Contacts of the strand formed by residues 177 - 183 (chain F) in PDB entry 1R4N
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 LEU 177 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141F ILE* 3.4 14.6 - - + +
143F CYS* 4.0 22.9 - - + -
154F ILE* 4.3 18.6 - - + -
155F ASN* 4.3 15.9 - - - +
158F LEU* 3.4 30.1 - - + -
175F VAL 3.3 1.5 + - - +
176F PRO* 1.3 71.7 - - - +
178F ILE* 1.3 71.6 + - - +
179F ASP* 3.9 3.3 + - + +
192F ILE* 3.0 60.4 + - + +
194F PRO* 4.9 0.9 - - + -
200F ILE* 4.4 7.4 - - + -
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Residues in contact with ILE 178 (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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140F ILE* 3.7 22.2 - - + -
141F ILE 2.8 9.9 + - - +
142F VAL* 3.1 12.1 - - + +
143F CYS 2.7 25.6 + - - -
176F PRO 4.2 3.1 - - - -
177F LEU* 1.3 79.4 - - - +
179F ASP* 1.3 61.3 + - - +
190F ARG 3.4 10.5 - - - +
191F VAL* 4.1 20.9 - - + -
303F CYS* 3.3 42.2 - - + -
306F GLU* 4.3 11.7 - - + -
307F VAL* 4.2 6.7 - - + -
310F ILE* 3.6 26.5 - - + -
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Residues in contact with ASP 179 (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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143F CYS* 3.6 18.3 - - + +
151F ARG* 2.6 42.5 + - - +
177F LEU* 3.9 8.1 + - + +
178F ILE* 1.3 73.7 - - - +
180F GLY* 1.3 68.5 + - - +
181F GLY* 4.3 0.5 + - - -
188F ASN* 4.5 4.9 + - - -
189F ALA* 3.3 5.4 - - - -
190F ARG* 3.0 63.8 + - + +
192F ILE* 5.4 0.2 - - + -
200F ILE* 4.5 9.9 - - + -
207F TYR* 4.5 0.2 + - - -
303F CYS* 3.9 7.1 - - - -
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Residues in contact with GLY 180 (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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59F LEU* 3.9 16.3 - - - +
143F CYS 3.2 18.3 + - - +
144F GLY* 4.4 1.2 - - - -
151F ARG* 2.9 19.1 + - - -
179F ASP* 1.3 83.0 - - - +
181F GLY* 1.3 59.1 + - - -
188F ASN 3.5 4.0 - - - -
299F ILE* 3.9 14.6 - - - -
303F CYS* 4.1 5.1 - - - -
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Residues in contact with GLY 181 (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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59F LEU* 4.8 0.9 - - - -
151F ARG* 3.8 5.6 - - - -
179F ASP* 4.8 0.4 - - - -
180F GLY* 1.3 75.3 - - - -
182F THR* 1.3 63.3 + - - -
187F GLY* 3.2 4.6 - - - -
188F ASN* 2.7 52.6 + - - +
299F ILE* 3.5 8.6 - - - +
173K LEU* 4.0 4.9 - - - -
175K GLY 3.7 6.5 - - - -
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Residues in contact with THR 182 (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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59F LEU* 4.7 2.2 - - - +
181F GLY* 1.3 76.5 + - - -
183F GLU* 1.3 75.2 + - - +
184F GLY 4.4 4.9 - - - +
186F LYS 3.7 5.6 - - - -
187F GLY* 4.2 0.2 - - - -
289F ILE* 6.0 0.4 - - + -
291F ALA* 4.6 13.5 - - + -
292F VAL 5.8 0.2 - - - +
295F THR* 3.3 24.0 - - + +
296F ASN* 3.0 35.6 + - - +
299F ILE* 4.2 4.0 - - - +
173K LEU* 3.7 4.3 - - - +
175K GLY* 3.0 33.1 + - - -
176K GLY* 4.4 11.9 - - - +
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Residues in contact with GLU 183 (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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182F THR* 1.3 83.5 - - - +
184F GLY* 1.3 63.8 + - - +
185F PHE 3.3 0.2 + - - -
186F LYS* 3.0 25.5 + - - +
208F PRO* 5.7 5.7 - - - +
289F ILE* 3.3 27.6 - - + -
290F PRO* 5.7 1.1 - - + -
173K LEU* 3.8 23.4 - - + +
174K ARG* 3.1 54.5 + - - +
175K GLY 4.9 0.4 - - - -
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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