Contacts of the helix formed by residues 170 - 185 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLU* 4.7 0.4 - - - -
112D LYS* 3.4 19.7 - - - +
120D VAL* 5.8 1.3 - - + -
121D ASP* 3.4 14.1 - - - -
124D MET* 6.5 0.4 - - - -
167D PRO 4.8 0.4 - - - -
168D TRP 4.7 0.4 - - - -
169D ASN* 1.3 111.3 + - - +
171D PRO* 1.3 59.4 - - - +
172D LEU 3.5 1.8 - - - -
173D LEU* 4.0 24.9 - - + -
174D MET* 2.8 53.3 + - + +
296D PHE* 3.4 38.4 - + - -
297D ASN* 3.7 18.6 - - + -
300D GLN 3.8 3.8 - - - -
301D CYS* 4.4 13.9 - - - -
302D CYS* 6.1 1.1 - - - -
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Residues in contact with PRO 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLU* 3.1 28.9 - - - +
110D ASN* 4.0 8.5 - - + +
112D LYS* 4.4 2.5 - - - +
166D ILE* 4.0 9.5 - - + +
167D PRO 4.4 9.6 - - - +
168D TRP 3.3 10.5 - - - +
169D ASN 3.6 3.1 - - - +
170D PHE* 1.3 89.0 - - - +
172D LEU* 1.3 61.5 + - - +
175D GLN* 3.3 19.6 + - - +
197D THR* 3.2 42.2 - - + +
200D THR* 3.6 10.5 - - - +
201D ALA* 5.2 5.0 - - + +
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ILE* 6.0 0.4 - - + -
102D LEU* 4.1 20.4 - - + +
106D GLU* 3.0 23.5 + - - +
121D ASP* 5.7 0.7 - - + -
122D LEU* 3.5 33.0 - - + -
125D VAL* 3.7 19.4 - - + +
171D PRO* 1.3 75.2 - - - +
173D LEU* 1.3 66.6 + - - +
175D GLN* 3.1 13.5 + - - +
176D ALA* 3.0 21.5 + - - +
200D THR* 3.6 32.5 - - + +
201D ALA 4.3 0.2 - - - +
204D VAL* 3.6 31.0 - - + -
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLU* 4.6 0.8 + - - -
120D VAL* 6.0 0.4 - - + -
121D ASP* 4.6 10.9 + - - +
124D MET* 3.8 39.5 - - + +
125D VAL* 3.5 32.8 - - + +
170D PHE* 3.4 30.5 + - + -
172D LEU* 1.3 78.4 - - - +
174D MET* 1.3 60.6 + - + +
176D ALA* 3.1 3.2 + - + +
177D TRP* 2.9 68.3 + - + +
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Residues in contact with MET 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ILE* 4.0 21.1 - - + -
167D PRO* 3.8 20.9 - - + +
169D ASN* 4.7 2.2 - - - +
170D PHE* 2.8 50.0 + - + +
171D PRO 4.2 2.0 - - - +
173D LEU* 1.3 76.3 - - + +
175D GLN* 1.3 60.7 + - - +
177D TRP* 3.5 51.3 + - + +
178D LYS* 3.2 31.5 + - - +
244D THR* 4.1 25.1 - - - -
302D CYS* 6.1 6.1 - - - -
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Residues in contact with GLN 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ILE* 4.0 10.7 - - + +
171D PRO 3.3 12.2 + - - +
172D LEU* 3.1 14.4 + - - +
173D LEU 3.1 0.4 - - - -
174D MET* 1.3 78.8 - - - +
176D ALA* 1.3 56.2 + - - +
178D LYS* 3.3 2.1 + - - +
179D LEU* 2.9 47.3 + - + +
191D MET* 3.6 18.6 - - - -
201D ALA* 3.2 37.9 + - + +
204D VAL* 3.5 35.9 - - - +
208D ILE* 4.8 0.2 - - - +
220D ILE* 3.4 20.0 - - - +
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Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D VAL* 3.9 30.7 - - + +
128D CYS* 3.5 23.4 - - + -
129D LEU* 4.3 14.6 - - + -
172D LEU 3.0 12.1 + - - +
173D LEU* 3.1 7.6 + - + +
175D GLN* 1.3 73.3 - - - +
177D TRP* 1.3 59.1 + - - +
178D LYS 3.0 1.8 - - - -
179D LEU* 4.5 1.8 - - - +
180D GLY* 2.9 28.6 + - - -
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Residues in contact with TRP 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D MET* 5.8 1.3 - - + +
128D CYS* 3.7 14.3 - - - +
132D TYR* 4.8 1.7 - - - -
173D LEU* 2.9 51.1 + - + +
174D MET* 3.5 38.1 - - + +
176D ALA* 1.3 76.1 - - - +
178D LYS* 1.3 60.7 + - + +
181D PRO* 3.1 22.9 - - - +
244D THR* 6.4 0.2 - - + -
268D GLU* 5.6 0.2 - - - -
302D CYS* 6.0 2.2 - - - -
459D PHE* 3.7 36.6 - + + -
465D PHE* 4.0 22.7 - + + -
476D GLU* 3.6 33.0 - - + +
477D LEU* 3.7 43.8 + - + +
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Residues in contact with LYS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D GLN* 3.1 37.8 + - + +
165D ILE 4.5 1.3 - - - -
166D ILE* 3.6 20.5 - - + +
174D MET* 3.2 21.7 + - - +
175D GLN 3.7 3.4 - - - +
176D ALA 3.0 0.2 - - - -
177D TRP* 1.3 79.0 - - - +
179D LEU* 1.3 63.7 + - - +
181D PRO* 3.3 14.9 - - - +
182D ALA* 3.4 4.5 - - - +
191D MET* 3.8 5.2 - - + -
242D ALA* 3.9 28.0 - - + -
243D PHE 4.6 0.7 - - - +
244D THR* 2.6 31.7 + - - +
476D GLU* 3.1 29.2 + - - +
485D TYR* 3.9 15.5 - - - +
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Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU* 5.2 4.9 - - + -
129D LEU* 4.9 6.3 - - + -
164D GLN* 3.6 16.4 - - - +
175D GLN* 2.9 44.2 + - + +
176D ALA* 4.3 2.9 - - - +
178D LYS* 1.3 69.3 - - - +
180D GLY* 1.3 69.0 + - - +
182D ALA* 4.5 1.3 - - - -
183D LEU* 2.9 44.1 + - + +
189D VAL* 4.0 20.0 - - + -
191D MET* 3.7 10.8 - - + -
204D VAL* 5.0 3.1 - - + -
208D ILE* 4.1 26.7 - - + -
218D VAL* 4.2 16.2 - - + -
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D LEU* 3.9 7.0 - - - +
129D LEU* 4.1 16.7 - - - +
132D TYR* 3.5 20.8 - - - +
176D ALA 2.9 15.4 + - - -
179D LEU* 1.3 80.1 - - - +
181D PRO* 1.3 59.6 - - - +
184D ALA* 3.1 26.9 + - - +
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Residues in contact with PRO 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D TYR* 3.6 31.4 - - + +
177D TRP 3.1 29.6 - - - +
178D LYS 3.3 7.2 - - - +
180D GLY* 1.3 84.9 - - - +
182D ALA* 1.3 57.2 + - - +
184D ALA* 3.5 1.1 + - + +
185D THR* 2.7 39.0 + - - +
476D GLU* 6.5 0.7 - - + -
477D LEU 6.1 0.4 - - - +
481D GLY* 3.4 25.6 - - - +
482D LEU* 4.1 6.5 - - + -
485D TYR* 3.9 16.9 - - + +
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Residues in contact with ALA 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D CYS* 5.1 0.2 - - - -
164D GLN* 3.6 16.4 - - - +
178D LYS 3.4 16.6 - - - +
179D LEU 3.4 2.6 + - - +
181D PRO* 1.3 81.0 - - - +
183D LEU* 1.3 59.7 + - - +
185D THR* 3.1 10.4 + - - -
186D GLY 3.4 0.2 + - - -
187D ASN* 2.9 30.6 + - + -
189D VAL* 4.0 17.7 - - + -
485D TYR* 3.7 22.2 - - + -
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TRP* 3.6 12.1 - - + -
84D ARG* 3.5 16.1 - - - +
88D LEU* 3.9 28.3 - - + -
91D LEU* 5.1 4.5 - - + -
179D LEU* 2.9 44.6 + - + +
182D ALA* 1.3 68.8 - - + +
184D ALA* 1.3 64.9 + - - +
185D THR 3.1 2.0 - - - -
186D GLY 3.1 10.4 + - - -
187D ASN 4.1 6.7 - - - +
189D VAL* 4.7 5.6 - - + -
208D ILE* 5.9 0.7 - - + -
213D PHE* 4.0 18.6 - - + -
217D VAL* 3.4 34.8 - - + +
218D VAL* 3.7 20.4 - - + -
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Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ARG* 2.9 22.2 + - - +
88D LEU* 3.8 10.2 - - + +
132D TYR* 3.3 26.0 - - + +
135D TRP 4.8 1.1 - - - -
136D ALA* 3.4 22.4 - - - +
180D GLY 3.1 21.6 + - - +
181D PRO* 3.8 7.0 - - + +
183D LEU* 1.3 77.2 - - - +
185D THR* 1.3 58.8 + - - +
482D LEU* 4.7 9.2 - - + -
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Residues in contact with THR 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A SER* 5.2 0.3 - - - -
84D ARG* 3.8 10.1 + - - +
139D TYR* 4.6 10.1 - - + -
157D GLU 4.9 1.0 - - - -
158D PRO* 3.1 24.1 - - - +
181D PRO 2.7 22.1 + - - +
182D ALA 3.1 0.3 + - - -
184D ALA* 1.3 80.1 - - - +
186D GLY* 1.3 55.9 + - - +
187D ASN* 2.8 24.9 + - - -
482D LEU* 4.2 26.7 - - + +
485D TYR* 3.4 10.8 - - + +
486D THR* 3.9 18.4 - - - +
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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
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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