Contacts of the strand formed by residues 174 - 181 (chain Q) in PDB entry 1ZGL
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 LYS 174 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14Q GLU* 5.6 4.3 - - - +
82Q VAL* 6.6 0.2 - - + -
116Q PRO* 4.3 21.1 - - + +
165Q VAL* 5.0 1.1 - - + -
166Q LEU 4.2 11.9 - - - +
167Q ASP* 4.3 8.5 - - - +
172Q ASP 3.9 2.4 + - - +
173Q PHE* 1.3 98.0 - - - +
175Q SER* 1.3 71.1 + - - +
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Residues in contact with SER 175 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116Q PRO* 5.0 2.7 - - - +
142Q THR* 6.1 1.1 - - - -
143Q ASP* 4.9 8.5 - - - +
165Q VAL* 4.4 5.1 - - - +
166Q LEU* 2.6 58.1 + - - +
167Q ASP 4.3 0.3 + - - -
168Q MET* 5.9 1.0 - - - +
173Q PHE* 3.5 22.7 - - - -
174Q LYS* 1.3 82.5 + - - +
176Q ASN* 1.3 63.7 + - - +
177Q SER* 4.8 0.9 + - - -
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Residues in contact with ASN 176 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116Q PRO* 5.6 6.1 - - + +
142Q THR* 3.5 1.6 - - - -
143Q ASP* 3.1 21.3 + - - +
144Q PHE* 3.3 37.0 + - + +
145Q ASP 5.7 0.2 - - - -
146Q SER* 5.6 7.4 - - - +
164Q THR 4.2 14.6 - - - +
165Q VAL* 4.4 6.9 - - + +
175Q SER* 1.3 76.3 - - - +
177Q SER* 1.3 69.1 + - - +
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Residues in contact with SER 177 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140Q LEU* 4.1 11.5 - - - +
141Q PHE 3.3 10.3 - - - -
142Q THR* 3.2 28.1 - - - -
144Q PHE* 3.5 6.5 - - - -
163Q LYS 2.7 26.3 + - - +
164Q THR* 4.1 2.6 + - - +
165Q VAL* 6.1 0.2 - - - -
166Q LEU* 5.7 3.1 + - - +
175Q SER 4.8 1.9 + - - -
176Q ASN* 1.3 81.1 + - - +
178Q ALA* 1.3 57.3 + - - +
145R THR* 5.9 0.9 - - - +
196R ARG* 3.9 25.7 + - - -
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Residues in contact with ALA 178 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Q LEU* 4.0 1.6 - - - +
141Q PHE 3.2 28.0 + - - -
144Q PHE* 3.8 5.3 - - + -
150Q VAL* 4.3 22.2 - - + -
161Q THR 5.3 0.2 - - - -
162Q ASP* 3.4 22.4 - - + +
163Q LYS* 4.1 6.1 - - - +
177Q SER* 1.3 73.1 - - - +
179Q VAL* 1.3 71.8 + - - +
193Q PHE* 3.8 17.2 - - + -
196R ARG* 4.2 0.4 - - - +
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Residues in contact with VAL 179 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q VAL* 4.5 2.7 - - + -
139Q CYS 3.4 15.7 - - - +
140Q LEU* 4.1 9.2 - - + -
160Q ILE 3.0 17.2 - - - +
161Q THR 3.2 11.8 - - - +
162Q ASP* 3.4 5.6 - - + +
178Q ALA* 1.3 80.6 - - - +
180Q ALA* 1.3 78.2 + - - +
181Q TRP* 3.7 30.6 - - + -
193Q PHE* 3.7 5.0 - - - -
147R VAL* 4.2 20.6 - - + -
194R SER* 4.6 5.4 - - - +
196R ARG* 2.8 42.4 - - - +
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Residues in contact with ALA 180 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q SER 3.8 0.2 - - - +
138Q VAL* 3.5 0.9 - - - -
139Q CYS* 2.7 37.4 + - - +
159Q TYR* 5.0 2.2 - - + -
160Q ILE 3.8 17.5 - - - +
179Q VAL* 1.3 79.6 - - - +
181Q TRP* 1.3 65.6 + - - +
187Q PHE* 4.1 16.5 - - + -
192Q ALA* 4.9 3.4 - - + -
193Q PHE* 3.8 24.7 - - + -
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Residues in contact with TRP 181 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q SER* 3.0 23.8 - - - +
138Q VAL* 4.2 3.4 - - + -
158Q VAL* 6.2 0.4 - - + -
159Q TYR* 2.7 40.1 + - - +
160Q ILE 5.2 6.2 - - - +
161Q THR 5.1 4.0 - - - -
179Q VAL* 3.7 28.9 - - + -
180Q ALA* 1.3 76.1 - - - +
182Q SER* 1.3 58.9 + - - +
187Q PHE* 4.5 3.4 - - - -
131R PHE* 5.9 2.0 - - + -
149R LEU* 3.3 39.5 - - + +
151R THR* 4.6 6.7 - - + +
176R ASP* 5.2 0.7 - - - -
180R LEU* 4.4 24.5 - - + +
192R SER* 4.3 22.0 + - - -
193R LEU 5.0 0.4 - - - -
194R SER* 3.6 31.9 - - - -
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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