Contacts of the helix formed by residues 170 - 185 (chain B) in PDB entry 1NZX
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 PHE 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU* 4.6 0.2 - - - -
112B LYS* 3.3 26.9 - - - +
120B VAL* 6.1 0.9 - - + -
121B ASP* 3.3 13.0 - - - +
167B PRO 4.8 0.4 - - - -
168B TRP 4.6 0.4 - - - -
169B ASN* 1.3 103.3 + - - +
171B PRO* 1.3 61.8 - - - +
172B LEU 3.6 1.8 - - - -
173B LEU* 3.9 28.9 - - + -
174B MET* 2.8 46.3 + - + +
296B PHE* 4.0 26.7 - + - -
297B ASN* 3.6 27.4 - - + -
300B GLN 3.9 2.9 - - - -
301B CYS* 4.2 20.2 - - - -
302B CYS* 5.3 2.7 - - - -
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Residues in contact with PRO 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU* 3.2 32.1 - - - +
110B ASN* 4.0 7.4 - - + +
112B LYS* 4.6 2.2 - - - +
166B ILE* 4.0 6.3 - - + +
167B PRO 4.4 9.2 - - - +
168B TRP 3.2 22.2 - - - +
169B ASN 3.6 3.1 - - - +
170B PHE* 1.3 83.8 - - - +
172B LEU* 1.3 61.4 + - - +
174B MET* 4.0 1.9 - - - +
175B GLN* 3.2 19.2 + - - +
197B THR* 3.3 35.0 - - + +
200B THR* 3.6 10.1 - - - +
201B ALA* 5.4 5.0 - - + +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 6.1 0.7 - - + -
102B LEU* 4.0 21.3 - - + +
106B GLU* 2.9 27.0 + - - +
121B ASP* 5.8 1.3 - - + -
122B LEU* 3.7 31.4 - - + -
125B VAL* 3.6 19.6 - - + +
171B PRO* 1.3 73.1 - - - +
173B LEU* 1.3 63.6 + - - +
175B GLN* 3.2 16.2 + - - +
176B ALA* 3.0 22.0 + - - +
200B THR* 3.6 29.6 - - - +
201B ALA 4.3 0.4 - - - +
204B VAL* 3.4 32.5 - - + -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU* 4.7 0.4 + - - -
121B ASP* 4.7 12.0 + - - +
124B MET* 3.7 61.7 - - + +
125B VAL* 3.6 11.8 - - + +
170B PHE* 3.5 32.4 + - + -
171B PRO 3.4 0.4 - - - -
172B LEU* 1.3 78.4 - - - +
174B MET* 1.3 60.9 + - + +
176B ALA* 3.1 5.1 + - + +
177B TRP* 2.9 69.2 + - + +
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Residues in contact with MET 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 3.9 22.7 - - + -
167B PRO* 3.8 20.9 - - + +
169B ASN* 4.3 3.4 - - - +
170B PHE* 2.8 44.1 + - + +
171B PRO 4.0 2.5 - - - +
173B LEU* 1.3 79.7 - - + +
175B GLN* 1.3 62.2 + - - +
177B TRP* 3.4 50.4 + - + +
178B LYS* 3.2 30.0 + - - +
244B THR* 4.0 26.9 - - - -
302B CYS* 6.4 1.6 - - - -
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Residues in contact with GLN 175 (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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166B ILE* 3.7 16.3 - - + +
171B PRO 3.2 10.3 + - - +
172B LEU* 3.2 15.7 + - - +
173B LEU 3.2 0.4 - - - -
174B MET* 1.3 78.8 - - - +
176B ALA* 1.3 56.9 + - - +
178B LYS* 3.2 1.7 + - - +
179B LEU* 2.8 53.9 + - + +
191B MET* 3.8 13.5 - - - +
201B ALA* 3.3 36.2 - - + +
204B VAL* 3.3 42.3 - - - +
220B ILE* 3.8 12.5 - - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 4.1 35.7 - - + +
128B CYS* 3.5 17.8 - - + -
129B LEU* 4.1 14.8 - - + +
172B LEU 3.0 12.0 + - - +
173B LEU* 3.4 9.6 - - + +
175B GLN* 1.3 76.5 - - - +
177B TRP* 1.3 59.6 + - - +
179B LEU* 4.8 1.3 - - - -
180B GLY* 2.9 26.5 + - - -
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Residues in contact with TRP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B MET* 4.8 4.9 - - + +
128B CYS* 3.7 14.6 - - - +
132B TYR* 5.2 1.3 - - - -
173B LEU* 2.9 50.7 + - + +
174B MET* 3.4 36.3 - - + +
175B GLN 3.4 0.4 - - - -
176B ALA* 1.3 77.1 - - - +
178B LYS* 1.3 58.8 + - + +
181B PRO* 3.1 22.9 - - - +
244B THR* 6.5 0.2 - - + -
268B GLU* 5.3 0.7 - - - -
302B CYS* 6.1 2.0 - - - -
459B PHE* 4.3 24.0 - + - -
465B PHE* 3.9 33.9 - + + -
476B GLU* 3.5 39.7 - - + +
477B LEU* 3.7 42.0 + - + +
485B TYR* 5.4 0.2 - - - -
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Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLN* 2.9 37.3 + - + +
165B ILE 4.7 0.9 - - - -
166B ILE* 3.6 21.0 - - + +
174B MET* 3.2 19.1 + - - +
175B GLN 3.6 3.4 - - - +
176B ALA 3.1 0.2 - - - -
177B TRP* 1.3 79.0 - - - +
179B LEU* 1.3 64.3 + - - +
181B PRO* 3.4 9.0 - - - +
182B ALA* 3.4 8.7 - - - +
191B MET* 3.8 6.3 - - + -
242B ALA* 3.5 31.9 - - + -
243B PHE 4.4 0.4 - - - +
244B THR* 2.9 27.4 + - - -
476B GLU* 2.8 31.6 + - - +
485B TYR* 3.7 17.5 - - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 5.1 0.4 - - + -
91B LEU* 5.1 7.2 - - + -
129B LEU* 4.8 7.2 - - + -
164B GLN* 3.7 9.6 - - - +
175B GLN* 2.8 44.8 + - + +
176B ALA* 4.5 2.7 - - - +
178B LYS* 1.3 72.8 - - - +
180B GLY* 1.3 66.9 + - - +
182B ALA* 4.5 2.2 - - - -
183B LEU* 2.9 37.4 + - + +
189B VAL* 4.1 16.8 - - + -
191B MET* 3.6 20.6 - - + -
204B VAL* 5.0 3.1 - - + -
208B ILE* 3.8 27.1 - - + -
218B VAL* 4.2 19.1 - - + -
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 4.0 7.0 - - - +
129B LEU* 4.1 16.8 - - - +
132B TYR* 3.5 21.1 - - - +
176B ALA 2.9 15.9 + - - -
179B LEU* 1.3 75.6 - - - +
181B PRO* 1.3 60.2 - - - +
184B ALA* 3.1 30.1 + - - +
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Residues in contact with PRO 181 (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 TYR* 3.8 33.8 - - + +
176B ALA 4.1 0.2 - - - +
177B TRP 3.1 29.8 - - - +
178B LYS 3.4 6.5 - - - +
180B GLY* 1.3 86.0 - - - +
182B ALA* 1.3 67.8 + - - +
184B ALA* 3.8 0.7 - - + +
185B THR* 2.9 33.4 + - - +
476B GLU* 6.6 0.2 - - + -
477B LEU 6.2 0.4 - - - +
481B GLY* 3.5 23.6 - - - +
482B LEU* 4.1 3.4 - - + -
485B TYR* 3.6 18.1 - - + +
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Residues in contact with ALA 182 (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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162B CYS* 5.2 0.2 - - - -
164B GLN* 3.6 15.5 - - - +
178B LYS 3.4 17.0 - - - +
179B LEU 3.9 2.0 - - - +
180B GLY 3.4 0.4 - - - -
181B PRO* 1.3 80.6 - - - +
183B LEU* 1.3 60.2 - - - +
185B THR* 3.1 13.5 + - - -
187B ASN* 2.9 32.0 + - + +
189B VAL* 3.9 18.8 - - + -
485B TYR* 3.9 19.0 - - + -
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Residues in contact with LEU 183 (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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76B TRP* 3.7 9.6 - - + -
84B ARG* 3.4 17.0 - - - +
88B LEU* 4.2 17.5 - - + -
91B LEU* 5.4 4.0 - - + -
179B LEU* 2.9 34.3 + - + +
182B ALA* 1.3 75.5 - - - +
184B ALA* 1.3 65.4 + - - +
186B GLY 3.0 10.4 + - - -
187B ASN 3.7 11.4 - - - +
189B VAL* 4.4 8.3 - - + -
208B ILE* 5.5 1.1 - - + -
213B PHE* 3.5 31.4 - - + -
217B VAL* 3.6 30.1 - - + +
218B VAL* 3.8 23.1 - - + -
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Residues in contact with ALA 184 (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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84B ARG* 3.1 23.4 + - - -
88B LEU* 3.9 10.5 - - + +
132B TYR* 3.4 31.6 - - + +
135B TRP* 4.8 0.7 - - + -
136B ALA* 3.3 22.9 - - - +
180B GLY 3.1 21.9 + - - +
181B PRO* 3.8 5.8 - - + +
182B ALA 3.3 0.2 - - - -
183B LEU* 1.3 76.4 - - - +
185B THR* 1.3 58.8 + - - +
482B LEU* 4.6 5.4 - - + -
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 4.1 8.8 + - - +
139B TYR* 4.7 9.4 - - + -
156B HIS 5.7 0.7 - - - +
157B GLU 4.9 0.7 - - - -
158B PRO* 3.2 24.0 - - - +
181B PRO 2.9 17.9 + - - +
182B ALA 3.1 0.2 + - - -
184B ALA* 1.3 75.9 - - + +
186B GLY* 1.3 56.4 + - - +
187B ASN* 2.7 25.1 + - - -
482B LEU* 3.7 29.8 - - + +
485B TYR* 3.4 12.9 + - + +
486B THR* 4.2 16.2 - - - +
500C SER* 5.2 0.3 - - - -
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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