Contacts of the strand formed by residues 184 - 189 (chain B) in PDB entry 6IEH
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 ARG 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ALA* 4.1 5.1 - - - +
183B GLN* 1.3 76.3 - - - +
185B VAL* 1.3 66.2 + - - +
222B ALA 4.9 3.6 - - - +
223B SER* 3.5 19.5 - - - +
242B VAL 5.6 0.9 - - - +
245B GLU* 2.7 26.3 + - + +
246B VAL* 3.9 19.3 - - + -
247B ALA* 3.2 18.4 + - - +
248B TRP 3.8 3.1 + - - -
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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
----------------------------------------------------------
175B ILE* 3.8 36.1 - - + +
178B ALA* 3.9 17.3 - - + -
179B LEU* 4.0 5.4 - - + -
184B ARG* 1.3 80.2 - - - +
186B ILE* 1.3 72.2 + - - +
187B PHE 4.7 0.4 - - - +
223B SER 3.1 11.1 + - - +
224B CYS* 3.5 8.4 - - - -
225B LEU* 3.0 21.3 + - - +
246B VAL* 4.6 0.2 - - - -
248B TRP* 3.3 18.2 - - + +
250B ILE* 3.6 30.5 - - + -
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Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG* 5.9 0.2 - - + -
185B VAL* 1.3 81.5 - - - +
187B PHE* 1.3 60.4 + - - +
188B THR* 4.3 6.7 - - + -
225B LEU* 3.1 16.6 - - + +
227B MET* 3.9 18.8 - - + -
232B LEU* 3.8 31.4 - - + -
242B VAL* 5.0 3.6 - - + -
243B MET* 3.9 11.4 - - + -
246B VAL* 3.6 22.7 - - + -
248B TRP 3.2 5.7 + - - +
249B VAL* 3.3 33.2 - - + +
250B ILE* 2.9 21.1 + - - +
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Residues in contact with PHE 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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168B THR* 5.0 4.5 - - - -
171B ALA* 4.0 14.6 - - + -
175B ILE* 5.2 3.4 - - + -
185B VAL* 4.2 0.6 - - + -
186B ILE* 1.3 73.7 - - - +
188B THR* 1.3 61.4 + - - +
189B SER* 4.5 4.7 - - - -
198B LYS* 3.5 40.6 - - + -
202B MET* 4.7 14.1 - - + -
224B CYS* 4.9 9.6 - - - -
225B LEU 2.8 8.7 + - - +
226B VAL* 3.0 26.1 - - + +
227B MET 2.8 23.0 + - - -
250B ILE* 3.3 44.9 - - + -
252B ASP* 3.8 27.6 - - + -
282B LEU* 5.1 0.7 - - + -
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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
----------------------------------------------------------
186B ILE* 4.3 8.3 - - + -
187B PHE* 1.3 79.5 - - - +
189B SER* 1.3 62.6 + - - +
227B MET* 2.8 25.4 - - + +
229B THR* 3.9 17.9 - - - +
232B LEU* 3.8 27.4 - - + -
249B VAL* 4.8 0.9 - - + -
250B ILE 3.0 15.4 + - - +
251B PHE* 3.8 20.8 - - - -
252B ASP* 3.3 24.6 + - - +
266B TRP* 5.2 0.2 - - - -
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 4.3 2.8 + - - -
188B THR* 1.3 73.7 + - - +
190B PRO* 1.3 74.0 - - - +
191B ILE 3.5 0.4 - - - -
194B LEU* 3.9 12.7 + - - +
195B SER* 3.2 32.9 + - - -
198B LYS* 4.0 13.7 - - - +
226B VAL* 5.6 0.9 - - - +
227B MET 2.9 5.5 + - - -
228B THR* 3.0 10.7 - - - +
229B THR* 3.0 22.5 + - - -
252B ASP* 4.1 11.8 + - - +
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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