Contacts of the strand formed by residues 154 - 163 (chain D) in PDB entry 1ZQ1
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 VAL 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D LYS* 3.5 3.2 - - - -
147D VAL* 2.9 31.4 + - - +
149D THR* 4.9 0.2 - - + -
152D GLY 4.3 2.2 - - - +
153D ALA* 1.3 74.7 - - - +
155D GLY* 1.3 60.4 + - - +
156D ILE* 3.6 2.9 - - + +
192D THR* 3.0 36.1 - - + -
195D ASP* 3.6 11.7 - - - +
196D ILE* 3.3 24.9 - - + -
201D GLN* 3.4 29.4 - - + +
205D VAL* 3.6 27.4 - - + -
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Residues in contact with GLY 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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145D GLY 3.5 7.9 - - - -
146D LYS* 4.3 2.9 - - - -
153D ALA 4.2 0.6 - - - -
154D VAL* 1.3 75.3 - - - +
156D ILE* 1.3 62.7 + - - -
157D PRO* 3.2 2.7 - - - +
192D THR* 3.3 12.6 - - - +
193D THR* 2.6 25.8 + - - -
195D ASP* 4.0 8.9 + - - -
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Residues in contact with ILE 156 (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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111D LEU* 4.9 7.2 - - + +
143D THR 3.9 0.9 - - - -
144D ASP* 3.2 2.3 + - - -
145D GLY* 2.6 42.9 + - - +
146D LYS* 3.6 11.0 - - - +
147D VAL* 3.5 33.0 - - + -
154D VAL* 3.6 9.9 - - + +
155D GLY* 1.3 77.2 - - - +
157D PRO* 1.3 64.7 - - - +
158D THR 3.3 23.1 - - - +
159D ILE* 3.7 15.7 - - + -
190D ILE* 3.7 23.8 - - + -
191D SER 3.4 9.6 - - - +
192D THR* 4.8 4.3 - - - +
205D VAL* 5.2 4.3 - - + -
209D ILE* 4.9 5.8 - - + -
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Residues in contact with PRO 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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53B ASN* 6.2 0.4 - - - +
143D THR* 3.1 30.9 - - - +
144D ASP* 3.2 10.9 + - - +
155D GLY 3.2 4.9 - - - +
156D ILE* 1.3 80.8 - - - +
158D THR* 1.3 64.2 + - - +
191D SER* 2.9 23.8 - - - +
192D THR 2.9 14.8 - - - +
193D THR* 3.2 19.7 - - + +
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Residues in contact with THR 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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53B ASN* 4.0 16.9 + - - +
55B TYR* 5.8 1.3 - - + -
140D ILE* 3.3 42.0 - - + -
142D ALA 3.7 3.6 - - - +
143D THR* 5.2 0.2 - - + -
156D ILE* 3.3 4.6 - - - +
157D PRO* 1.3 88.7 - - - +
159D ILE* 1.3 74.5 + - - +
160D CYS* 3.5 14.6 - - - -
189D GLU* 4.3 3.8 - - - -
191D SER* 3.3 36.1 + - - -
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Residues in contact with ILE 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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104D ALA 5.1 2.7 - - - +
107D ILE* 5.5 1.8 - - + -
108D ALA* 3.8 26.5 - - + +
111D LEU* 4.3 12.8 - - + -
113D ALA* 3.4 33.2 - - + -
140D ILE* 3.9 1.6 - - - -
141D ILE* 2.9 30.4 + - + +
142D ALA* 3.1 16.3 + - + +
156D ILE* 3.7 15.3 - - + +
158D THR* 1.3 82.5 - - - +
160D CYS* 1.3 61.7 - - - +
188D ILE* 3.7 26.5 - - + -
189D GLU 3.2 7.0 - - - +
190D ILE* 4.4 9.0 - - + -
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Residues in contact with CYS 160 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B TYR* 3.9 25.6 - - - -
138D THR* 4.0 12.8 - - + -
139D ALA 3.2 15.3 - - - +
140D ILE* 4.0 2.5 - - - -
141D ILE* 4.5 1.1 - - - +
158D THR* 3.5 27.6 - - - -
159D ILE* 1.3 74.9 - - - +
161D LEU* 1.3 60.8 + - - +
162D GLU* 3.9 0.9 - - - +
187D LEU 3.6 0.7 - - - +
188D ILE* 3.5 10.7 - - - +
189D GLU* 2.8 59.0 + - + +
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Residues in contact with LEU 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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25D LEU* 4.2 22.9 - - + -
30D LEU* 3.9 22.9 - - + -
96D PRO* 4.5 4.3 - - + -
100D ALA* 3.7 4.9 - - + +
101D LEU* 3.6 31.9 - - + +
104D ALA* 4.0 5.6 - - + -
121D TYR* 2.5 40.3 + - - +
139D ALA 3.2 11.4 + - - +
141D ILE* 3.2 33.3 - - + +
160D CYS* 1.3 73.0 - - - +
162D GLU* 1.3 58.1 + - - +
186D PRO* 4.4 2.0 - - + -
187D LEU 3.4 18.8 - - - +
188D ILE* 4.9 1.6 - - + +
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D HIS* 3.4 29.0 + - - -
30D LEU* 3.2 14.4 - - - +
124D LYS* 3.4 12.7 + - - -
136D GLN* 3.3 24.8 + - - +
137D ARG 3.2 14.4 - - - +
138D THR* 3.0 34.3 + - + +
160D CYS* 3.9 0.9 - - - +
161D LEU* 1.3 72.8 - - - +
163D GLU* 1.3 59.8 + - - +
186D PRO 3.8 0.3 - - - -
187D LEU* 2.9 46.9 + - + +
189D GLU* 3.4 17.0 - - + +
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Residues in contact with GLU 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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30D LEU* 4.1 8.7 - - + -
31D PHE* 3.4 16.2 - - + -
87D TYR* 2.8 38.9 + - - +
131D ASN* 5.2 3.8 - - - +
135D PHE 4.4 3.1 - - - +
136D GLN* 2.5 40.3 + - + +
137D ARG* 2.9 64.3 + - + +
162D GLU* 1.3 78.1 - - - +
164D ASP* 1.3 64.7 + - - +
165D ALA 3.9 0.2 + - - -
183D LEU* 5.7 2.0 - - + +
184D GLY* 4.6 4.9 - - - +
185D ILE 4.1 3.8 - - - -
187D LEU* 4.2 2.8 - - - +
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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