Contacts of the strand formed by residues 184 - 192 (chain B) in PDB entry 1SMN
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 HIS 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A PRO 2.6 23.9 + - - -
181A ALA 3.2 21.4 + - - -
182A VAL* 3.1 12.8 + - - -
183A ASN 3.1 28.9 + - - -
184A HIS* 4.5 7.3 + - - -
185A TYR* 3.8 18.6 - + - -
230A LEU* 3.9 6.5 - - + +
175B PHE* 3.5 2.3 - - - +
176B ILE* 3.3 28.0 + - + +
183B ASN* 1.3 75.9 - - - +
185B TYR* 1.3 61.2 + - - +
236B VAL* 3.5 18.1 - - + +
237B LEU* 3.8 27.0 - - + +
240B LEU* 4.2 14.1 - - + -
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Residues in contact with TYR 185 (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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184A HIS* 4.0 17.3 - + - -
236A VAL* 4.2 9.5 - - + +
174B ILE 3.2 13.7 - - - +
175B PHE* 3.8 11.0 - - + -
180B PRO* 4.0 11.7 - - + -
183B ASN 3.7 12.3 - - - -
184B HIS* 1.3 75.3 - - - +
186B ALA* 1.3 67.3 + - - +
187B ALA* 6.2 0.2 - - + -
207B VAL* 5.1 6.1 - - + -
219B TRP* 3.9 23.6 - + + -
230B LEU* 3.3 38.1 + - + +
233B LYS* 2.8 39.8 + - - +
235B GLY* 3.1 31.2 - - - -
236B VAL 4.7 1.2 - - - +
237B LEU* 3.1 23.2 + - - +
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Residues in contact with ALA 186 (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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172B LYS 4.6 0.4 - - - -
173B VAL* 3.4 5.4 - - - +
174B ILE* 2.8 34.7 + - + +
185B TYR* 1.3 83.5 - - - +
187B ALA* 1.3 63.2 + - - +
188B PHE* 3.8 15.9 - - + -
207B VAL* 5.5 0.4 - - - -
235B GLY* 4.8 3.8 - - - +
237B LEU* 3.9 13.7 - - + -
238B PRO* 3.6 29.8 - - + -
241B MET* 5.1 0.7 - - - -
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Residues in contact with ALA 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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172B LYS 3.3 6.7 - - - -
173B VAL* 4.0 2.5 - - + -
186B ALA* 1.3 77.9 - - - +
188B PHE* 1.3 64.5 + - - +
204B ARG* 3.3 9.4 - - - +
205B VAL* 2.9 43.1 + - + +
206B THR 4.1 0.7 - - - -
207B VAL* 4.0 20.9 - - + -
210B ILE* 4.0 22.0 - - + -
235B GLY 5.6 1.0 - - - +
238B PRO* 5.4 0.4 - - - +
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Residues in contact with PHE 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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126B LEU* 3.6 27.1 - - + -
171B TRP* 3.2 6.2 - - - +
172B LYS 2.9 37.8 + - - +
174B ILE* 4.1 11.0 - - + -
186B ALA* 3.8 18.8 - - + -
187B ALA* 1.3 78.1 - - - +
189B LEU* 1.3 62.1 + - - +
190B PHE* 3.7 21.5 - + + -
200B PHE* 3.5 51.4 - + - -
201B CYS* 4.7 0.7 - - - -
203B PHE 3.2 15.7 - - - +
204B ARG* 3.6 18.4 - - + -
205B VAL* 3.9 2.5 - - - -
210B ILE* 4.0 1.9 - - - +
238B PRO* 4.0 20.6 - - + -
241B MET* 4.4 5.6 - - - -
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Residues in contact with LEU 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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149B LEU* 4.0 15.7 - - + -
169B ALA* 4.2 15.3 - - + -
170B TYR 3.4 8.7 - - - +
171B TRP* 4.2 6.3 - - + -
188B PHE* 1.3 77.7 - - - +
190B PHE* 1.3 73.4 + - - +
191B ASP* 4.4 2.2 + - + +
203B PHE* 3.1 28.0 + - - +
205B VAL* 3.8 15.8 - - + +
209B GLU* 4.2 11.0 - - + +
210B ILE* 4.1 22.0 - - + -
213B ARG* 3.5 35.4 - - - +
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Residues in contact with PHE 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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118B LEU* 3.7 26.8 - - + +
122B ALA* 3.7 29.8 - - + -
123B TRP* 3.7 28.5 - + + -
126B LEU* 3.6 27.6 - - + -
169B ALA* 3.2 3.6 - - - -
170B TYR* 2.8 40.2 + - - +
188B PHE* 3.7 18.4 - - + -
189B LEU* 1.3 75.9 - - - +
191B ASP* 1.3 62.4 + - - +
194B THR* 3.8 5.4 - - - +
200B PHE* 3.7 21.8 - - + -
203B PHE* 3.6 39.3 - + + -
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Residues in contact with ASP 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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118B LEU* 3.8 5.0 - - - +
151B GLU* 5.6 1.7 - - - +
152B ARG* 2.7 47.1 + - - -
168B SER* 3.4 9.7 - - - +
169B ALA* 3.9 7.3 - - + +
189B LEU* 4.4 3.3 + - + +
190B PHE* 1.3 74.9 - - - +
192B GLN* 1.3 65.6 + - - +
193B ASN* 2.9 22.0 + - + +
194B THR* 2.8 27.2 + - - +
203B PHE* 5.5 2.0 - - - -
213B ARG* 5.7 1.7 + - - -
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Residues in contact with GLN 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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85B VAL* 5.4 0.8 - - - +
113B PRO 3.1 23.0 + - - -
114B GLN* 3.6 1.4 - - - +
115B LYS* 2.9 53.8 + - + +
117B ASP* 5.9 0.2 - - - +
118B LEU* 4.0 13.3 + - - +
152B ARG* 4.3 0.7 - - - +
154B MET* 3.7 21.5 - - + +
166B ILE* 3.8 8.3 - - - +
167B PRO 2.8 29.6 + - - +
168B SER* 2.8 25.9 + - - +
169B ALA* 3.9 2.0 - - - +
170B TYR* 3.4 22.3 + - + -
190B PHE 3.8 0.4 + - - -
191B ASP* 1.3 72.5 + - - +
193B ASN* 1.3 57.9 + - - +
194B THR 3.2 5.7 + - - +
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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