Contacts of the strand formed by residues 146 - 152 (chain F) in PDB entry 1Z6Z
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 ASN 146 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90F GLN 2.9 15.0 + - - +
91F ARG* 3.3 26.0 + - - +
92F LEU 2.9 26.0 + - - +
144F GLY 3.9 1.2 + - - -
145F LEU* 1.3 70.0 - - - +
147F ARG* 1.3 63.7 + - - +
148F THR* 2.7 26.3 + - - -
187F ASN 5.9 0.2 - - - -
189F ARG* 4.1 8.8 - - - +
245F ASP* 3.2 30.9 + - - -
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Residues in contact with ARG 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F LEU* 3.6 20.6 - - + -
136F LEU* 3.2 29.6 + - + +
139F PHE 2.8 36.5 + - - -
140F PRO* 3.5 8.6 - - - +
141F ASP* 3.3 36.0 - - - +
145F LEU* 3.6 24.9 + - + +
146F ASN* 1.3 77.2 + - - +
148F THR* 1.3 61.8 + - - +
149F VAL* 5.6 0.2 - - - -
185F GLU* 3.9 14.5 + - - -
187F ASN* 4.3 16.1 + - - +
188F VAL* 3.5 37.4 - - + +
189F ARG* 2.9 25.5 + - - +
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Residues in contact with THR 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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91F ARG* 3.9 10.3 + - - -
92F LEU* 2.9 17.6 + - - +
93F LEU* 3.4 11.9 - - + +
94F LEU 3.0 24.3 + - - -
146F ASN* 2.7 25.3 + - - -
147F ARG* 1.3 73.2 + - - +
149F VAL* 1.3 69.8 + - - +
150F VAL* 4.1 7.0 - - + -
189F ARG* 3.2 22.3 - - + +
242F LEU* 3.8 29.4 - - + -
245F ASP* 4.9 1.9 + - - -
247F PHE* 4.5 7.2 - - + -
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Residues in contact with VAL 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F LEU* 5.9 1.8 - - + -
94F LEU* 3.5 19.1 - - + +
132F THR* 4.0 16.6 - - + -
135F VAL* 5.6 1.1 - - + -
136F LEU* 4.1 23.8 - - + -
148F THR* 1.3 78.5 - - - +
150F VAL* 1.3 63.7 - - - +
178F PHE* 3.7 23.8 - - + -
181F LEU* 3.7 22.2 - - + -
188F VAL* 4.1 4.5 - - + +
189F ARG 3.0 7.9 + - - +
190F VAL* 3.6 15.4 - - + -
191F LEU* 2.9 25.8 + - - +
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Residues in contact with VAL 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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93F LEU* 4.2 7.9 - - + -
94F LEU 2.7 16.0 + - - +
95F ILE* 4.1 13.5 - - + -
96F ASN* 2.8 37.2 + - - +
148F THR* 4.1 6.3 - - + -
149F VAL* 1.3 80.2 - - - +
151F ASN* 1.3 61.5 + - - +
152F ILE* 3.9 25.8 - - + -
178F PHE* 3.7 2.7 - - - -
191F LEU* 3.3 15.7 - - + +
193F TYR* 4.4 4.5 - - + -
238F LEU* 4.2 16.2 - - + -
242F LEU* 4.0 27.4 - - + -
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Residues in contact with ASN 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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96F ASN* 4.1 3.8 - - - -
128F MET* 3.8 12.3 - - + -
150F VAL* 1.3 74.2 - - - +
152F ILE* 1.3 63.2 + - - +
153F SER* 3.2 7.5 + - - +
171F LYS 5.0 0.2 + - - -
174F ARG* 2.9 51.2 + - - +
175F ASP* 3.0 18.2 + - - -
178F PHE* 3.6 18.0 - - + -
191F LEU 2.8 8.5 + - - -
192F ASN* 2.8 28.1 + - - +
193F TYR* 2.9 25.8 + - - -
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Residues in contact with ILE 152 (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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16F PHE* 3.9 21.3 - - + -
95F ILE* 4.0 10.8 - - + -
96F ASN 3.1 22.0 + - - +
97F ASN* 3.8 24.7 - - + +
150F VAL* 3.9 20.9 - - + -
151F ASN* 1.3 75.2 + - - +
153F SER* 1.3 61.2 + - - +
171F LYS* 2.9 24.4 + - - -
174F ARG* 3.5 1.9 + - - -
193F TYR* 3.4 9.0 - - + -
195F PRO* 3.8 22.7 - - + -
238F LEU* 4.1 7.6 - - + -
806F NAP 3.4 28.9 - - - +
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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