Contacts of the strand formed by residues 224 - 230 (chain B) in PDB entry 3E88
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 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B MET* 3.7 26.2 - - + +
165B LYS* 6.1 1.0 - - - +
182B ILE* 3.6 26.1 - - + +
183B LEU 3.3 12.1 - - - +
184B ARG* 3.6 24.7 - - + +
185B LYS* 3.7 3.8 - - - +
220B GLN* 3.4 4.7 - - - +
221B THR* 2.8 38.7 + - - +
222B HIS* 5.2 3.8 - - - -
223B ASP* 1.3 105.4 + - - +
225B LEU* 1.3 62.7 + - - +
226B CYS* 4.2 2.6 - - - -
450B ILE* 3.8 15.4 - - - +
451B TPO 3.2 41.0 + - - -
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Residues in contact with LEU 225 (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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181B LYS 3.5 2.6 - - - +
182B ILE* 3.5 2.4 - - - -
183B LEU* 2.9 42.1 + - + +
185B LYS* 3.9 17.5 - - + -
188B ILE* 3.4 30.7 - - + -
197B THR* 3.8 16.2 - - + -
219B PHE 4.0 1.1 - - - -
220B GLN* 3.8 23.3 - - + +
224B ARG* 1.3 74.3 - - - +
226B CYS* 1.3 61.5 + - - +
227B PHE* 4.3 2.2 - - + -
470B PHE* 3.8 33.2 - - + -
473B PHE* 3.9 25.8 - - + -
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Residues in contact with CYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B MET* 3.8 24.9 - - - -
180B MET* 4.3 7.4 - - + -
181B LYS 3.5 4.3 - - - +
182B ILE* 4.1 19.5 - - - -
217B TYR 4.0 0.5 - - - +
218B ALA* 3.5 5.7 - - - +
219B PHE* 2.9 77.1 + - + +
221B THR* 5.3 0.2 - - - -
224B ARG* 4.7 3.8 - - - -
225B LEU* 1.3 79.2 - - - +
227B PHE* 1.3 62.8 + - - +
228B VAL 4.1 0.4 + - - -
473B PHE* 4.4 2.7 - - - -
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Residues in contact with PHE 227 (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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1B G96 3.7 15.9 - - + -
180B MET* 3.2 6.4 - - - +
181B LYS* 2.9 51.1 + - + +
183B LEU* 4.0 25.1 - - + -
197B THR* 4.0 8.3 - - + -
200B GLU* 3.7 36.1 - - + -
201B SER* 4.0 16.2 - - - -
204B LEU* 4.6 0.7 - - + -
215B LEU* 4.0 17.9 - - + -
217B TYR 3.8 3.1 - - - -
218B ALA* 4.9 1.1 - - + -
225B LEU* 5.1 2.2 - - + -
226B CYS* 1.3 73.7 - - - +
228B VAL* 1.3 60.7 + - - +
229B MET* 3.2 18.4 - - + +
473B PHE* 3.6 33.9 - + - -
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Residues in contact with VAL 228 (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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152B PHE* 4.0 14.8 - - + -
169B VAL* 5.1 1.3 - - + -
178B TYR* 3.9 29.2 - - + -
179B ALA 3.5 4.0 - - - +
180B MET* 3.9 22.4 - - + -
215B LEU* 3.3 2.6 - - - +
216B LYS* 2.8 26.5 + - + -
217B TYR* 2.9 39.6 + - + +
219B PHE* 3.8 28.5 - - + -
227B PHE* 1.3 74.2 - - - +
229B MET* 1.3 62.1 + - - +
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Residues in contact with MET 229 (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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1B G96 3.3 60.8 - - + +
166B VAL* 5.1 0.7 - - + -
178B TYR* 3.4 11.6 - - - +
179B ALA* 2.9 40.8 + - + +
180B MET 4.0 0.9 - - - -
181B LYS* 3.2 33.4 - - + +
213B THR* 3.6 11.4 - - + -
214B ALA 3.2 18.2 - - - +
215B LEU* 4.1 7.6 - - + -
216B LYS 4.2 1.8 - - - +
227B PHE* 3.2 28.7 - - + +
228B VAL* 1.3 76.3 - - - +
230B GLU* 1.3 62.8 + - - +
231B TYR 3.4 0.2 + - - -
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Residues in contact with GLU 230 (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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1B G96 3.5 13.7 + - - -
178B TYR* 4.2 12.9 - - + -
212B LEU 4.0 0.2 - - - +
213B THR* 3.9 7.9 - - + +
214B ALA* 3.3 43.1 + - + +
216B LYS 5.3 0.2 - - - +
229B MET* 1.3 75.4 - - - +
231B TYR* 1.3 65.2 + - - +
232B ALA* 3.3 5.9 + - + +
290B LYS* 2.8 44.4 + - + +
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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