Contacts of the strand formed by residues 183 - 188 (chain B) in PDB entry 1I2M
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 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B HIS* 3.7 4.9 - - - -
146B PHE* 4.0 5.4 - - - -
179B SER* 3.4 2.9 - - - -
180B GLY* 2.9 51.6 + - - -
181B ASN 3.8 0.4 - - - -
182B ASP* 1.3 81.4 + - - +
184B LEU* 1.3 58.9 + - - +
185B VAL* 3.9 15.3 - - + -
196B LEU 3.4 12.8 - - - +
198B CYS 3.7 15.9 - - - +
203B GLN* 3.5 31.7 + - + +
204B LEU* 4.0 5.2 - - + -
247B CYS* 3.6 8.6 - - - -
248B GLY 3.8 3.4 - - - -
249B ALA 4.2 5.6 + - - -
251B PHE 3.8 17.7 - - - -
252B THR* 2.8 27.8 + - - -
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Residues in contact with LEU 184 (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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125B SER* 3.7 3.4 - - - +
130B HIS* 4.2 7.9 - - - +
132B ALA* 3.7 20.9 - - + -
140B VAL* 4.5 5.8 - - + -
142B LEU* 3.9 29.4 - - + -
146B PHE* 4.2 5.1 - - + -
168B VAL* 5.1 0.7 - - + -
177B VAL* 4.3 5.4 - - + -
178B ALA 3.4 18.6 - - - +
179B SER* 3.5 13.7 - - - +
183B HIS* 1.3 75.7 - - - +
185B VAL* 1.3 69.5 + - - +
186B MET* 4.1 18.4 - - + -
195B THR* 3.3 4.3 - - - -
196B LEU* 2.9 56.9 + - + +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LYS 3.9 0.5 - - - +
177B VAL* 3.5 4.5 - - - -
178B ALA* 2.9 53.3 + - + +
183B HIS* 3.9 12.1 - - + -
184B LEU* 1.3 79.9 - - - +
186B MET* 1.3 63.0 + - - +
187B LEU 4.3 0.2 - - - -
193B LEU* 4.3 10.5 - - + -
194B TYR 3.3 5.8 - - - +
195B THR* 3.7 17.5 - - + -
245B ALA* 4.4 16.8 - - + -
247B CYS* 3.5 20.0 - - - -
252B THR* 3.9 15.3 - - + +
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Residues in contact with MET 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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140B VAL* 3.8 29.6 - - + -
168B VAL* 4.2 6.1 - - + -
170B LEU* 3.9 12.6 - - + -
174B VAL* 3.9 16.4 - - + -
176B LYS 3.4 4.5 - - - -
177B VAL* 4.2 12.6 - - + -
184B LEU* 4.1 12.8 - - + -
185B VAL* 1.3 78.0 - - - +
187B LEU* 1.3 61.6 + - - +
188B THR* 3.8 2.5 + - - +
192B ASP 3.6 0.7 - - - +
193B LEU* 3.6 4.1 - - - -
194B TYR* 2.8 52.7 + - + +
196B LEU* 3.4 30.1 - - + -
226B PRO* 3.8 26.2 - - + -
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Residues in contact with LEU 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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27B HIS* 3.8 20.0 - - + +
174B VAL* 3.3 4.0 - - - +
175B VAL* 2.8 28.8 + - + +
176B LYS* 2.9 21.0 + - + +
185B VAL* 4.3 0.6 - - - +
186B MET* 1.3 71.7 - - - +
188B THR* 1.3 65.6 + - - +
191B GLY* 4.0 6.1 - - - -
192B ASP 3.5 14.8 - - - +
193B LEU* 4.3 13.9 - - + +
242B PHE* 3.5 36.6 - - + +
243B GLN* 3.5 30.7 - - - +
244B ASP* 3.7 9.4 - - - +
245B ALA* 4.7 4.0 - - + +
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Residues in contact with THR 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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170B LEU* 5.6 0.4 - - + -
172B VAL* 3.6 25.8 - - + -
173B PRO 3.4 11.9 - - - +
174B VAL* 4.1 7.6 - - + +
175B VAL* 3.9 8.7 - - - +
186B MET* 4.4 2.5 - - + +
187B LEU* 1.3 79.3 - - - +
189B ALA* 1.3 63.5 + - - +
190B ASP* 3.0 12.7 + - - +
191B GLY* 3.0 13.7 + - - -
192B ASP* 2.8 41.1 + - - +
194B TYR* 3.6 27.6 - - + -
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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