Contacts of the strand formed by residues 201 - 209 (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 ALA 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ALA 2.9 14.4 + - - +
198A PHE* 3.2 29.7 - - - +
200A VAL* 1.4 77.9 - - + +
202A ASP* 1.3 59.6 + - - +
203A LYS 3.6 17.9 - - - +
204A VAL* 4.0 6.7 - - + -
222A ALA* 4.9 0.9 - - - +
245A LEU* 3.7 24.2 - - + -
246A HIS 3.5 10.1 - - - +
247A LEU 4.5 0.2 - - - +
248A LYS* 3.9 5.8 + - - -
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Residues in contact with ASP 202 (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 PHE* 4.2 1.8 - - - -
201A ALA* 1.3 73.2 - - - +
203A LYS* 1.3 61.1 + - - +
221A THR* 3.7 8.1 - - - +
222A ALA* 3.1 39.7 + - + +
246A HIS* 3.2 21.3 + - - +
247A LEU 4.6 1.6 - - - +
248A LYS* 3.6 30.5 - - + +
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Residues in contact with LYS 203 (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 PHE* 4.4 0.2 - - - -
201A ALA* 3.5 3.0 - - - +
202A ASP* 1.3 83.9 + - - +
204A VAL* 1.3 70.5 + - - +
205A ILE* 4.1 17.4 - - + +
219A GLU* 3.2 34.2 + - + +
220A SER 3.3 14.1 - - - +
221A THR* 4.8 14.1 - - + +
246A HIS* 3.0 47.8 + - + +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 3.6 28.7 - - + -
197A ALA* 3.8 15.5 - - + -
198A PHE* 3.7 26.2 - - + -
201A ALA* 4.0 7.2 - - + -
203A LYS* 1.3 78.6 - - - +
205A ILE* 1.3 61.6 + - - +
206A VAL* 4.2 3.1 - - + +
218A TRP 3.6 3.6 - - - +
219A GLU* 3.5 1.2 - - - -
220A SER* 2.9 37.0 + - - -
243A ILE* 3.8 11.2 - - + -
244A SER 3.4 3.8 - - - -
245A LEU* 3.7 31.6 - - + -
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Residues in contact with ILE 205 (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* 4.1 14.1 - - + +
204A VAL* 1.3 70.8 - - - +
206A VAL* 1.3 62.5 + - - +
207A TYR* 3.5 36.7 - - + +
217A ILE* 3.7 24.5 - - + -
218A TRP 3.9 2.2 - - - +
219A GLU* 3.7 29.2 - - + +
229A TYR* 5.6 0.9 - - - +
244A SER* 2.9 41.3 + - - +
246A HIS* 3.5 30.5 + - + +
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Residues in contact with VAL 206 (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* 4.3 11.4 - - + -
194A PHE* 3.7 35.4 - - + -
204A VAL* 4.2 1.8 - - + -
205A ILE* 1.3 73.7 - - - +
207A TYR* 1.3 64.2 + - - +
208A THR* 4.2 5.2 + - + +
216A TYR 3.9 0.3 - - - +
217A ILE* 3.3 5.2 - - - +
218A TRP* 2.7 66.0 + - + +
241A THR* 3.8 24.9 - - + -
242A ARG 3.3 3.6 - - - -
243A ILE* 3.8 17.7 - - + -
1001A BC2 5.1 1.1 - - + -
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Residues in contact with TYR 207 (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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205A ILE* 3.5 37.2 - - + +
206A VAL* 1.3 71.2 - - - +
208A THR* 1.3 59.8 + - - +
215A GLN* 4.4 7.4 - - - +
216A TYR 3.5 5.2 - - - +
217A ILE* 3.6 33.7 - - + -
231A ASP* 4.5 9.4 - - - -
236A THR* 6.0 0.2 - - - -
237A LEU* 3.3 11.3 - - + +
241A THR* 3.3 3.1 - - - +
242A ARG* 2.7 75.1 + - + +
244A SER* 3.5 22.0 + - - -
246A HIS* 5.9 0.2 - - - -
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Residues in contact with THR 208 (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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152A GLY 3.6 0.2 - - - -
153A MET* 2.8 64.4 + - + +
158A LEU* 4.4 15.9 - - + -
206A VAL* 4.5 5.2 - - + +
207A TYR* 1.3 74.5 - - - +
209A LYS* 1.4 59.3 + - - +
214A GLU 4.1 1.0 - - - +
215A GLN* 3.3 6.1 - - - +
216A TYR* 2.8 50.2 + - + +
218A TRP 6.0 0.2 - - - +
237A LEU* 3.9 1.5 - - - +
240A GLY 3.5 4.7 - - - -
241A THR* 3.2 17.5 + - - -
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Residues in contact with LYS 209 (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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151A ILE 3.9 0.9 - - - +
152A GLY* 3.6 5.0 - - - -
153A MET 4.6 0.4 - - - -
208A THR* 1.4 75.4 + - - +
210A ASN* 1.3 86.4 + - - +
211A ASN* 3.7 11.7 + - - +
213A ASP 3.1 15.0 + - - +
214A GLU* 3.8 4.7 - - - +
215A GLN* 3.5 38.8 - - + +
235A ALA* 3.8 22.4 - - + -
237A LEU* 4.1 9.2 - - + -
238A LYS 3.3 30.7 + - - +
239A ARG* 3.5 4.3 - - - -
240A GLY 2.9 31.4 + - - +
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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