Contacts of the strand formed by residues 183 - 187 (chain B) in PDB entry 4X61
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 PHE 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 4.2 15.3 - - + -
141B VAL* 3.8 35.4 - - + -
149B ILE* 4.3 11.7 - - + -
151B VAL* 4.4 11.7 - - + -
163B TYR* 5.1 1.6 - + - -
173B VAL* 5.1 0.7 - - + -
174B ALA 3.3 15.0 - - - +
175B ALA* 3.5 12.3 - - + +
176B SER 3.8 2.5 - - - +
181B SER 4.4 4.0 - - - -
182B VAL* 1.3 82.3 - - - +
184B LEU* 1.3 76.1 + - - +
185B SER* 5.1 0.4 - - - -
194B LEU* 3.8 2.6 - - - +
195B TRP* 2.8 76.9 + + + +
197B THR* 4.4 19.1 - - + -
220B TRP* 4.2 3.4 - - - -
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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
----------------------------------------------------------
173B VAL* 3.3 3.1 - - - -
174B ALA* 2.8 33.0 + - + +
183B PHE* 1.3 82.0 - - - +
185B SER* 1.3 63.1 - - - +
192B ILE* 4.7 3.1 - - + -
193B LEU 3.3 13.7 - - - +
194B LEU* 3.9 24.5 - - + -
206B ILE* 4.1 15.7 - - + -
218B LEU* 3.8 23.8 - - + -
220B TRP* 3.5 31.6 - - + +
228B PHE* 3.5 43.5 - - + -
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ILE* 3.5 24.1 - - - +
166B HIS* 3.2 17.4 + - - -
170B VAL* 4.6 1.3 - - - -
172B CYS 3.3 7.4 - - - -
173B VAL* 3.8 8.7 - - - -
183B PHE* 5.1 0.7 - - - -
184B LEU* 1.3 76.8 - - - +
186B CYS* 1.3 60.4 + - - +
191B ARG 3.9 0.2 - - - +
192B ILE* 3.4 4.7 - - - +
193B LEU* 2.8 33.6 + - - +
195B TRP* 2.7 26.4 + - - -
218B LEU* 3.7 3.8 - - - -
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Residues in contact with CYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B HIS* 4.2 2.2 - - - -
170B VAL* 3.7 3.3 - - - +
171B THR* 3.0 21.2 + - - -
172B CYS* 3.1 25.7 + - - -
185B SER* 1.3 77.0 - - - +
187B SER* 1.3 61.8 + - - +
191B ARG 3.3 7.4 - - - +
192B ILE* 4.1 6.5 - - + -
215B PRO* 3.5 45.3 - - + -
216B THR 4.1 5.4 - - - -
218B LEU* 3.8 24.9 - - + -
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B HIS* 3.2 30.7 - - - -
168B ALA* 2.7 19.6 + - - -
169B GLN 2.6 23.9 + - - -
170B VAL* 3.9 4.7 - - - -
171B THR* 3.8 7.0 - - - -
186B CYS* 1.3 76.6 - - - +
188B GLU* 1.3 62.7 + - - +
189B ASP* 3.0 14.5 + - - +
190B ASN* 3.0 16.3 + - - -
191B ARG 3.4 5.1 + - - -
215B PRO* 3.9 13.0 - - - +
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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
------------------------------------------------------------
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