Contacts of the strand formed by residues 215 - 221 (chain B) in PDB entry 4IX8
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 THR 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.2 7.6 + - - -
167B ASN* 2.5 28.9 + - - +
169B LEU* 4.1 22.0 - - + +
210B MET 3.8 1.9 + - - -
211B VAL* 3.8 12.8 - - + -
212B ASP 3.0 31.5 + - - +
213B SER 3.3 2.1 - - - +
214B HIS* 1.3 77.4 - - - +
216B LYS* 1.3 65.0 + - - +
217B ALA 4.1 10.5 - - - +
248B ILE* 3.5 28.3 - - + +
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 6.2 0.4 - - - +
161B LEU* 3.5 19.8 - - + +
162B CYS* 3.8 23.1 - - - -
163B ASN* 5.9 1.6 - - - +
166B ASP* 2.9 45.5 + - + +
167B ASN 3.0 7.4 + - - +
213B SER 4.0 17.9 + - - +
214B HIS* 3.5 14.3 + - - +
215B THR* 1.3 78.6 - - - +
217B ALA* 1.3 65.0 + - - +
248B ILE* 4.4 2.7 - - - -
249B PRO* 3.1 26.0 - - - +
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Residues in contact with ALA 217 (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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158B LEU* 5.8 0.2 - - + -
161B LEU* 3.8 17.3 - - + -
168B ILE* 3.5 17.5 - - + +
169B LEU* 2.9 27.5 + - - +
215B THR* 3.7 6.3 - - - +
216B LYS* 1.3 83.3 - - - +
218B PHE* 1.3 61.4 + - - +
219B VAL* 4.2 0.9 - - + -
248B ILE* 4.1 6.9 - - - +
249B PRO* 3.5 12.6 - - + +
251B ILE* 3.9 20.4 - - + -
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Residues in contact with PHE 218 (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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169B LEU* 3.5 22.0 - - + -
192B TYR* 3.5 37.2 - + - -
202B CYS* 4.8 0.4 - - + -
204B LEU* 4.1 18.6 - - + -
207B ALA* 4.2 3.8 - - + -
217B ALA* 1.3 73.6 - - - +
219B VAL* 1.3 61.5 + - - +
220B ILE* 3.8 21.8 - - + -
239B ILE* 4.0 17.7 - - + -
242B PHE* 3.6 29.8 - + - -
243B CYS* 3.8 23.1 - - - -
248B ILE* 3.9 6.9 - - + +
249B PRO 3.0 6.1 + - - -
250B LEU* 3.4 20.8 - - + +
251B ILE* 2.8 27.4 + - - +
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Residues in contact with VAL 219 (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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158B LEU* 5.0 0.7 - - + -
168B ILE* 4.2 22.2 - - + -
169B LEU 2.7 16.9 + - - +
170B VAL* 4.1 14.6 - - + -
171B CYS* 3.6 12.0 + - - -
178B TYR* 3.8 36.3 - - + +
192B TYR* 2.7 23.9 + - - -
217B ALA* 5.0 1.1 - - + -
218B PHE* 1.3 79.0 - - - +
220B ILE* 1.3 71.0 + - - +
221B ILE* 5.0 1.8 - - + -
251B ILE* 3.4 32.1 - - + +
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Residues in contact with ILE 220 (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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171B CYS* 4.7 0.9 - - - -
192B TYR* 3.4 19.5 - - - +
202B CYS* 4.1 5.6 - - - -
218B PHE* 3.8 19.1 - - + -
219B VAL* 1.3 76.8 - - - +
221B ILE* 1.3 61.8 + - - +
222B ASN* 4.6 12.8 - - + +
231B PHE* 4.7 7.4 - - + -
236B VAL* 5.5 3.4 - - + -
239B ILE* 4.1 26.2 - - + -
250B LEU* 4.0 10.1 - - + -
251B ILE 2.9 14.8 + - - +
252B SER* 3.5 27.0 - - - +
253B ASP* 2.8 32.9 + - - +
269B VAL* 4.1 15.3 - - + -
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Residues in contact with ILE 221 (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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171B CYS* 4.1 24.6 - - - -
174B SER* 4.1 3.1 - - - -
175B PHE* 3.6 39.0 - - + +
178B TYR* 4.0 16.2 - - + -
219B VAL* 5.0 2.2 - - + -
220B ILE* 1.3 78.0 - - - +
222B ASN* 1.3 63.0 + - - +
223B PRO 3.4 15.3 - - - +
224B SER* 3.7 26.1 - - - +
225B ASN 3.9 6.3 - - - +
229B SER* 5.1 0.2 + - - -
231B PHE* 4.3 10.6 - - - -
253B ASP* 3.7 16.8 - - + +
286B LLP 3.6 23.3 - - + -
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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