Contacts of the strand formed by residues 184 - 192 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PHE* 3.4 2.3 - - - +
176A ILE* 3.3 28.3 + - + +
183A ASN* 1.3 77.8 - - - +
185A TYR* 1.3 58.3 + - - +
236A VAL* 3.4 27.5 - - + +
237A LEU* 3.8 26.4 - - + +
240A LEU* 4.1 15.5 - - + -
180B PRO 2.8 21.3 + - - -
181B ALA 3.1 22.7 + - - -
182B VAL* 3.1 10.2 + - - -
183B ASN 3.1 31.2 + - - -
184B HIS* 4.5 8.6 + - - -
185B TYR* 4.0 9.2 - + - -
230B LEU* 4.0 5.3 - - - +
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Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE 3.1 13.5 - - - +
175A PHE* 3.8 10.3 - - + -
180A PRO* 4.0 10.3 - - + -
183A ASN 3.7 12.8 - - - -
184A HIS* 1.3 76.3 - - - +
186A ALA* 1.3 68.6 + - - +
207A VAL* 5.1 6.1 - - + -
219A TRP* 3.9 22.0 - + + -
230A LEU* 3.2 38.8 + - + +
233A LYS* 2.9 40.8 + - - +
235A GLY* 3.2 37.4 - - - -
236A VAL 4.8 1.6 - - - +
237A LEU* 3.2 16.5 + - - +
184B HIS* 3.8 20.2 - + - -
236B VAL* 4.1 9.5 - - + +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LYS 4.5 0.4 - - - -
173A VAL* 3.3 5.7 - - - +
174A ILE* 2.8 35.9 + - + +
185A TYR* 1.3 83.9 - - - +
187A ALA* 1.3 62.0 + - - +
188A PHE* 3.7 15.5 - - + -
207A VAL* 5.2 0.3 - - - +
235A GLY* 4.9 4.0 - - - +
237A LEU* 3.9 13.0 - - + -
238A PRO* 3.5 30.7 - - + -
241A MET* 5.1 0.7 - - - -
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LYS 3.3 9.0 - - - +
173A VAL* 4.2 7.2 - - + -
185A TYR* 6.2 0.2 - - + -
186A ALA* 1.3 76.4 - - - +
188A PHE* 1.3 61.1 + - - +
204A ARG* 3.2 10.0 - - - +
205A VAL* 2.9 47.1 + - - +
206A THR 4.1 8.7 - - - -
207A VAL* 4.2 7.0 - - + +
210A ILE* 4.1 17.5 - - + -
235A GLY 5.6 1.4 - - - +
238A PRO* 5.3 0.2 - - - +
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.8 26.7 - - + -
171A TRP* 3.2 7.0 - - - +
172A LYS 2.9 37.3 + - - +
174A ILE* 4.2 9.0 - - + -
186A ALA* 3.7 20.0 - - + -
187A ALA* 1.3 75.1 - - - +
189A LEU* 1.3 60.9 + - - +
190A PHE* 3.6 20.6 - + + -
200A PHE* 3.6 49.8 - + - -
201A CYS* 4.7 0.7 - - - -
203A PHE 3.1 7.6 - - - +
204A ARG* 3.5 29.4 - - + -
205A VAL* 4.0 3.1 - - - -
210A ILE* 4.1 1.6 - - - +
238A PRO* 3.8 20.9 - - + -
241A MET* 4.4 5.6 - - - -
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.7 29.8 - - + -
169A ALA* 4.0 9.2 - - + -
170A TYR 3.2 24.7 - - - +
171A TRP* 3.8 11.0 - - + -
188A PHE* 1.3 76.4 - - - +
190A PHE* 1.3 62.8 + - - +
191A ASP 4.5 0.2 + - - -
203A PHE* 2.9 28.7 + - - +
205A VAL* 4.0 16.1 - - + +
209A GLU* 3.8 13.9 - - + +
210A ILE* 4.8 9.4 - - + -
213A ARG* 3.5 33.7 - - - +
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.9 24.0 - - + -
122A ALA* 3.9 19.5 - - + -
123A TRP* 3.6 28.3 - + + -
126A LEU* 3.6 28.7 - - + -
169A ALA* 3.1 6.1 - - - +
170A TYR* 2.8 42.7 + - + +
172A LYS* 5.5 0.4 - - + -
188A PHE* 3.6 27.1 - + + -
189A LEU* 1.3 75.8 - - - +
191A ASP* 1.3 61.2 + - - +
194A THR* 3.9 5.4 - - - +
200A PHE* 3.8 23.3 - - + -
203A PHE* 3.6 37.2 - + + -
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Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.7 5.5 - - - +
152A ARG* 2.7 44.0 + - - -
168A SER 3.4 7.1 - - - +
169A ALA* 3.8 6.5 - - + +
189A LEU 4.3 0.4 + - - -
190A PHE* 1.3 74.6 - - - +
192A GLN* 1.3 64.2 + - - +
193A ASN* 2.9 23.3 + - - +
194A THR* 2.7 28.2 + - - +
203A PHE* 5.7 1.2 - - - -
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Residues in contact with GLN 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 5.3 1.2 - - - +
113A PRO 3.0 24.5 + - - -
114A GLN* 4.2 1.4 - - - +
115A LYS* 2.9 55.3 + - + +
118A LEU* 3.8 12.9 - - - +
152A ARG* 4.3 2.5 - - - +
154A MET* 3.6 22.7 - - + +
166A ILE* 3.7 7.7 - - - +
167A PRO 2.9 29.2 + - - +
168A SER 2.8 24.6 + - - +
169A ALA* 3.9 1.5 - - - +
170A TYR* 3.3 23.0 + - + -
190A PHE 3.9 0.2 + - - -
191A ASP* 1.3 72.8 + - - +
193A ASN* 1.3 59.3 + - - +
194A THR 3.3 5.1 + - - +
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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