Contacts of the helix formed by residues 140 - 159 (chain B) in PDB entry 4NY0
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 ASP 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS 4.1 2.6 - - - +
77B VAL 4.1 0.2 - - - -
78B LYS* 3.2 30.7 + - + +
79B HIS* 3.1 41.5 + - + +
137B PHE 3.1 14.3 + - - +
138B THR 3.2 0.2 - - - -
139B GLU* 1.3 80.4 - - - +
141B LYS* 1.3 57.7 + - - +
142B PRO* 3.6 13.0 - - - +
143B THR* 3.0 36.9 + - - -
144B LEU 3.3 1.7 + - - -
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PHE 4.2 0.7 - - - -
138B THR 4.5 8.2 + - - +
139B GLU 4.1 0.2 - - - -
140B ASP* 1.3 70.6 - - - +
142B PRO* 1.4 71.8 - - + +
143B THR 3.2 0.2 - - - -
144B LEU* 3.8 17.3 - - + -
145B ASN* 3.2 44.0 + - - +
236B ARG* 4.5 31.8 - - - +
237B GLU* 5.0 21.1 - - - +
240B ILE* 6.1 1.6 - - - -
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Residues in contact with PRO 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.9 15.1 - - + -
75B HIS* 3.5 26.9 - - + +
76B LYS* 3.9 14.4 - - + +
77B VAL* 4.0 12.8 - - + -
140B ASP* 3.3 13.0 - - - +
141B LYS* 1.4 92.2 - - + +
143B THR* 1.3 54.8 + - - +
145B ASN* 4.0 4.2 - - + +
146B PHE* 3.2 25.3 + - - +
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Residues in contact with THR 143 (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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77B VAL* 3.4 14.7 - - - +
79B HIS* 4.5 3.0 + - + -
82B CYS* 5.6 0.4 - - + -
83B TYR* 2.9 32.6 + - + +
126B ILE* 3.6 15.7 - - + -
137B PHE* 3.7 31.0 - - + -
140B ASP* 3.0 28.2 + - - +
142B PRO* 1.3 72.7 - - - +
144B LEU* 1.3 66.8 + - - +
145B ASN 3.2 1.1 - - - -
146B PHE* 3.6 0.4 - - - +
147B PHE* 2.9 23.9 + - - +
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Residues in contact with LEU 144 (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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134B LEU* 4.8 4.5 - - + +
137B PHE* 3.3 36.2 + - + +
138B THR* 4.1 28.7 - - + -
140B ASP 3.3 4.0 + - - -
141B LYS* 3.8 15.3 - - + +
143B THR* 1.3 78.0 - - - +
145B ASN* 1.3 61.8 + - - +
147B PHE* 3.6 2.4 + - - +
148B TYR* 3.0 24.3 + - - +
237B GLU* 4.3 22.9 - - + +
240B ILE* 3.9 31.6 - - + -
241B LEU* 4.6 6.7 - - + -
244B PHE* 4.5 10.5 - - + -
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Residues in contact with ASN 145 (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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42B TYR 4.9 0.4 - - - -
44B GLU* 4.7 8.4 + - + +
141B LYS* 3.2 49.2 + - - +
142B PRO* 4.0 4.0 - - + +
144B LEU* 1.3 80.2 - - - +
146B PHE* 1.3 53.6 + - - +
148B TYR* 3.1 7.9 + - - +
149B GLN* 2.7 43.6 + - + +
178B ARG* 3.4 27.1 - - - +
240B ILE* 3.6 21.0 - - - +
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Residues in contact with PHE 146 (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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42B TYR* 3.4 44.2 - + + +
43B PHE* 3.5 43.5 - + + +
83B TYR* 3.8 24.7 - + - +
124B LEU* 3.3 33.0 - - + -
126B ILE* 3.6 19.1 - - + -
142B PRO 3.2 17.2 + - - +
143B THR 3.2 4.7 + - - +
145B ASN* 1.3 76.7 - - - +
147B PHE* 1.3 56.8 + - - +
149B GLN* 3.2 2.9 + - - +
150B GLN* 2.9 45.7 + - - +
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Residues in contact with PHE 147 (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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126B ILE* 3.7 29.6 - - + -
129B LEU* 3.8 28.3 - - + -
133B PHE* 3.8 24.2 - + - -
134B LEU* 4.1 2.9 - - + -
137B PHE* 3.9 18.8 - + + -
143B THR 2.9 16.0 + - - +
144B LEU* 3.7 3.6 - - + +
146B PHE* 1.3 78.7 - - - +
148B TYR* 1.3 63.5 + - - +
150B GLN* 3.1 15.5 + - - +
151B VAL* 2.8 42.7 + - + +
244B PHE* 3.6 26.5 - + - -
253B PHE* 3.8 28.0 - + - -
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Residues in contact with TYR 148 (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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144B LEU 3.0 16.4 + - - +
145B ASN* 3.1 12.3 + - - +
147B PHE* 1.3 75.9 - - - +
149B GLN* 1.3 79.5 + - - +
151B VAL* 4.0 0.7 - - - +
152B LYS* 3.0 38.4 + - + +
174B LEU 4.7 1.0 - - - -
175B GLU* 2.9 46.2 + - - +
178B ARG* 3.5 22.3 - - + +
239B SER 5.6 0.4 - - - -
240B ILE* 3.8 33.9 - - + -
243B PHE* 3.5 44.3 - + + -
244B PHE* 3.6 12.2 - + - -
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Residues in contact with GLN 149 (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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42B TYR* 3.5 33.9 - - + +
44B GLU* 4.2 8.7 + - + -
49B PRO* 5.6 1.9 - - - +
52B TRP* 3.4 32.4 - - + -
145B ASN* 2.7 23.6 + - + +
146B PHE 3.5 1.3 - - - +
148B TYR* 1.3 89.0 - - - +
150B GLN* 1.3 58.5 + - - +
152B LYS* 3.6 24.4 + - - +
153B SER* 2.9 31.9 + - - -
175B GLU* 4.7 0.6 + - - -
178B ARG* 3.6 26.5 - - - +
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Residues in contact with GLN 150 (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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42B TYR* 3.5 23.1 - - + -
125B ARG* 3.3 41.8 - - - +
126B ILE* 2.7 50.1 + - - -
146B PHE* 2.9 23.2 + - - +
147B PHE* 3.5 20.5 - - - +
149B GLN* 1.3 76.3 - - - +
151B VAL* 1.3 65.4 + - - +
153B SER* 3.7 1.0 - - - -
154B ASP* 3.1 25.6 + - - +
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Residues in contact with VAL 151 (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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147B PHE* 2.8 49.8 + - + +
148B TYR 4.1 0.4 - - - +
150B GLN* 1.3 74.8 - - + +
152B LYS* 1.3 61.2 + - - +
154B ASP* 3.5 7.1 + - - +
155B TYR* 2.9 26.5 + - - +
243B PHE* 4.7 0.7 - - + -
244B PHE* 3.7 26.2 - - + -
247B LEU* 3.6 26.0 - - + +
251B TYR* 4.6 3.4 - - + -
253B PHE* 3.8 27.4 - - + -
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Residues in contact with LYS 152 (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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49B PRO* 5.7 7.1 - - - +
148B TYR* 3.0 49.3 + - + +
149B GLN* 3.6 26.4 + - - +
151B VAL* 1.3 74.1 - - - +
153B SER* 1.3 59.4 + - - +
155B TYR* 3.2 9.2 + - + +
156B MET* 2.9 46.4 + - + +
175B GLU* 3.9 29.0 + - + +
205B ARG 4.6 10.3 + - - -
243B PHE* 4.0 23.5 - - + -
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Residues in contact with SER 153 (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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42B TYR* 3.8 24.4 + - - -
149B GLN* 2.9 18.6 + - - -
150B GLN 3.7 4.7 - - - -
152B LYS* 1.3 75.3 - - - +
154B ASP* 1.3 65.0 + - - +
156B MET* 3.3 6.4 + - - +
157B LEU* 3.0 41.1 + - - +
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Residues in contact with ASP 154 (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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42B TYR* 4.3 3.5 + - - -
125B ARG* 2.4 42.7 + - - -
150B GLN* 3.1 20.4 + - - +
151B VAL* 3.8 7.6 - - - +
153B SER* 1.3 76.4 + - - +
155B TYR* 1.3 62.1 + - - +
157B LEU* 4.8 4.8 - - - +
158B GLU* 3.1 38.4 + - - +
251B TYR* 3.5 23.6 + - + +
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Residues in contact with TYR 155 (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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151B VAL 2.9 15.7 + - - +
152B LYS* 3.2 14.1 + - - +
154B ASP* 1.3 77.4 - - - +
156B MET* 1.3 87.2 + - + +
159B ILE* 3.2 33.0 + - + -
160B ALA* 2.9 48.7 + - + +
163B VAL* 4.5 7.2 - - + -
167B ILE* 5.3 0.4 - - + -
168B ALA* 3.4 33.4 + - - +
171B LEU* 3.5 31.4 - - + +
172B GLY 5.2 0.4 + - - -
206B PHE 5.4 2.4 + - - -
208B PRO* 4.6 3.6 - - + +
243B PHE* 4.2 12.3 - + - -
247B LEU* 3.8 23.1 - - + -
251B TYR* 4.9 3.8 + - + -
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Residues in contact with MET 156 (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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152B LYS* 2.9 37.9 + - + +
153B SER* 3.3 8.0 + - - +
155B TYR* 1.3 98.6 - - + +
157B LEU* 1.3 66.3 + - + +
158B GLU 3.1 5.2 + - - -
159B ILE 4.4 0.2 + - - -
160B ALA* 3.7 20.9 + - - +
161B ASP* 4.9 6.2 + - - +
175B GLU* 6.3 0.7 - - + -
204B LYS 5.1 2.9 - - - +
205B ARG 3.7 16.2 - - - +
206B PHE* 3.5 35.7 - - - +
207B PHE 4.2 10.8 - - - +
208B PRO* 5.1 1.3 - - - -
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Residues in contact with LEU 157 (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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153B SER* 3.0 33.3 + - - +
154B ASP* 4.2 5.2 - - - +
156B MET* 1.3 82.7 - - + +
158B GLU* 1.3 67.8 + - + +
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Residues in contact with GLU 158 (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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154B ASP* 3.1 22.7 + - - +
156B MET 3.1 2.2 + - - -
157B LEU* 1.3 90.2 - - + +
159B ILE* 1.3 72.7 + - + +
160B ALA 3.9 0.7 - - - -
161B ASP* 6.5 0.2 - - - -
162B GLN* 3.4 14.4 + - - +
251B TYR* 3.8 21.8 + - + -
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Residues in contact with ILE 159 (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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155B TYR* 3.2 31.3 + - + +
158B GLU* 1.3 84.6 - - + +
160B ALA* 1.3 68.2 + - - +
161B ASP 3.3 2.5 - - - +
162B GLN* 3.5 18.8 + - + +
163B VAL* 3.4 26.6 + - + +
247B LEU* 4.0 3.8 - - + -
250B VAL* 4.1 14.6 - - + +
251B TYR* 3.5 53.4 - - + -
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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