Contacts of the strand formed by residues 183 - 188 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D HIS* 3.8 7.6 - - - -
146D PHE* 4.1 1.8 - - - -
179D SER* 3.5 3.1 - - - -
180D GLY* 2.9 53.0 + - - -
181D ASN 3.8 0.4 - - - -
182D ASP* 1.3 82.0 + - - +
184D LEU* 1.3 60.6 + - - +
185D VAL* 3.8 15.3 - - + -
195D THR* 5.7 0.2 - - - -
196D LEU 3.4 12.1 - - - +
198D CYS 3.8 15.0 - - - +
203D GLN* 3.5 39.9 + - + +
204D LEU* 3.9 4.7 - - + -
247D CYS* 3.6 7.4 - - - -
248D GLY 3.8 11.0 - - - -
249D ALA 4.1 5.8 + - - -
251D PHE 3.8 8.3 + - - -
252D THR* 2.9 22.3 + - - -
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D SER* 3.8 3.6 - - - +
130D HIS* 4.3 7.4 - - - +
132D ALA* 3.7 20.2 - - + -
140D VAL* 4.6 5.4 - - + -
142D LEU* 3.8 28.5 - - + -
146D PHE* 4.3 5.1 - - + -
168D VAL* 5.0 1.1 - - + -
177D VAL* 4.3 6.1 - - + -
178D ALA 3.5 10.8 - - - +
179D SER* 3.5 19.7 - - - +
183D HIS* 1.3 75.1 - - - +
185D VAL* 1.3 68.7 + - - +
186D MET* 4.1 19.7 - - + -
195D THR* 3.3 6.2 - - - -
196D LEU* 2.8 54.6 + - + +
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Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LYS 3.9 0.3 - - - +
177D VAL* 3.4 4.5 - - - -
178D ALA* 2.8 40.5 + - + +
183D HIS* 3.8 14.4 - - + -
184D LEU* 1.3 80.2 - - - +
186D MET* 1.3 65.3 + - - +
187D LEU 5.1 0.2 - - - +
193D LEU* 3.4 39.9 - - + -
194D TYR 3.5 4.5 - - - +
195D THR* 4.0 10.3 - - + -
245D ALA* 4.1 12.3 - - + -
247D CYS* 3.5 25.8 - - - -
252D THR* 3.9 12.3 - - + +
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Residues in contact with MET 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 4.0 19.1 - - + -
168D VAL* 4.3 5.2 - - + -
170D LEU* 3.8 19.3 - - + -
174D VAL* 3.9 15.3 - - + -
176D LYS 3.4 4.7 - - - -
177D VAL* 4.3 10.5 - - + -
184D LEU* 4.1 20.6 - - + -
185D VAL* 1.3 79.1 - - - +
187D LEU* 1.3 59.7 + - - +
188D THR* 3.9 1.7 + - + +
192D ASP 3.6 0.5 - - - +
193D LEU* 3.5 8.0 - - - +
194D TYR* 2.8 53.7 + - + +
196D LEU* 3.5 27.6 - - + -
226D PRO* 4.0 24.9 - - + -
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Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D HIS* 3.7 14.6 - - + +
174D VAL* 3.2 4.5 - - - +
175D VAL* 2.7 40.5 + - + +
176D LYS* 2.8 24.8 + - + +
185D VAL* 4.3 0.6 - - - +
186D MET* 1.3 71.4 - - - +
188D THR* 1.3 60.7 + - - +
191D GLY 4.0 9.0 - - - +
192D ASP 3.5 14.4 - - - +
193D LEU* 3.8 17.7 - - + -
242D PHE* 3.8 25.8 - - + +
243D GLN* 3.7 30.3 - - - +
244D ASP* 3.8 9.0 - - - +
245D ALA* 4.7 3.8 - - + +
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Residues in contact with THR 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D LEU* 5.5 1.1 - - + -
172D VAL* 3.7 25.1 - - + -
173D PRO 3.4 11.9 - - - +
174D VAL* 4.1 7.6 - - + +
175D VAL* 3.8 7.5 - - - +
186D MET 4.6 2.2 - - - +
187D LEU* 1.3 81.2 - - - +
189D ALA* 1.3 58.6 + - - +
190D ASP* 3.0 12.2 + - - +
191D GLY* 3.0 18.5 + - - -
192D ASP* 2.9 31.1 + - - +
194D TYR* 3.5 34.3 - - + -
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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