Contacts of the strand formed by residues 141 - 151 (chain F) in PDB entry 2ZUQ
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138F THR* 6.0 0.4 - - - -
140F SER* 1.3 85.0 + - - +
142F VAL* 1.3 64.9 + - - +
143F THR* 3.7 9.7 + - - +
188F THR* 5.1 8.1 - - - +
189F VAL 3.7 11.7 - - - -
190F THR* 4.6 5.1 - - - +
191F SER 3.9 5.4 + - - +
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Residues in contact with VAL 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F PRO* 5.3 4.3 - - + -
138F THR* 4.6 12.1 - - - +
141F SER* 1.3 73.3 - - - +
143F THR* 1.3 58.3 + - - +
144F LEU* 3.4 31.2 - - + -
188F THR* 3.4 3.2 - - - +
189F VAL* 2.7 47.4 + - + +
190F THR 4.6 2.5 - - - +
191F SER* 3.7 24.7 - - - +
194F TRP* 4.0 18.4 - - + -
195F PRO* 4.1 17.5 - - + -
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Residues in contact with THR 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E THR* 5.1 13.0 - - + +
141E SER* 3.4 31.3 + - - -
143E PHE* 3.2 16.3 - - - -
160E PHE* 5.3 0.5 - - - -
162E ASN* 4.6 9.9 + - - -
132F PRO* 3.8 8.0 - - - +
141F SER 4.2 9.0 - - - +
142F VAL* 1.3 75.1 - - - +
144F LEU* 1.3 72.5 + - - +
186F SER* 5.3 1.6 - - - -
187F VAL 3.3 8.0 + - - -
188F THR* 3.6 22.9 + - + -
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Residues in contact with LEU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PHE* 3.9 9.0 - - - -
160E PHE* 4.7 0.9 - - - -
130F LEU 4.4 4.0 - - - +
132F PRO* 3.6 20.6 - - + -
142F VAL* 3.4 27.4 - - + -
143F THR* 1.3 81.3 + - - +
145F GLY* 1.3 59.8 + - - +
160F TRP* 3.2 19.0 - - + -
186F SER* 3.4 5.0 - - - -
187F VAL* 2.8 35.2 + - + +
189F VAL* 4.7 2.7 - - + -
194F TRP* 3.6 43.3 - - + +
199F ILE* 3.7 26.2 - - + -
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Residues in contact with GLY 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PHE* 3.8 3.0 - - - -
160E PHE* 3.6 16.6 - - - -
129F PRO* 5.1 0.3 - - - +
130F LEU* 3.3 32.1 + - - +
144F LEU* 1.3 76.2 - - - +
146F CYS* 1.3 64.6 + - - +
160F TRP* 3.4 11.6 - - - -
185F SER 3.3 9.2 - - - -
201F CYS* 5.0 1.0 - - - +
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Residues in contact with CYS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F VAL* 3.7 23.1 - - - -
128F TYR 4.1 4.9 - - - -
129F PRO* 5.1 2.9 - - - -
130F LEU* 3.6 8.4 - - - +
145F GLY* 1.3 73.0 - - - -
147F LEU* 1.3 60.2 + - - +
158F LEU* 4.0 11.2 - - + +
160F TRP* 4.0 3.1 - - + -
184F SER* 3.1 5.7 - - - -
185F SER 3.0 31.3 + - - +
201F CYS* 2.0 52.5 - - - -
203F VAL* 4.1 5.6 - - - -
214F LYS* 5.9 0.7 - - - -
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Residues in contact with LEU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E GLN* 3.9 12.3 - - - +
156E SER* 4.4 12.6 - - - +
158E VAL* 3.9 22.9 - - + -
203E THR* 5.0 6.5 - - + +
126F SER 3.5 0.2 - - - +
127F VAL* 3.0 7.6 - - - +
128F TYR* 2.8 73.9 + - + +
130F LEU* 3.7 19.9 - - + +
146F CYS* 1.3 71.5 - - - +
148F VAL* 1.3 66.8 + - - +
149F LYS* 4.2 9.9 - - + -
182F THR* 4.8 11.7 - - + -
183F LEU 3.5 16.6 - - - +
184F SER* 4.0 7.0 - - - -
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Residues in contact with VAL 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F PRO* 3.3 32.8 - - + -
126F SER 3.8 2.9 - - - -
127F VAL* 3.7 25.6 - - + -
147F LEU* 1.3 79.6 - - - +
149F LYS* 1.3 57.9 + - - +
151F TYR* 3.6 12.1 - - + -
156F VAL* 4.8 8.1 - - + -
158F LEU* 4.1 23.6 - - + -
182F THR* 3.5 2.4 - - - -
183F LEU* 2.7 52.3 + - + +
203F VAL* 4.1 11.0 - - + -
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Residues in contact with LYS 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E GLN* 4.3 7.6 - - - +
156E SER* 3.5 26.6 + - - +
185E LEU* 4.9 6.7 - - - +
203E THR* 5.2 4.8 - - + +
205E THR* 3.8 25.8 + - - +
125F PRO* 3.7 16.6 - - - +
126F SER* 3.6 16.4 + - - +
128F TYR* 4.7 10.5 - - + -
147F LEU* 4.2 15.0 - - + -
148F VAL* 1.3 75.4 - - - +
150F GLY* 1.3 66.1 + - - +
151F TYR* 3.7 2.6 + - - -
177F GLN* 3.1 37.6 + - - +
181F TYR 3.7 2.5 - - - -
182F THR* 3.2 22.8 - - + +
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Residues in contact with GLY 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F THR* 4.1 4.0 - - - +
124F ALA 3.0 17.5 - - - +
126F SER* 5.5 0.3 + - - -
149F LYS* 1.3 75.3 - - - +
151F TYR* 1.3 55.9 + - - -
177F GLN* 3.1 13.4 + - - -
180F LEU* 3.5 23.0 - - - +
181F TYR 2.9 13.5 + - - -
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Residues in contact with TYR 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F THR 3.7 12.8 - - - +
124F ALA 4.0 0.9 - - - -
125F PRO* 3.8 21.8 - - + -
148F VAL* 3.6 23.6 - - + -
149F LYS 4.0 4.9 - - - -
150F GLY* 1.3 75.0 - - - +
152F PHE* 1.3 67.6 + - - +
153F PRO 4.2 10.3 - - - -
154F GLU* 4.0 8.2 + - - -
155F PRO 4.4 1.1 - - - -
156F VAL* 3.5 42.5 - - + +
174F ALA* 3.4 23.8 - - + +
180F LEU* 3.3 12.6 - - - +
181F TYR* 3.0 56.0 + + + -
182F THR* 3.6 11.0 - - - -
183F LEU* 3.7 7.7 - - + +
205F HIS* 4.1 5.6 - + + -
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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