Contacts of the strand formed by residues 225 - 233 (chain K) in PDB entry 6Y5D
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217K HIS* 2.9 24.7 + - - -
218K VAL 5.0 2.3 + - - -
219K LYS* 2.7 40.1 + - + +
222K ALA* 3.0 29.7 + - + +
223K PRO 3.3 0.4 - - - -
224K ASN* 1.3 82.2 - - + +
226K PHE* 1.3 61.5 + - - +
227K ASP 4.3 0.2 + - - -
317K SER* 3.5 21.8 - - - +
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Residues in contact with PHE 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K ILE* 3.7 14.4 - - + -
182K ALA* 3.7 8.5 - - + -
183K ALA* 3.6 34.8 - - + -
186K VAL* 3.8 13.0 - - + -
214K TYR 4.5 0.2 - - - -
215K TYR* 3.4 34.8 - - + -
216K GLU 4.3 2.2 - - - -
217K HIS* 3.6 15.0 - + - -
223K PRO 3.9 8.3 - - - -
224K ASN 3.7 9.6 - - - -
225K GLU* 1.3 75.7 - - - +
227K ASP* 1.3 62.6 + - - +
228K VAL* 4.3 2.0 - - + -
316K ILE* 3.6 33.4 - - + -
317K SER 2.9 11.1 + - - +
318K VAL* 3.5 14.1 - - + -
319K ASP* 2.9 29.6 + - - +
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Residues in contact with ASP 227 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K ASN* 5.3 0.5 + - - -
216K GLU* 3.1 44.6 + - + +
218K VAL* 3.6 29.9 - - + +
226K PHE* 1.3 76.5 - - - +
228K VAL* 1.3 72.6 + - - +
229K MET* 5.9 1.0 - - - +
319K ASP* 3.5 21.9 - - + +
321K THR* 4.6 11.3 + - - -
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Residues in contact with VAL 228 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K VAL* 4.5 9.6 - - + -
190K VAL* 4.5 7.0 - - + -
208K LEU* 4.6 11.2 - - + -
210K ASN* 5.9 2.0 - - - +
214K TYR* 3.2 34.8 - - - +
215K TYR* 4.4 1.6 - - - -
226K PHE* 5.1 0.4 - - + -
227K ASP* 1.3 85.3 - - - +
229K MET* 1.3 60.5 + - - +
230K PHE* 4.0 17.0 - - + -
318K VAL* 4.1 9.0 - - + -
319K ASP 3.0 8.7 + - - +
320K ILE* 3.8 26.6 - - + +
321K THR* 3.0 24.4 + - - -
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Residues in contact with MET 229 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208K LEU* 3.5 10.2 - - - +
209K LEU* 3.1 59.9 + - + +
210K ASN* 4.9 9.2 + - - +
227K ASP* 5.9 1.3 - - - +
228K VAL* 1.3 77.1 - - - +
230K PHE* 1.3 67.5 + - - +
231K LYS* 5.1 0.4 - - - -
321K THR* 3.2 32.5 - - + +
323K ALA* 3.4 29.6 - - + -
358K TYR* 5.1 1.8 - - - -
360K VAL* 4.5 3.1 - - + -
378K SER* 4.3 12.6 - - - +
380K SER* 3.7 20.2 - - - +
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Residues in contact with PHE 230 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K VAL* 3.7 28.5 - - + -
193K LEU* 4.4 20.4 - - + -
194K LEU* 4.2 14.6 - - + -
197K LEU* 3.6 28.0 - - + -
206K VAL* 3.8 11.4 - - + -
207K GLY 3.4 3.1 - - - -
208K LEU* 3.7 21.5 - - + -
228K VAL* 4.0 13.0 - - + -
229K MET* 1.3 79.5 - - - +
231K LYS* 1.3 60.3 + - - +
280K PHE* 3.5 30.3 - + + -
284K ILE* 4.5 1.8 - - + -
320K ILE* 3.9 16.6 - - + -
321K THR 2.8 8.6 + - - +
322K LEU* 3.3 8.0 - - - +
323K ALA 2.9 23.5 + - - -
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Residues in contact with LYS 231 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205K GLY 4.1 1.4 - - - +
206K VAL* 3.3 7.6 - - - +
207K GLY* 2.7 45.0 + - - +
208K LEU 3.7 16.4 - - - -
209K LEU* 4.0 24.0 - - + +
211K THR* 5.4 2.0 - - - -
229K MET 3.9 1.2 + - - -
230K PHE* 1.3 73.5 - - - +
232K LEU* 1.3 61.9 + - - +
233K GLU* 5.7 4.0 - - - +
323K ALA* 3.2 11.7 - - + +
325K GLU* 3.6 36.0 + - + +
358K TYR* 4.2 19.1 - - + -
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Residues in contact with LEU 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K ALA 3.7 13.9 - - - +
203K PHE* 3.9 34.1 - - + -
205K GLY* 4.4 7.4 - - - +
206K VAL* 4.2 15.5 - - + +
231K LYS* 1.3 75.1 - - - +
233K GLU* 1.3 72.0 + - - +
234K VAL 3.5 0.2 + - - -
262K LEU* 3.9 28.0 - - + -
276K MET* 4.0 24.5 - - + -
322K LEU* 4.4 9.6 - - + -
323K ALA 2.7 11.5 + - - +
324K LEU* 3.2 12.2 - - + +
325K GLU* 2.9 22.8 + - - -
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Residues in contact with GLU 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205K GLY* 5.0 5.9 + - - +
231K LYS* 4.3 4.2 - - - +
232K LEU* 1.3 78.3 - - - +
234K VAL* 1.3 71.8 + - - +
235K PRO* 4.1 18.7 - - + +
262K LEU* 4.1 9.4 - - - +
325K GLU* 3.8 27.3 - - + +
327K LYS* 4.1 30.2 + - + +
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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