Contacts of the strand formed by residues 229 - 236 (chain A) in PDB entry 3PEI
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 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A THR* 3.8 22.9 - - - -
183A ASP* 3.0 29.0 + - - -
186A LEU* 3.9 24.0 - - + +
203A TYR* 4.2 13.9 - + - -
204A LEU 3.2 14.6 - - - +
205A ASP* 4.0 15.0 - - + -
209A MSE 4.0 4.1 - - - +
227A SER* 3.6 38.5 - - - -
228A ASN* 1.3 78.4 - - - +
230A THR* 1.3 62.9 + - - +
231A VAL* 3.8 17.9 - - + -
300A MSE 3.5 0.9 - - - +
301A GLY* 3.8 0.9 - - - -
302A LEU* 2.9 37.1 + - + +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A TYR* 3.2 4.2 - - - -
204A LEU* 3.0 44.2 + - + +
209A MSE 3.5 24.9 - - - +
214A MSE 3.6 10.9 - - + +
229A TYR* 1.3 72.8 + - - +
231A VAL* 1.3 60.1 + - - +
232A CYS* 3.9 3.2 + - - -
299A VAL* 4.2 16.2 - - + -
300A MSE 3.3 7.0 - - - +
301A GLY* 4.8 1.3 - - - -
342A THR* 4.2 14.3 + - + +
345A TYR* 4.2 26.2 - - + -
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.6 26.7 - - + -
189A ALA* 3.7 29.6 - - + -
201A LEU* 3.8 13.5 - - + -
203A TYR* 3.8 7.0 - - + -
229A TYR* 3.8 9.0 - - + -
230A THR* 1.3 77.0 - - - +
232A CYS* 1.3 63.5 + - - +
233A MSE 4.2 3.1 - - + +
298A GLY 3.6 1.4 - - - +
299A VAL* 3.2 5.0 - - - +
300A MSE 2.8 53.9 + - + +
302A LEU* 3.8 24.5 - - + -
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Residues in contact with CYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A SER 3.5 1.4 - - - +
201A LEU* 3.5 6.3 - - - +
202A ASP* 2.7 47.1 + - + +
203A TYR* 5.5 0.4 - - - -
204A LEU* 6.4 0.4 - - - -
230A THR* 4.5 6.3 - - - -
231A VAL* 1.3 77.6 - - - +
233A MSE 1.3 63.4 + - - +
234A GLU* 3.6 1.7 + - + +
297A VAL* 4.1 6.3 - - + -
298A GLY 3.4 4.0 - - - -
299A VAL* 4.1 19.1 - - - -
345A TYR* 4.2 25.8 - - - -
349A TYR* 3.4 28.5 - - - +
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Residues in contact with MSE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA* 4.0 11.7 - - + -
192A LEU* 4.2 18.2 - - - -
193A THR* 3.6 23.6 - - + -
199A PHE* 4.1 9.8 - - + -
200A SER 3.5 4.5 - - - -
201A LEU* 3.9 10.5 - - + -
231A VAL* 4.2 2.2 - - + -
232A CYS* 1.3 74.5 - - - +
234A GLU* 1.3 63.1 + - - +
235A TYR 3.4 1.4 + - - -
280A VAL* 4.3 12.6 - - + -
281A MSE 3.5 34.5 - - - +
284A MSE 4.4 10.8 - - + +
296A VAL 3.7 0.7 - - - +
297A VAL* 3.4 2.7 - - - -
298A GLY* 2.7 43.0 + - - +
300A MSE 3.8 28.9 - - + -
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR 3.4 5.7 - - - +
199A PHE* 3.4 2.3 - - - -
200A SER* 2.9 52.7 + - - +
201A LEU 5.7 0.2 - - - -
202A ASP* 4.1 17.9 - - - +
232A CYS 4.5 3.6 - - - +
233A MSE 1.3 71.1 - - - +
235A TYR* 1.3 58.5 + - - +
236A LYS* 3.7 22.9 + - - -
296A VAL 3.9 3.6 - - - -
297A VAL* 4.1 9.4 - - + -
348A LYS* 5.5 1.4 + - - -
349A TYR* 2.8 36.0 + - + +
513A SO4 3.9 20.2 - - - +
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Residues in contact with TYR 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR* 3.5 29.4 - - - -
199A PHE* 3.6 32.5 - + + -
233A MSE 3.4 0.8 + - - +
234A GLU* 1.3 72.7 - - - +
236A LYS* 1.3 57.5 + - - +
237A GLY* 3.1 10.3 + - - -
284A MSE 4.8 1.8 - - - -
287A ILE* 3.4 33.6 + - + -
288A ALA* 3.9 17.9 - - + -
291A ASN* 3.3 14.7 + - - -
292A LEU* 3.0 43.8 + - + -
294A VAL* 3.3 13.9 - - + -
295A ASN* 3.4 1.4 - - - -
296A VAL* 2.7 43.9 + - + +
513A SO4 4.0 2.0 + - - -
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Residues in contact with LYS 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR* 2.9 31.3 + - + +
200A SER* 3.9 12.6 - - - +
234A GLU* 3.7 24.1 + - - +
235A TYR* 1.3 73.8 - - - +
237A GLY* 1.3 60.0 + - - +
238A GLY 3.4 7.9 - - - +
240A GLU* 5.2 16.1 + - - +
295A ASN* 3.6 11.0 - - - +
513A SO4 3.6 31.5 + - - +
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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