Contacts of the strand formed by residues 228 - 237 (chain B) in PDB entry 1EQR
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 GLU 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PRO* 4.0 6.5 - - - +
164A MET* 3.2 21.8 + - - +
165A LEU* 3.0 36.6 + - + +
214B LYS* 3.2 34.1 + - + +
215B CYS 3.1 11.9 - - - +
216B PHE* 3.7 16.6 - - + -
226B GLN* 3.3 21.6 - - + +
227B PRO* 1.3 82.6 - - + +
229B PHE* 1.3 63.9 + - - +
552B ILE* 5.5 2.9 - - - +
556B LYS* 3.6 8.9 + - + +
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Residues in contact with PHE 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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192B GLN* 4.3 5.6 - - - -
214B LYS* 4.5 4.7 - - - +
215B CYS* 2.9 53.6 + - + +
216B PHE 4.3 0.9 - - - -
217B ARG* 3.2 65.5 - - + +
226B GLN* 5.4 1.6 - - + -
228B GLU* 1.3 78.6 - - - +
230B THR* 1.3 64.9 + - - +
231B GLN* 3.4 39.7 - - + -
534B GLY* 5.6 3.6 - - - -
536B ASP* 3.4 17.9 - - - +
548B ILE* 6.1 1.6 - - + -
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Residues in contact with THR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLU* 2.3 38.6 + - - +
141B ARG* 4.3 3.9 + - - -
212B ILE* 3.6 31.4 - - + -
213B VAL 3.5 15.0 - - - +
214B LYS* 3.8 12.5 + - - +
229B PHE* 1.3 73.9 - - - +
231B GLN* 1.3 62.5 + - - +
534B GLY* 3.7 1.9 - - - -
535B LEU* 2.8 40.5 + - + +
536B ASP* 3.4 13.1 + - - +
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Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B SER* 3.8 13.4 - - - -
211B GLN 3.4 0.2 - - - +
212B ILE* 3.6 1.9 - - - -
213B VAL* 2.9 38.4 + - + +
215B CYS* 3.6 19.6 - - - -
229B PHE* 3.4 36.5 - - + -
230B THR* 1.3 78.7 - - - +
232B ILE* 1.3 66.3 + - - +
233B ASP* 3.3 7.9 + - + +
532B ALA* 3.6 27.3 + - + +
533B PHE 3.3 9.4 + - - +
534B GLY* 4.7 5.3 - - - +
535B LEU 4.2 0.4 - - - +
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Residues in contact with ILE 232 (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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144B ILE* 5.8 0.4 - - + -
148B VAL* 4.0 33.0 - - + -
152B MET* 5.4 3.6 - - + -
210B TYR* 5.1 4.9 - - + -
211B GLN 3.8 4.0 - - - +
212B ILE* 3.8 26.5 - - + -
231B GLN* 1.3 71.1 - - - +
233B ASP* 1.3 58.1 + - - +
234B VAL* 3.8 17.6 + - + +
251B LEU* 4.9 5.8 - - + -
255B LEU* 5.4 1.1 - - + -
532B ALA* 3.2 5.4 - - - -
533B PHE* 2.8 48.1 + - + +
535B LEU* 4.4 20.0 - - + -
538B LEU* 3.8 30.1 - - + -
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Residues in contact with ASP 233 (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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193B SER* 5.5 1.6 - - - -
194B PRO* 3.4 24.2 - - - +
198B LYS* 2.8 31.8 + - - +
209B TYR* 2.7 30.9 + - - +
210B TYR* 2.8 36.2 - - - +
211B GLN 2.9 21.9 + - - +
213B VAL* 3.9 13.0 - - + -
231B GLN* 3.3 6.4 + - + +
232B ILE* 1.3 69.3 - - - +
234B VAL* 1.3 56.8 + - - +
531B LEU 3.9 1.8 - - - +
532B ALA* 3.9 9.5 - - - +
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Residues in contact with VAL 234 (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 MET* 4.5 7.9 - - + -
157B PHE* 3.4 31.9 - - + -
198B LYS* 3.2 6.5 + - - -
209B TYR* 3.5 7.0 - - - +
232B ILE* 3.9 21.8 - - + +
233B ASP* 1.3 80.4 + - - +
235B GLU* 1.3 72.7 + - - +
236B THR* 4.5 4.3 - - + -
244B VAL* 6.2 1.6 - - + -
248B MET* 4.0 31.2 - - + -
530B GLY* 5.6 0.9 - - - -
531B LEU* 2.7 49.7 + - + +
533B PHE* 5.2 0.4 - - + -
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Residues in contact with GLU 235 (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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157B PHE* 4.3 0.3 - - - -
198B LYS* 3.0 29.5 - - + +
199B GLN* 3.9 3.5 - - - +
202B MET* 3.3 28.5 - - + -
208B ARG* 3.5 0.9 - - - -
209B TYR* 2.9 50.6 + - + +
234B VAL* 1.3 74.2 - - - +
236B THR* 1.3 68.6 + - - +
489B ARG* 2.7 45.1 + - - +
528B HIS* 3.6 17.0 - - - -
529B ALA 3.5 13.3 + - - -
530B GLY* 3.1 2.3 - - - -
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Residues in contact with THR 236 (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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157B PHE* 3.7 25.1 - - + -
202B MET* 3.7 2.4 - - - +
207B ASP 3.8 5.6 - - - -
208B ARG* 4.5 3.1 - - + -
234B VAL* 4.5 5.2 - - + -
235B GLU* 1.3 81.2 - - - +
237B SER* 1.3 62.0 + - - +
239B MET* 3.6 41.3 - - + +
244B VAL* 3.8 17.2 - - + +
247B VAL* 5.7 1.6 - - + -
248B MET* 6.1 0.2 - - + -
528B HIS* 3.1 7.1 - - - +
529B ALA 2.5 52.4 + - - +
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Residues in contact with SER 237 (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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2A ARG* 4.5 1.2 + - - -
23A TRP* 5.7 0.7 - - - -
202B MET* 3.2 36.1 + - - +
206B PHE 4.3 1.0 + - - -
207B ASP* 3.1 35.5 + - - +
236B THR* 1.3 73.2 - - - +
238B PHE* 1.3 84.9 + - - +
239B MET* 3.2 14.9 + - - +
526B PRO* 4.0 8.8 - - - +
527B PRO 3.3 8.5 - - - -
528B HIS* 4.1 0.7 - - - +
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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