Contacts of the strand formed by residues 214 - 221 (chain D) in PDB entry 1ZXN
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 TYR 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119D TRP* 3.6 38.6 - + + +
120D ASN 3.6 7.4 - - - -
121D ASN* 4.5 0.2 - - - +
122D GLY 4.0 1.3 + - - -
124D GLY* 5.0 0.9 - - - -
180D GLU* 2.8 50.4 + - + +
181D THR* 3.3 1.0 - - - -
182D ALA* 2.8 62.1 + - + -
189D MET* 3.1 15.7 - - + +
209D PHE* 4.4 13.9 - + - -
212D GLU 4.4 2.2 - - - +
213D ASP* 1.3 81.9 - - - +
215D THR* 1.3 66.0 + - - +
216D CYS* 4.2 8.5 - - + -
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Residues in contact with THR 215 (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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118D ILE 3.9 0.6 - - - +
119D TRP* 3.4 1.6 - - - -
120D ASN* 2.9 58.0 + - - +
122D GLY 5.3 0.4 + - - -
123D LYS 4.8 0.3 + - - -
124D GLY* 3.8 11.3 - - - -
125D ILE* 4.0 9.5 + - + +
179D VAL* 5.7 0.2 - - + -
180D GLU 3.4 7.0 - - - +
181D THR* 3.2 22.9 + - - +
214D TYR* 1.3 74.3 - - - +
216D CYS* 1.3 63.1 + - - +
217D ILE* 3.5 24.0 - - + -
907D ADP 3.7 20.9 + - + +
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Residues in contact with CYS 216 (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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117D SER* 3.8 22.2 - - - -
118D ILE 3.5 4.7 - - - -
119D TRP* 3.7 32.5 - - + -
178D THR 3.9 1.7 - - - +
180D GLU* 2.6 48.0 + - + +
214D TYR* 4.2 9.9 - - + -
215D THR* 1.3 77.1 - - - +
217D ILE* 1.3 64.6 + - - +
218D THR* 4.0 9.7 + - - -
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Residues in contact with ILE 217 (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 ILE* 4.0 24.2 - - + -
116D ILE 4.1 0.2 - - - +
117D SER* 3.5 1.9 - - - -
118D ILE* 2.9 36.9 + - - +
120D ASN* 5.6 0.2 - - - +
142D PHE* 4.0 31.2 - - + -
177D PHE* 3.8 28.9 - - + -
178D THR 3.4 9.6 - - - +
179D VAL* 4.3 10.5 - - + -
215D THR* 3.5 26.0 - - + -
216D CYS* 1.3 79.8 - - - +
218D THR* 1.3 64.2 + - - +
219D PHE* 4.0 12.9 + - + -
907D ADP 5.1 4.3 - - - +
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Residues in contact with THR 218 (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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115D LEU* 5.1 10.1 - - + -
116D ILE 3.4 16.6 - - - +
117D SER* 3.4 19.8 + - - -
176D LYS 4.8 0.3 - - - -
177D PHE* 3.8 0.3 - - - -
178D THR* 2.8 45.0 + - - +
180D GLU* 5.8 0.2 + - - -
216D CYS* 4.0 10.3 + - - -
217D ILE* 1.3 73.4 - - - +
219D PHE* 1.3 63.6 + - - +
220D GLN* 6.1 1.1 - - + -
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Residues in contact with PHE 219 (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 ILE* 5.1 4.7 - - + -
85D PHE* 4.2 20.6 - + + -
88D ILE* 3.9 13.5 - - + -
115D LEU* 3.8 2.1 - - - +
116D ILE* 3.0 75.0 + - + -
118D ILE* 4.1 8.1 - - + -
170D CYS* 3.7 26.0 - - - -
174D SER* 3.6 15.5 - - - +
176D LYS 3.4 7.9 - - - +
177D PHE* 3.5 21.3 - - + -
217D ILE* 4.0 16.2 - - + -
218D THR* 1.3 75.5 - - - +
220D GLN* 1.3 64.0 + - - +
221D PRO* 3.5 17.2 - - + +
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Residues in contact with GLN 220 (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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113D ASN 4.0 9.1 - - - +
114D ASN* 3.1 26.5 + - - +
115D LEU* 4.5 7.2 - - + -
174D SER* 3.5 3.7 - - - -
175D THR* 3.0 33.7 + - - +
176D LYS* 2.9 29.8 + - + +
218D THR* 6.1 1.8 - - + -
219D PHE* 1.3 76.7 - - - +
221D PRO* 1.3 72.3 - - - +
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Residues in contact with PRO 221 (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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81D LEU* 4.0 28.5 - - + -
84D ILE* 4.7 2.0 - - + -
114D ASN* 3.1 33.5 + - - +
116D ILE* 4.1 13.2 - - + -
173D PHE 3.9 7.9 - - - +
174D SER* 4.0 3.4 - - - +
175D THR* 4.4 2.8 + - - +
219D PHE* 3.5 31.6 - - + +
220D GLN* 1.3 86.5 - - - +
222D ASP* 1.3 60.2 + - - +
223D LEU* 3.2 18.6 + - + +
231D LEU* 5.4 5.2 - - + -
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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