Contacts of the strand formed by residues 215 - 221 (chain A) in PDB entry 3PEJ
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 GLN 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A TYR* 4.4 8.5 - - - +
208A THR 3.3 13.7 - - - +
209A LYS* 3.5 11.2 - - + +
214A GLU* 1.3 75.0 - - - +
216A TYR* 1.3 60.7 + - - +
230A LYS* 3.6 6.2 - - - +
231A ASP* 2.6 54.5 + - + +
234A GLY 3.3 20.4 - - - +
235A ALA* 3.4 13.1 - - - +
236A THR* 2.8 21.2 + - - -
237A LEU* 2.9 46.9 + - - +
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Residues in contact with TYR 216 (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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153A MET 5.2 3.1 - - - +
154A THR 6.1 0.2 - - - -
155A LYS* 3.6 55.1 + - + +
158A LEU* 5.1 4.5 - - + -
206A VAL 3.9 0.3 - - - +
207A TYR* 3.5 3.1 - - - -
208A THR* 2.8 45.7 + - + +
213A ASP* 3.2 33.7 + - + -
214A GLU* 3.2 30.4 + - + -
215A GLN* 1.3 75.0 - - - +
217A ILE* 1.3 66.0 + - - +
228A ILE* 4.4 9.0 - - + -
229A TYR* 3.4 23.8 - - - +
230A LYS* 3.3 39.7 - - + -
231A ASP 4.1 0.2 - - - +
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Residues in contact with ILE 217 (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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158A LEU* 5.4 0.2 - - - -
205A ILE* 3.7 25.4 - - + -
206A VAL 3.3 2.9 - - - +
207A TYR* 3.6 27.8 - - + -
216A TYR* 1.3 77.2 - - - +
218A TRP* 1.4 63.5 + - - +
219A GLU* 4.0 3.8 - - + +
227A THR 3.7 1.2 - - - +
228A ILE* 3.3 6.4 - - - +
229A TYR* 2.6 81.5 + - + +
231A ASP* 3.4 34.1 - - + +
232A PRO* 4.1 3.4 - - + -
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Residues in contact with TRP 218 (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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77A TYR* 3.7 9.9 - - - -
153A MET* 5.1 0.4 - - + -
158A LEU* 3.7 39.0 - - + -
162A LEU* 3.4 39.4 - - + +
194A PHE* 3.6 36.1 - + - -
195A TYR* 4.4 2.5 - + - -
204A VAL 3.6 3.1 - - - +
206A VAL* 2.7 61.8 + - + +
208A THR* 6.0 0.2 - - + -
216A TYR 4.3 0.2 - - - -
217A ILE* 1.4 73.1 - - - +
219A GLU* 1.3 66.6 + - - +
220A SER* 3.3 21.0 + - - -
226A PHE* 3.7 11.8 - + - +
227A THR 3.4 3.6 - - - -
228A ILE* 3.5 21.8 - - + -
1001A BC2 4.5 22.0 - - + -
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Residues in contact with GLU 219 (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 LYS* 3.2 38.9 + - + -
204A VAL 3.5 3.8 - - - -
205A ILE* 3.7 29.8 - - + +
217A ILE* 4.0 5.2 - - + +
218A TRP* 1.3 73.8 - - - +
220A SER* 1.3 63.2 + - - +
221A THR* 5.2 4.3 + - - +
226A PHE* 3.2 8.4 - - - +
227A THR* 3.0 52.7 + - + +
229A TYR* 3.9 15.9 + - - -
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Residues in contact with SER 220 (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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77A TYR* 4.8 2.6 + - - -
85A MET* 5.7 1.3 - - - -
194A PHE* 4.6 5.0 - - - -
195A TYR* 5.6 1.4 - - - -
198A PHE* 3.7 21.6 - - - -
203A LYS* 3.3 7.3 - - - +
204A VAL* 2.9 39.1 + - - -
218A TRP* 3.3 34.5 + - - -
219A GLU* 1.3 71.6 + - - +
221A THR* 1.3 63.8 + - - +
225A LYS 3.6 5.4 - - - -
226A PHE* 4.1 4.8 - - - +
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Residues in contact with THR 221 (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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85A MET* 3.4 13.0 - - - +
198A PHE* 3.7 4.5 - - - -
202A ASP 3.7 12.3 - - - +
203A LYS* 4.6 16.9 - - - +
219A GLU* 5.2 4.5 + - - +
220A SER* 1.3 74.8 - - - +
222A ALA* 1.4 64.2 + - + +
223A ASP* 3.1 35.6 + - - +
224A ALA* 3.2 12.8 + - - -
225A LYS* 2.8 18.4 + - - +
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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