contact with HIS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 4.6 18.7 + - - -
44B TYR* 4.1 18.6 - + - -
79B TRP* 4.2 12.3 - + + -
80B HIS* 3.0 55.6 + + + +
120B ALA 3.0 18.3 + - - +
121B ILE 3.6 4.3 - - - +
123B ALA* 1.3 77.2 - - - +
125B PHE* 1.3 65.0 + - - +
127B SER* 3.2 8.5 + - - -
128B CYS* 3.0 47.9 + - - -
188B ARG* 6.0 1.8 - - - -
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Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR* 3.7 20.4 - + + +
121B ILE 2.9 17.7 + - - +
122B GLU 3.2 3.1 + - - +
124B HIS* 1.3 81.9 - - - +
126B MET* 1.3 74.7 + - - +
128B CYS* 3.2 7.2 + - - +
129B MET* 3.1 41.8 + - - +
153B LEU 4.3 15.9 - - - -
154B TRP* 4.0 26.2 - + + -
157B LEU* 3.6 26.5 - - + -
165B PHE* 3.9 12.1 - + - -
261B PRO* 3.5 37.7 - - + -
262B ASP* 3.7 7.2 - - + -
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLY 3.6 18.4 - - - +
122B GLU* 2.8 36.3 + - + +
123B ALA* 4.0 4.3 - - - +
125B PHE* 1.3 92.3 - - + +
127B SER* 1.3 56.7 + - - +
129B MET* 3.3 11.4 + - + +
130B LYS* 2.8 41.1 + - - +
142B ILE* 4.8 11.2 - - + -
150B HIS* 3.7 56.5 - - + +
153B LEU* 4.9 1.3 - - + -
154B TRP* 4.8 4.3 - - - -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.8 7.5 - - - +
109A ALA* 2.4 41.8 + - - -
110A PRO* 4.2 1.7 - - - +
111A SER 4.9 0.5 + - - -
140A GLY 4.8 1.3 + - - -
123B ALA 3.0 20.5 + - - -
124B HIS* 3.5 8.5 - - - -
125B PHE 3.2 0.2 - - - -
126B MET* 1.3 77.2 - - - +
128B CYS* 1.3 57.0 + - - +
130B LYS* 3.4 8.6 + - - +
131B GLU* 2.9 29.7 + - - +
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Residues in contact with CYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR* 5.1 0.7 - - - -
124B HIS* 3.0 48.6 + - - -
125B PHE* 3.5 9.0 - - - +
127B SER* 1.3 74.3 - - - +
129B MET* 1.3 59.7 - - - +
131B GLU* 3.2 10.1 + - - +
132B ALA* 2.9 28.8 + - - +
188B ARG* 5.0 13.9 - - - -
262B ASP* 3.7 31.2 - - + +
264B PHE* 3.5 9.9 - - + -
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Residues in contact with MET 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PHE* 3.1 44.4 + - + +
126B MET* 3.6 14.8 - - + +
128B CYS* 1.3 76.2 - - - +
130B LYS* 1.3 59.6 + - - +
132B ALA* 3.3 4.0 + - - +
133B ASP* 3.0 29.8 + - - +
142B ILE* 4.7 11.0 - - + +
153B LEU* 3.7 23.3 - - + -
165B PHE* 4.6 0.4 - - + -
169B ASN* 3.5 6.3 - - - +
172B LEU* 3.2 36.3 - - + +
261B PRO 3.8 2.9 - - - +
262B ASP* 3.8 22.4 - - - +
263B ASN* 3.3 21.1 - - - +
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 3.7 26.2 + - - +
108A PHE* 3.6 22.6 - - + -
139A TRP* 3.5 2.0 - - - +
140A GLY* 1.3 80.8 - - - +
126B MET* 2.8 23.7 + - + +
127B SER* 3.7 1.3 - - - +
128B CYS 3.3 0.2 - - - -
129B MET* 1.3 72.7 - - - +
131B GLU* 1.3 65.8 + - - +
133B ASP* 3.4 5.4 + - - +
134B ALA* 3.1 23.6 + - - +
139B SER* 4.6 0.7 + - - -
142B ILE* 4.3 21.3 - - + +
143B ASN* 5.4 5.6 - - - +
150B HIS* 4.6 21.0 + - - -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.5 41.3 - - + -
110A PRO* 5.3 1.0 - - - +
114A GLN* 3.3 16.2 + - - +
123A PHE* 3.6 13.8 - - + -
127B SER* 2.9 14.9 + - - +
128B CYS* 3.5 11.7 - - - +
130B LYS* 1.3 75.0 - - - +
132B ALA* 1.3 63.5 + - - +
134B ALA* 3.3 12.1 + - - +
135B LEU* 3.3 14.7 + - + +
188B ARG* 3.0 26.5 + - - -
200B GLN* 2.9 25.6 + - - +
264B PHE* 4.0 9.2 - - + -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B CYS 2.9 15.7 + - - +
129B MET 3.3 5.8 + - - +
131B GLU* 1.3 77.3 - - - +
133B ASP* 1.3 56.5 + - - +
135B LEU* 3.2 6.8 + - - +
136B LYS* 3.0 32.5 + - - +
186B PRO* 3.6 20.4 - - + +
262B ASP 3.8 2.9 - - - +
263B ASN* 3.6 29.6 - - + +
264B PHE* 3.9 10.7 - - + -
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B MET 3.0 16.9 + - - +
130B LYS 4.1 0.4 - - - +
132B ALA* 1.3 75.6 - - - +
134B ALA* 1.3 61.0 + - - +
136B LYS* 4.1 6.6 - - - +
137B HIS* 2.7 55.5 + - - -
139B SER* 2.9 28.8 + - - -
140B GLN 3.6 0.3 + - - -
141B VAL* 3.3 3.6 + - - +
142B ILE* 2.9 45.0 + - + -
172B LEU* 3.6 15.8 - - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASN* 4.2 15.0 + - + +
107A SER* 5.1 0.9 - - - +
108A PHE* 4.7 6.5 - - + -
123A PHE* 4.0 18.2 - - + -
130B LYS 3.1 12.7 + - - +
131B GLU* 3.3 11.9 + - - +
133B ASP* 1.3 76.9 - - - +
135B LEU* 1.3 60.3 + - - +
138B LYS* 3.1 24.3 + - - +
139B SER* 3.3 23.0 + - - +
183B ARG* 5.3 4.3 + - - -
184B TYR* 5.7 0.2 - - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A CYS* 4.5 4.5 - - + +
123A PHE* 3.6 26.2 - - + -
131B GLU 3.3 14.8 + - - +
132B ALA 3.2 6.4 + - - +
134B ALA* 1.3 81.6 - - - +
136B LYS* 1.3 59.8 + - - +
183B ARG* 3.5 7.3 - - - +
184B TYR* 3.0 43.1 + - + +
185B ILE 4.7 3.1 - - - +
186B PRO* 4.0 28.0 - - + -
187B PHE 5.3 0.4 - - - +
200B GLN* 4.0 21.8 - - + +
201B LYS 5.9 2.0 - - - +
202B LEU* 3.7 30.5 - - + -
264B PHE* 4.4 5.2 - - + -
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA 3.0 26.0 + - - +
133B ASP* 4.2 9.0 - - - +
135B LEU* 1.3 76.6 - - - +
137B HIS* 1.3 76.5 + - + +
138B LYS 3.9 0.4 - - - -
172B LEU* 2.9 23.1 + - - +
173B MET* 3.5 14.5 - - - +
182B PHE* 3.4 35.1 - - + -
183B ARG* 3.1 24.8 + - - +
184B TYR 3.6 8.3 - - - +
186B PRO* 3.5 27.8 - - + -
255B SER* 4.7 0.7 - - - +
263B ASN* 2.8 33.9 + - - +
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASP* 2.7 38.7 + - - +
136B LYS* 1.3 89.2 - - + +
138B LYS* 1.3 72.1 + - - +
139B SER 3.1 0.2 - - - -
140B GLN* 3.1 24.7 - - + +
141B VAL* 3.5 30.8 - - + +
171B LYS 4.7 0.2 - - - -
172B LEU 3.2 28.3 - - - -
174B GLU 2.5 25.2 + - - -
175B TYR* 4.5 8.5 - - + -
176B PRO* 4.8 8.3 - - + -
182B PHE* 3.9 8.3 - + - -
183B ARG* 5.4 1.3 - - - -
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA* 3.1 17.6 + - - +
135B LEU 4.7 0.4 + - - -
136B LYS 3.9 0.2 - - - -
137B HIS* 1.3 79.6 - - - +
139B SER* 1.3 67.6 + - - +
140B GLN* 3.1 26.0 + - + +
143B ASN* 5.0 0.3 + - - -
183B ARG* 3.9 47.5 - - - +
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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
------------------------------------------------------------
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