Contacts of the strand formed by residues 186 - 192 (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 LYS 186 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177E ASP* 3.0 40.5 + - - +
178E ASN* 5.9 1.2 - - - +
182F THR* 3.7 0.9 - - - -
183F GLU 3.0 35.4 + - - +
185F PHE* 1.3 82.1 - - + +
187F GLY* 1.3 60.7 + - - +
295F THR* 3.8 6.2 - - - +
323F VAL* 6.0 1.1 - - + -
324F PHE 3.2 8.3 - - - +
325F ASN* 3.5 23.6 - - - +
327F VAL* 5.8 1.1 - - - -
108K LEU* 4.6 11.6 - - + +
140K GLN* 6.0 1.8 - - - +
171K LEU* 4.6 21.4 - - + +
173K LEU* 3.3 15.8 - - + +
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Residues in contact with GLY 187 (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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181F GLY 3.2 11.0 - - - -
182F THR* 4.2 0.4 - - - -
186F LYS* 1.3 73.8 - - - +
188F ASN* 1.3 58.7 + - - +
295F THR* 4.6 1.6 - - - -
299F ILE* 3.6 17.5 - - - -
323F VAL* 3.5 2.9 - - - +
324F PHE* 2.7 36.5 + - - +
173K LEU* 3.0 16.7 - - - +
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Residues in contact with ASN 188 (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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179F ASP* 4.1 7.7 + - - +
180F GLY* 3.5 1.4 - - - -
181F GLY* 2.7 41.9 + - - +
187F GLY* 1.3 74.5 - - - +
189F ALA* 1.3 59.6 + - - +
190F ARG* 4.3 13.9 - - - +
207F TYR* 4.8 0.6 + - - -
299F ILE* 3.3 6.2 - - - +
321F TYR* 3.5 21.7 + - + +
322F LEU 3.0 14.8 - - - +
323F VAL* 4.4 0.4 - - - -
171K LEU 3.9 13.7 - - - +
172K ALA* 3.9 5.5 - - - +
173K LEU* 2.8 43.8 + - - +
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Residues in contact with ALA 189 (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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178F ILE* 5.8 0.2 - - + -
179F ASP 3.3 6.1 - - - -
188F ASN* 1.3 75.4 - - - +
190F ARG* 1.3 61.6 + - - +
299F ILE* 4.1 10.9 - - + +
302F VAL* 4.0 22.2 - - + -
303F CYS* 3.8 24.9 - - - -
318F LEU* 4.5 3.3 - - + +
321F TYR* 3.4 3.0 + - - -
322F LEU* 2.9 37.0 + - + +
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Residues in contact with ARG 190 (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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178F ILE* 3.4 9.0 - - - +
179F ASP* 3.0 57.8 + - + +
188F ASN* 4.3 11.0 - - - +
189F ALA* 1.3 77.1 - - - +
191F VAL* 1.3 65.3 + - - +
192F ILE* 4.7 10.9 - - + +
199F CYS 4.0 1.6 + - - -
200F ILE* 3.6 33.6 + - - +
203F THR* 2.5 39.0 + - - -
206F LEU* 5.5 0.2 - - - +
207F TYR* 3.1 31.5 + - - -
318F LEU* 4.3 1.6 - - - -
320F ASN 3.6 20.2 - - - +
321F TYR* 3.8 20.9 + - + +
172K ALA* 4.9 0.6 - - - +
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Residues in contact with VAL 191 (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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177F LEU 4.2 1.8 - - - -
178F ILE* 4.1 11.7 - - + -
190F ARG* 1.3 76.6 - - - +
192F ILE* 1.3 77.5 + - - +
193F LEU* 4.6 11.4 - - + -
197F THR* 3.5 3.9 - - + +
306F GLU* 3.2 34.8 - - + -
310F ILE* 4.3 20.0 - - + -
317F PRO* 4.8 6.5 - - + -
318F LEU* 3.8 29.8 - - + +
320F ASN* 3.2 30.2 - - - +
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Residues in contact with ILE 192 (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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155F ASN* 4.6 2.0 - - - +
176F PRO* 3.4 1.0 - - - +
177F LEU* 3.0 54.4 + - + +
179F ASP* 5.4 0.7 - - + -
190F ARG* 4.7 13.9 - - + +
191F VAL* 1.3 82.7 - - - +
193F LEU* 1.3 76.4 + - - +
194F PRO* 3.3 24.2 - - + -
197F THR* 4.2 2.9 - - - -
198F ALA 3.6 17.0 - - - +
199F CYS* 4.0 9.2 - - + +
200F ILE* 3.6 47.8 - - + +
320F ASN* 5.8 0.2 - - + -
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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