Contacts of the strand formed by residues 168 - 177 (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 SER 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B LEU 2.9 8.0 + - - -
150B TYR* 4.4 0.6 - - - +
151B GLU* 2.7 39.8 + - - +
152B ARG* 3.8 35.8 + - - -
154B MET* 3.8 7.0 - - - -
166B ILE 3.7 0.4 + - - -
167B PRO* 1.3 72.1 - - - +
169B ALA* 1.3 64.4 + - - +
191B ASP* 3.4 8.7 + - - +
192B GLN* 2.8 33.4 + - - +
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Residues in contact with ALA 169 (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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148B PRO* 3.2 6.4 - - - +
149B LEU* 2.9 51.1 + - + +
151B GLU* 4.8 3.4 - - - +
167B PRO* 3.5 1.9 - - - +
168B SER* 1.3 85.4 + - - +
170B TYR* 1.3 72.4 + - - +
189B LEU* 4.2 6.1 - - + -
190B PHE 3.2 15.7 - - - +
191B ASP* 3.9 9.6 - - - +
192B GLN* 3.9 3.1 - - - +
213B ARG* 5.2 1.1 - - - +
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Residues in contact with TYR 170 (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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90B GLN* 5.0 6.1 - - + -
112B THR* 2.6 38.3 + - + -
113B PRO 3.2 18.7 + - - -
114B GLN* 3.6 26.0 - - + -
118B LEU* 3.7 14.6 - - + -
123B TRP* 3.7 26.7 - + + -
146B THR* 6.1 0.2 - - - -
147B GLY 3.4 15.0 - - - +
148B PRO* 4.1 6.5 - - + -
167B PRO* 3.6 18.0 - - + +
169B ALA* 1.3 81.4 - - - +
171B TRP* 1.3 60.8 + - - +
189B LEU* 3.4 3.4 - - - +
190B PHE* 2.8 37.7 + - + +
192B GLN* 3.4 30.7 + - + -
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Residues in contact with TRP 171 (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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40B ASN 4.0 4.5 - - - -
41B TRP* 4.1 1.3 - - + -
123B TRP* 4.0 3.9 - - - -
145B VAL* 3.4 44.0 - - + -
146B THR* 2.7 37.5 + - - -
147B GLY* 2.9 39.1 + - - -
148B PRO 3.1 22.5 + - - -
149B LEU* 3.9 19.5 - - + -
170B TYR* 1.3 75.1 - - - +
172B LYS* 1.3 59.3 + - - +
173B VAL* 4.1 7.9 - - + -
188B PHE 3.2 12.6 - - - +
189B LEU* 4.2 5.4 - - + -
210B ILE* 3.6 33.7 - - + -
214B THR* 3.3 12.0 - - + +
216B LEU* 3.6 30.5 - - + -
218B ILE* 4.1 14.1 - - + -
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Residues in contact with LYS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.3 15.2 + - - -
90B GLN 4.8 3.6 + - - -
92B PRO* 4.9 0.8 - - - +
123B TRP* 3.9 31.1 + - + -
126B LEU* 4.1 22.7 - - + +
127B GLU* 3.6 27.1 + - - +
130B GLU* 2.9 33.8 + - - +
144B THR* 3.4 19.3 - - + -
145B VAL 3.5 4.3 - - - +
146B THR* 4.0 8.5 - - - +
171B TRP* 1.3 76.4 - - - +
173B VAL* 1.3 60.1 + - - +
174B ILE* 3.9 13.5 - - + -
187B ALA* 3.3 1.9 - - - -
188B PHE* 2.9 37.4 + - + +
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Residues in contact with VAL 173 (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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143B TYR 3.9 0.5 - - - +
144B THR* 3.3 4.7 - - - +
145B VAL* 2.9 36.6 + - + +
171B TRP* 4.1 9.6 - - + -
172B LYS* 1.3 71.0 - - - +
174B ILE* 1.3 62.4 + - - +
186B ALA 3.4 7.4 - - - +
187B ALA* 4.0 6.1 - - + -
207B VAL* 4.0 11.2 - - + -
210B ILE* 3.6 30.1 - - + -
218B ILE* 4.1 20.9 - - + -
219B TRP* 3.2 45.3 + - + +
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Residues in contact with ILE 174 (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* 4.3 9.0 - - + -
130B GLU* 4.4 10.5 - - + +
133B LEU* 4.7 3.6 - - + -
142B VAL* 3.5 31.2 - - + -
143B TYR 3.5 4.3 - - - -
144B THR* 3.6 11.4 - - - +
172B LYS* 3.9 27.1 - - + -
173B VAL* 1.3 79.5 - - - +
175B PHE* 1.3 66.2 + - - +
185B TYR* 3.2 5.8 - - - +
186B ALA* 2.8 37.4 + - + +
188B PHE* 4.1 26.2 - - + -
219B TRP* 4.4 2.0 - - - -
237B LEU* 3.8 19.5 - - + -
241B MET* 4.5 7.0 - - + -
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Residues in contact with PHE 175 (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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9B CYS 3.9 13.5 - - - -
10B ALA* 4.1 6.5 - - + -
11B VAL* 4.1 6.3 - - + -
142B VAL* 3.6 4.0 - - - +
143B TYR* 2.9 74.1 + + + +
145B VAL* 6.4 0.7 - - + -
174B ILE* 1.3 77.4 - - - +
176B ILE* 1.3 76.4 + - - +
178B ASN 3.6 22.0 - - - -
179B SER* 3.6 11.4 - - - -
180B PRO* 3.6 22.2 - - + -
183B ASN 5.0 0.2 - - - +
184B HIS 3.5 14.1 - - - +
185B TYR* 3.8 10.8 - - + -
219B TRP* 3.5 34.8 - + + -
237B LEU* 4.6 0.7 - - - -
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Residues in contact with ILE 176 (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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181A ALA 4.6 0.4 - - - +
182A VAL* 4.0 35.9 - - + +
133B LEU* 4.2 16.8 - - + -
139B ILE* 4.0 33.0 - - + -
141B SER 3.4 11.4 - - - +
142B VAL* 4.3 3.6 - - + -
143B TYR* 5.3 0.2 - - - -
175B PHE* 1.3 86.5 - - - +
177B ASN* 1.3 65.2 + - - +
178B ASN 3.1 4.7 + - - -
183B ASN* 3.0 29.9 - - + +
184B HIS* 3.3 19.4 + - + +
237B LEU* 3.9 27.4 - - + -
240B LEU* 5.0 0.2 - - + -
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Residues in contact with ASN 177 (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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182A VAL* 4.0 23.8 - - - +
138B ASP 3.1 22.1 + - - -
139B ILE* 3.4 6.1 - - - +
140B SER* 2.9 35.3 + - - +
141B SER* 3.0 22.3 + - - +
143B TYR* 3.5 22.8 - - - -
175B PHE* 4.7 0.2 - - - -
176B ILE* 1.3 72.3 - - - +
178B ASN* 1.3 76.5 + - - +
183B ASN* 3.7 10.7 - - - +
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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