Contacts of the helix formed by residues 141 - 152 (chain D) in PDB entry 2ZVW
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 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D MET 3.5 2.6 + - - -
140D PRO* 1.3 71.4 - - - +
142D GLY* 1.3 59.2 + - - +
144D PHE* 3.4 4.3 + - - +
145D SER* 3.0 28.4 + - - -
219D THR* 3.7 20.2 + - - +
222D SER 2.6 29.2 + - - -
223D GLU* 2.9 18.3 + - - -
224D THR 4.1 7.9 - - - -
225D VAL* 4.1 11.2 - - - -
239D TYR* 4.2 15.3 + - - -
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Residues in contact with GLY 142 (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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140D PRO* 3.2 2.4 - - - +
141D SER* 1.3 82.7 + - - +
143D GLU* 1.3 56.7 + - - +
145D SER* 3.2 8.6 + - - -
146D ARG* 3.0 50.0 + - - +
219D THR* 4.2 8.0 - - - +
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Residues in contact with GLU 143 (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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139D MET* 3.7 17.7 - - + -
140D PRO* 3.2 26.4 + - + +
142D GLY* 1.3 75.7 - - - +
144D PHE* 1.3 56.7 + - - +
146D ARG* 2.9 39.6 + - - +
147D ILE* 3.0 55.7 + - + +
180D ILE* 5.1 0.2 - - - +
182D LEU* 4.5 12.3 - - + +
192D GLU* 6.0 2.1 - - - +
110F LYS* 4.6 22.1 + - - +
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Residues in contact with PHE 144 (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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139D MET* 3.6 14.7 - - + +
140D PRO 3.1 6.9 + - - +
141D SER 3.8 4.7 - - - +
142D GLY 3.3 0.2 - - - -
143D GLU* 1.3 76.1 - - - +
145D SER* 1.3 62.1 + - - +
147D ILE* 3.4 4.8 + - + +
148D CYS* 3.1 50.5 + - - -
160D ILE* 5.4 0.4 - - + -
169D PHE* 4.1 18.4 - + - -
212D MET* 4.2 28.3 - - + -
215D PHE* 5.3 1.1 - - + -
216D THR* 4.0 13.2 - - + -
225D VAL* 3.7 28.5 - - + -
227D ILE* 3.7 27.8 - - + -
237D VAL* 4.0 21.5 - - + -
239D TYR* 3.9 14.4 - - - -
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Residues in contact with SER 145 (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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141D SER 3.0 14.3 + - - -
142D GLY* 3.4 12.3 - - - -
143D GLU 3.2 0.2 - - - -
144D PHE* 1.3 77.6 - - - +
146D ARG* 1.3 62.0 + - - +
148D CYS* 3.9 2.3 - - - +
149D LYS* 3.1 25.4 + - - +
213D ASN* 4.7 0.9 - - - +
216D THR* 3.7 25.8 + - - +
219D THR* 3.9 16.6 + - - -
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Residues in contact with ARG 146 (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 GLY* 3.0 33.2 + - - +
143D GLU* 2.9 46.2 + - - +
145D SER* 1.3 74.9 - - - +
147D ILE* 1.3 56.7 + - + +
149D LYS* 3.7 7.1 - - + -
150D ASP* 2.8 50.7 + - - +
192D GLU* 6.3 1.2 - - - +
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Residues in contact with ILE 147 (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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139D MET* 4.0 9.2 - - + -
143D GLU* 3.0 40.8 + - - +
144D PHE* 3.7 6.3 - - + +
145D SER 3.4 0.2 - - - -
146D ARG* 1.3 76.6 - - + +
148D CYS* 1.3 60.1 + - - +
150D ASP* 3.8 2.0 - - - +
151D LEU* 3.0 49.2 + - + +
169D PHE* 3.8 37.5 - - + -
180D ILE* 4.0 26.0 - - + -
182D LEU* 3.7 26.9 - - + -
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Residues in contact with CYS 148 (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 PHE* 3.1 55.7 + - - +
145D SER 3.9 2.7 - - - +
147D ILE* 1.3 80.6 - - - +
149D LYS* 1.3 61.8 + - - +
152D SER* 3.0 27.0 + - - -
158D VAL* 6.1 0.7 - - - -
169D PHE* 6.0 0.9 - - - -
209D LEU* 3.9 15.0 - - + +
212D MET* 3.7 20.6 - - + -
213D ASN* 3.0 21.8 + - - +
216D THR* 4.5 6.1 - - + -
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Residues in contact with LYS 149 (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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145D SER* 3.1 18.4 + - - +
146D ARG* 3.8 7.9 - - + +
148D CYS* 1.3 76.1 - - - +
150D ASP* 1.3 68.0 + - - +
152D SER* 2.9 20.8 + - - +
153D SER* 3.4 11.6 + - - -
213D ASN* 3.4 8.0 + - - +
80F LYS* 3.6 31.5 - - - +
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Residues in contact with ASP 150 (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 ARG* 2.8 37.1 + - - +
147D ILE* 3.8 5.3 - - - +
149D LYS* 1.3 82.7 + - - +
151D LEU* 1.3 61.8 + - - +
153D SER* 2.7 25.0 + - - -
154D ILE* 3.6 7.3 - - - +
180D ILE* 5.0 10.0 - - + +
80F LYS* 4.4 6.2 - - - +
81F CYS* 3.1 53.6 - - + +
114F PHE* 5.2 0.7 - - + -
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Residues in contact with LEU 151 (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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147D ILE* 3.0 27.5 + - + +
148D CYS 4.1 0.9 - - - +
150D ASP* 1.3 77.3 - - - +
152D SER* 1.3 54.7 + - - +
154D ILE* 2.7 28.0 + - - +
155D GLY 2.9 10.9 + - - +
158D VAL* 3.7 29.6 - - + -
169D PHE* 3.7 24.5 - - + +
170D SER 4.5 2.2 - - - +
171D THR* 3.5 21.9 - - + +
178D ALA* 4.1 19.7 - - + +
180D ILE* 4.0 21.3 - - + -
209D LEU* 3.7 16.4 - - + -
114F PHE* 4.7 3.1 - - + -
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Residues in contact with SER 152 (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 CYS 3.0 10.9 + - - -
149D LYS* 2.9 19.8 + - - +
151D LEU* 1.3 74.0 - - - +
153D SER* 1.3 58.2 + - - +
154D ILE 3.2 2.0 - - - -
155D GLY 3.2 19.8 + - - +
156D ASP* 5.3 2.1 - - - +
209D LEU* 3.5 15.6 - - - +
210D ARG 5.5 0.4 - - - -
213D ASN* 3.1 27.0 + - - -
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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