Contacts of the strand formed by residues 186 - 192 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ASP* 2.9 41.0 + - - +
178A ASN* 5.9 1.2 - - - +
182B THR* 3.7 1.2 - - - -
183B GLU* 3.0 36.0 + - + +
185B PHE* 1.3 83.1 - - + +
187B GLY* 1.3 58.0 + - - +
295B THR* 3.8 5.8 - - - +
323B VAL* 6.0 1.3 - - + -
324B PHE 3.2 7.0 - - - +
325B ASN* 3.5 23.3 - - - +
327B VAL* 5.8 1.1 - - - -
108I LEU* 4.8 10.9 - - + +
171I LEU* 4.8 20.0 - - + +
173I LEU* 3.4 16.8 - - + +
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Residues in contact with GLY 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLY 3.1 12.1 - - - -
182B THR* 4.2 0.2 - - - -
186B LYS* 1.3 73.5 - - - +
188B ASN* 1.3 58.4 + - - +
295B THR* 4.7 2.0 - - - -
299B ILE* 3.5 17.5 - - - -
323B VAL* 3.4 2.6 - - - +
324B PHE* 2.6 39.6 + - - +
173I LEU* 3.0 15.5 - - - +
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Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ASP* 4.1 7.3 + - - +
180B GLY* 3.6 1.4 - - - -
181B GLY* 2.7 39.0 + - - +
187B GLY* 1.3 73.7 - - - +
189B ALA* 1.3 60.3 + - - +
190B ARG* 4.3 16.2 - - - +
207B TYR* 4.8 0.2 + - - -
299B ILE* 3.3 6.6 - - - +
321B TYR* 3.5 22.2 + - + +
322B LEU 3.0 14.6 - - - +
323B VAL* 4.4 0.7 - - - -
171I LEU 4.0 12.6 - - - +
172I ALA* 3.9 2.6 - - - +
173I LEU* 2.8 50.1 + - + +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ILE* 5.8 0.2 - - + -
179B ASP 3.3 5.6 - - - -
188B ASN* 1.3 75.5 - - - +
190B ARG* 1.3 61.2 + - - +
299B ILE* 4.1 8.9 - - + +
302B VAL* 3.9 25.6 - - + -
303B CYS* 3.9 22.9 - - - -
318B LEU* 4.5 3.1 - - + +
321B TYR* 3.4 3.4 - - - -
322B LEU* 2.9 38.4 + - + +
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Residues in contact with ARG 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ILE* 3.4 9.1 - - - +
179B ASP* 3.0 58.8 + - + +
188B ASN* 4.3 12.4 - - - +
189B ALA* 1.3 74.0 - - - +
191B VAL* 1.3 63.6 + - - +
192B ILE* 4.7 11.5 - - + +
199B CYS 4.1 1.0 + - - -
200B ILE* 3.6 32.9 + - - +
203B THR* 2.4 40.2 + - - -
206B LEU* 6.0 0.2 - - - +
207B TYR* 3.1 32.1 + - - -
318B LEU* 4.3 1.6 - - - -
320B ASN* 3.5 21.1 - - + +
321B TYR* 3.9 22.3 + - + +
172I ALA* 4.9 0.8 - - - +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU 4.2 1.6 - - - -
178B ILE* 4.1 9.2 - - + -
190B ARG* 1.3 76.5 - - - +
192B ILE* 1.3 76.9 + - - +
193B LEU* 4.5 11.4 - - + -
197B THR* 3.5 4.6 - - - +
306B GLU* 3.2 37.5 - - + -
310B ILE* 4.3 19.7 - - + -
317B PRO* 4.8 6.5 - - + -
318B LEU* 3.8 29.8 - - + +
320B ASN* 3.2 29.0 - - + +
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ASN* 4.6 2.0 - - - +
176B PRO* 3.4 0.9 - - - +
177B LEU* 3.1 53.3 + - + +
179B ASP* 5.5 0.4 - - + -
190B ARG* 4.7 13.7 - - + +
191B VAL* 1.3 82.7 - - - +
193B LEU* 1.3 78.5 + - - +
194B PRO* 3.4 24.5 - - + -
197B THR* 4.2 3.6 - - - -
198B ALA 3.6 16.6 - - - +
199B CYS* 3.9 8.7 - - + -
200B ILE* 3.6 48.9 - - + +
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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