Contacts of the strand formed by residues 225 - 233 (chain A) in PDB entry 4KM5
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 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A HIS* 3.0 30.7 + - - -
218A VAL* 5.2 9.6 - - + -
219A LYS* 4.2 31.3 + - + +
222A ALA* 3.3 30.3 + - + +
223A PRO 3.2 0.6 - - - -
224A ASN* 1.3 80.2 - - - +
226A PHE* 1.3 59.7 + - - +
317A SER* 3.6 18.8 + - - +
319A ASP* 5.5 7.0 - - - +
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Residues in contact with PHE 226 (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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179A ILE* 3.5 26.9 - - + -
182A ALA* 4.4 8.3 - - + -
183A ALA* 4.1 20.6 - - + -
186A VAL* 3.9 28.0 - - + -
214A TYR* 4.6 11.9 - - - -
215A TYR 4.8 9.4 - - - -
216A GLU 4.1 1.3 - - - -
217A HIS* 3.4 20.6 - + - -
218A VAL* 5.8 2.8 - - - +
223A PRO 3.5 14.6 - - - -
224A ASN* 3.6 17.7 - - - -
225A GLU* 1.3 75.9 - - - +
227A ASP* 1.3 63.7 + - - +
228A VAL* 5.3 1.1 - - + -
316A ILE* 4.2 13.5 - - + -
317A SER 2.7 16.5 + - - +
318A VAL* 3.6 15.8 - - + -
319A ASP* 2.9 31.2 + - - +
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Residues in contact with ASP 227 (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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215A TYR* 3.1 31.0 + - - +
216A GLU* 3.1 42.0 + - + +
218A VAL* 4.7 19.7 - - + +
226A PHE* 1.3 75.1 - - - +
228A VAL* 1.3 66.6 + - - +
229A MET* 5.5 6.2 - - - +
319A ASP* 3.5 25.2 - - - +
321A THR* 5.0 7.3 + - - -
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Residues in contact with VAL 228 (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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186A VAL* 4.2 16.8 - - + -
190A VAL* 4.2 10.1 - - + -
208A LEU* 4.1 13.7 - - + -
212A GLY 5.0 5.8 - - - +
215A TYR* 3.9 11.7 - - + -
226A PHE* 5.3 1.8 - - + -
227A ASP* 1.3 83.5 - - - +
229A MET* 1.3 57.9 + - - +
230A PHE* 3.7 29.8 - - + -
318A VAL* 3.7 22.2 - - + -
319A ASP 2.6 17.3 + - - +
320A ILE* 4.3 7.6 - - + -
321A THR* 2.7 34.1 + - - -
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Residues in contact with MET 229 (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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208A LEU* 4.0 6.3 - - - +
209A LEU* 3.6 44.0 + - + +
210A ASN 5.4 0.5 + - - -
215A TYR* 4.0 24.5 - - + +
216A GLU* 5.8 2.5 - - - +
227A ASP* 5.5 6.3 - - - +
228A VAL* 1.3 77.3 - - - +
230A PHE* 1.3 70.8 + - - +
321A THR* 3.3 22.7 - - + +
323A ALA* 4.2 24.0 - - + -
358A TYR* 5.5 1.6 - - - -
360A VAL* 4.8 4.7 - - + -
378A SER* 4.4 14.8 - - - +
380A SER* 3.6 23.1 - - - +
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Residues in contact with PHE 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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190A VAL* 3.6 34.1 - - + -
193A LEU* 4.7 7.6 - - + -
194A LEU* 3.6 34.1 - - + -
197A LEU* 3.9 17.3 - - + -
206A VAL* 5.5 2.7 - - + -
207A GLY 3.6 7.2 - - - +
208A LEU* 4.0 5.8 - - + -
228A VAL* 3.7 14.1 - - + -
229A MET* 1.3 82.4 - - - +
231A LYS* 1.3 58.8 + - - +
280A PHE* 3.7 14.8 - + - -
284A ILE* 5.3 0.4 - - + -
320A ILE* 3.6 33.0 - - + -
321A THR 2.6 13.7 + - - +
322A LEU* 4.2 14.0 - - + +
323A ALA* 2.7 35.2 + - - +
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Residues in contact with LYS 231 (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 GLY 4.4 10.6 + - - -
206A VAL* 3.2 7.2 - - - +
207A GLY* 2.9 42.9 + - - +
208A LEU 3.6 12.1 - - - +
209A LEU* 3.5 24.9 - - + +
229A MET* 4.0 1.0 + - + -
230A PHE* 1.3 73.4 - - - +
232A LEU* 1.3 59.5 + - - +
233A GLU* 4.6 8.1 + - - +
323A ALA* 3.5 5.6 - - - -
325A GLU* 2.7 37.4 + - + +
327A LYS* 5.5 2.4 - - - +
358A TYR* 3.9 24.5 - - + +
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Residues in contact with LEU 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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202A ALA 4.1 15.0 - - - +
203A PHE* 3.9 27.8 - - + -
205A GLY* 3.7 23.6 - - - +
206A VAL* 3.7 21.5 - - + -
231A LYS* 1.3 74.2 - - - +
233A GLU* 1.3 70.2 + - - +
234A VAL* 3.4 3.7 + - + +
262A LEU* 4.5 16.8 - - + -
276A MET* 4.6 14.6 - - + -
322A LEU* 4.4 7.4 - - + -
323A ALA 2.8 14.8 + - - +
324A LEU* 3.5 12.8 - - + -
325A GLU* 2.9 21.3 + - - +
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Residues in contact with GLU 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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205A GLY* 3.9 12.6 + - - +
231A LYS* 4.1 6.6 + - - +
232A LEU* 1.3 84.5 - - - +
234A VAL* 1.3 67.7 + - - +
235A PRO* 4.1 15.0 - - + +
262A LEU* 5.4 2.1 - - - +
325A GLU* 3.2 34.3 + - + +
326A SER* 6.0 0.4 - - - -
327A LYS* 3.4 39.3 + - + +
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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