Contacts of the strand formed by residues 220 - 227 (chain I) in PDB entry 3PB1
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 TYR 220 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E ARG* 4.2 30.7 - - + -
212I GLU* 3.1 31.9 - - + -
213I PHE 3.5 1.8 - - - -
214I THR* 3.9 22.9 - - + -
218I GLY 4.8 8.5 - - - -
219I HIS* 1.3 75.0 - - - +
221I TYR* 1.3 63.9 + - - +
240I PRO* 3.5 6.1 - - - +
241I TYR* 3.0 28.2 + + + +
242I GLU* 4.7 10.6 + - - +
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Residues in contact with TYR 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I GLU* 3.5 6.2 - - - +
213I PHE* 3.1 60.9 + - + +
214I THR 3.7 18.9 + - - -
215I THR* 3.8 10.1 - - + -
219I HIS 3.8 9.4 - - - -
220I TYR* 1.3 76.0 - - - +
222I ASP* 1.3 65.6 + - - +
223I ILE* 3.3 35.4 - - + +
239I ALA 3.3 15.5 - - - +
240I PRO* 3.6 8.1 - - + -
241I TYR* 3.9 2.0 - - - +
250I LEU* 3.6 30.3 - - + -
253I ILE* 4.0 9.0 - - + +
258I LEU* 3.9 11.6 - - - +
262I TRP* 3.1 29.6 + + - -
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Residues in contact with ASP 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I TYR* 2.6 34.0 + - + -
211I THR 3.9 4.5 - - - -
212I GLU* 4.2 5.9 - - - +
221I TYR* 1.3 75.2 - - - +
223I ILE* 1.3 65.6 - - - +
224I LEU* 5.4 1.6 - - + +
237I ILE 4.2 1.1 - - - -
238I ALA* 3.1 23.4 - - - -
239I ALA* 2.9 17.0 + - - +
240I PRO 5.3 0.3 - - - +
241I TYR* 4.2 28.6 - - - +
352I ILE* 4.0 21.2 - - + +
354I ILE* 5.3 7.6 - - + +
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Residues in contact with ILE 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I TYR* 3.4 4.7 - - - -
211I THR* 2.9 41.8 + - + +
213I PHE* 4.9 2.2 - - + -
221I TYR* 3.3 37.2 - - + +
222I ASP* 1.3 82.0 - - - +
224I LEU* 1.3 63.9 + - - +
236I PHE* 4.1 9.2 - - + -
237I ILE 3.2 11.0 - - - +
238I ALA* 3.5 11.4 - - + -
262I TRP* 3.3 46.7 - - + -
266I MET* 3.5 21.7 - - + +
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Residues in contact with LEU 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I PHE* 3.4 38.6 - - + -
209I ASN 3.5 6.1 - - - +
210I TYR* 3.7 24.2 - - + -
222I ASP* 4.3 1.8 - - + -
223I ILE* 1.3 72.6 - - - +
225I GLU* 1.3 59.8 + - - +
226I LEU* 4.2 4.9 - - + -
235I MET 3.7 0.5 - - - +
236I PHE* 3.2 7.4 - - - +
237I ILE* 2.9 43.8 + - + +
266I MET* 3.9 3.6 - - - -
271I ARG* 5.2 0.9 - - + -
273I LEU* 3.5 35.7 - - + -
352I ILE* 3.6 31.4 - - + -
354I ILE* 5.2 4.3 - - + -
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Residues in contact with GLU 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I PHE* 3.9 11.1 - - - +
209I ASN* 2.8 50.2 + - + +
224I LEU* 1.3 73.4 - - - +
226I LEU* 1.3 71.3 + - - +
227I PRO* 3.6 13.9 - - + +
234I SER* 2.6 37.4 + - - +
235I MET 3.4 4.0 - - - +
236I PHE* 4.2 13.2 - - + +
263I LYS* 3.0 25.8 + - - +
266I MET* 3.8 17.0 - - + +
365I ASN* 4.0 5.4 + - - +
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Residues in contact with LEU 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I TRP* 3.5 31.5 - - + -
179I PHE* 4.5 9.4 - - + -
204I GLN* 5.0 1.1 - - - +
208I PHE* 3.5 36.1 - - + -
224I LEU* 4.2 3.8 - - + -
225I GLU* 1.3 76.5 - - - +
227I PRO* 1.3 68.9 - - + +
235I MET 2.7 34.0 + - - +
237I ILE* 3.2 31.6 - - + -
273I LEU* 3.7 17.5 - - + -
275I LEU* 3.9 19.7 - - + -
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Residues in contact with PRO 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I TRP* 3.8 7.1 - - - +
176I LYS* 3.0 32.7 + - + +
177I THR 4.5 1.4 + - - +
208I PHE* 5.3 6.1 - - + -
225I GLU* 3.6 15.2 - - + +
226I LEU* 1.3 86.1 - - + +
228I TYR* 1.3 64.6 + - - +
231I ASP* 3.4 26.2 - - - +
233I LEU 4.4 1.3 - - - +
234I SER* 3.5 17.0 - - - +
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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
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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