Contacts of the helix formed by residues 153 - 171 (chain D) in PDB entry 3NZG
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 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D ALA* 1.3 74.7 - - - +
154D LEU* 1.3 56.1 + - - +
155D ASP* 4.0 3.8 + - - +
156D VAL* 2.9 30.6 + - - +
157D ALA* 2.7 34.0 + - - +
186D TRP* 3.5 11.4 - - - +
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Residues in contact with LEU 154 (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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153D SER* 1.3 77.1 - - - +
155D ASP* 1.3 63.7 + - - +
157D ALA* 3.7 1.0 - - - +
158D ILE* 2.9 31.4 + - + +
186D TRP* 3.4 50.7 - - + +
190D GLU* 3.9 37.5 - - + +
193D TYR* 3.8 31.0 - - + -
194D TYR* 4.1 8.7 - - + -
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Residues in contact with ASP 155 (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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153D SER* 3.5 4.2 + - - +
154D LEU* 1.3 78.6 - - - +
156D VAL* 1.3 64.7 + - + +
158D ILE* 4.0 7.2 - - - +
159D LYS* 3.0 29.4 + - - +
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Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ILE* 3.9 13.3 - - + +
149D PRO* 4.4 10.8 - - + +
152D ALA* 3.4 19.5 - - + -
153D SER* 2.9 33.4 - - - +
154D LEU 3.2 0.8 - - - -
155D ASP* 1.3 79.1 - - + +
157D ALA* 1.3 61.9 + - - +
159D LYS* 3.8 4.6 - - - +
160D GLY* 3.1 20.1 + - - -
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Residues in contact with ALA 157 (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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148D ILE* 3.5 24.2 - - + +
152D ALA* 4.6 2.5 - - + -
153D SER 2.7 21.3 + - - +
154D LEU 3.7 0.4 - - - +
156D VAL* 1.3 71.5 - - - +
158D ILE* 1.3 65.0 + - - +
160D GLY* 3.2 2.3 + - - -
161D TYR* 3.0 27.9 + - - +
181D PRO* 4.8 1.8 - - + -
186D TRP* 3.6 26.2 - - + -
194D TYR* 3.7 13.2 - - + +
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Residues in contact with ILE 158 (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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154D LEU* 2.9 23.7 + - + +
155D ASP* 4.0 6.3 - - - +
157D ALA* 1.3 72.0 - - - +
159D LYS* 1.3 67.9 + - - +
161D TYR* 3.2 2.3 + - - +
162D ALA* 3.0 23.5 + - + +
193D TYR* 4.0 18.8 - - + +
194D TYR* 3.9 22.2 - - + -
197D GLU* 3.6 39.7 - - + +
198D LEU* 4.4 10.3 - - + -
201D ILE* 4.0 22.2 - - + +
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Residues in contact with LYS 159 (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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155D ASP* 3.0 25.1 + - - +
156D VAL* 3.8 5.2 - - - +
158D ILE* 1.3 77.4 - - - +
160D GLY* 1.3 61.7 + - - +
162D ALA* 3.6 5.9 + - - +
163D PRO* 3.1 20.8 - - - +
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Residues in contact with GLY 160 (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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146D PRO* 3.0 29.8 - - - +
148D ILE* 4.0 8.7 - - - -
156D VAL 3.1 15.0 + - - -
157D ALA 3.6 3.4 - - - -
158D ILE 3.2 0.2 - - - -
159D LYS* 1.3 79.4 - - - +
161D TYR* 1.3 57.7 + - - +
163D PRO* 3.6 15.2 - - - +
164D LEU* 4.0 3.6 - - - +
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Residues in contact with TYR 161 (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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144D LEU* 2.6 42.0 + - + -
145D TYR* 3.4 16.0 - + - -
146D PRO* 3.4 24.9 - - + -
148D ILE* 5.1 2.7 - - + -
157D ALA 3.0 17.5 + - - +
158D ILE 3.2 0.6 + - - +
160D GLY* 1.3 76.3 - - - +
162D ALA* 1.3 67.6 + - - +
164D LEU* 3.0 19.6 + - + +
165D LEU* 3.0 21.0 + - + +
178D VAL* 3.6 25.4 - - + -
179D CYS 2.7 26.7 + - - -
181D PRO* 5.9 0.2 - - + -
194D TYR* 3.2 29.8 - + - -
198D LEU* 3.6 23.6 - - + -
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Residues in contact with ALA 162 (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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158D ILE* 3.0 16.8 + - + +
159D LYS* 3.6 7.2 - - - +
161D TYR* 1.3 76.5 - - - +
163D PRO* 1.3 69.9 - - + +
165D LEU* 3.2 3.1 + - - +
166D GLU* 3.0 30.5 + - + +
201D ILE* 4.1 28.1 - - + +
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Residues in contact with PRO 163 (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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159D LYS 3.1 20.4 - - - +
160D GLY* 3.6 12.8 - - - +
162D ALA* 1.3 88.5 - - + +
164D LEU* 1.3 59.9 + - + +
166D GLU* 4.0 7.3 - - + +
167D LYS* 3.0 30.2 + - - +
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Residues in contact with LEU 164 (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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144D LEU* 4.0 28.2 - - + +
145D TYR 3.7 14.6 - - - +
146D PRO* 3.5 46.2 - - + -
160D GLY 4.0 6.3 - - - +
161D TYR* 3.0 10.8 + - + +
163D PRO* 1.3 78.9 - - + +
165D LEU* 1.3 58.8 + - - +
167D LYS* 3.3 11.8 + - + +
168D ALA* 2.9 28.6 + - - +
345D PHE* 4.4 20.5 - - + +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 4.0 19.1 - - + -
161D TYR* 3.0 19.4 + - + +
162D ALA 3.6 5.6 - - - +
164D LEU* 1.3 74.3 - - - +
166D GLU* 1.3 64.9 + - - +
168D ALA* 3.4 5.2 + - - +
169D LYS* 3.1 28.9 + - - +
176D VAL* 4.0 18.4 - - + -
178D VAL* 4.2 13.5 - - + -
198D LEU* 3.9 47.1 - - + +
201D ILE* 4.2 18.8 - - + -
202D LEU* 4.1 19.0 - - + +
208D MSE 5.8 0.7 - - - -
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Residues in contact with GLU 166 (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 ALA* 3.0 24.3 + - + +
163D PRO* 4.0 7.6 - - + +
165D LEU* 1.3 72.4 - - - +
167D LYS* 1.3 67.2 + - - +
169D LYS* 3.1 24.2 + - - +
170D ALA* 2.9 23.4 + - - +
201D ILE* 3.8 23.9 - - + +
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Residues in contact with LYS 167 (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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163D PRO 3.0 20.3 + - - +
164D LEU* 3.5 12.8 - - + +
165D LEU 3.3 0.2 - - - -
166D GLU* 1.3 76.9 - - - +
168D ALA* 1.3 56.9 + - - +
170D ALA* 3.1 7.0 + - - +
171D HIS* 3.0 57.4 + - + +
344D GLU* 3.0 37.0 + - - +
345D PHE* 3.5 23.6 - - + -
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Residues in contact with ALA 168 (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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142D LEU* 6.0 0.2 - - + -
144D LEU* 4.5 3.6 - - + -
164D LEU 2.9 17.6 + - - +
165D LEU* 3.7 7.4 - - - +
167D LYS* 1.3 75.0 - - - +
169D LYS* 1.3 63.5 + - + +
171D HIS 3.2 1.2 + - - -
172D ASN 3.1 4.3 + - - -
173D ILE* 2.9 38.4 + - + +
176D VAL* 3.8 29.4 - - + -
202D LEU* 5.4 1.8 - - + -
206D THR* 5.9 1.3 - - + -
345D PHE* 3.7 14.5 - - + -
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Residues in contact with LYS 169 (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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165D LEU 3.1 18.2 + - - +
166D GLU* 3.5 24.6 + - - +
168D ALA* 1.3 75.6 - - - +
170D ALA* 1.3 63.9 + - - +
172D ASN* 3.1 20.5 + - - +
173D ILE 5.0 1.6 - - - +
201D ILE 3.3 15.0 + - - +
202D LEU* 3.2 45.8 + - + +
203D GLY* 4.5 2.8 - - - +
206D THR* 4.4 10.3 - - + +
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Residues in contact with ALA 170 (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 GLU 2.9 13.2 + - - +
167D LYS* 3.1 12.8 + - - +
169D LYS* 1.3 78.8 - - - +
171D HIS* 1.3 67.1 + - + +
172D ASN* 3.4 9.4 + - - +
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Residues in contact with HIS 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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167D LYS* 3.0 54.5 + - + +
168D ALA 3.2 2.6 + - - +
170D ALA* 1.3 81.5 - - + +
172D ASN* 1.3 72.2 + - - +
173D ILE* 3.4 9.4 - - + +
344D GLU* 3.9 21.5 + - - -
345D PHE* 3.9 20.6 - + + -
363D ASP* 4.4 2.6 + - - -
364D GLY 4.0 11.3 + - - -
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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
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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