Contacts of the strand formed by residues 295 - 307 (chain K) in PDB entry 6R90
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 VAL 295 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225K PRO* 2.8 55.5 - - + +
226K PHE* 3.8 3.5 + - + -
287K LYS* 3.6 44.2 - - + -
288K GLU 3.6 4.9 - - - +
289K GLU* 5.0 6.3 - - + -
290K GLN* 3.3 2.9 - - - -
293K GLY 4.2 6.3 - - - +
294K THR* 1.3 84.2 - - - +
296K THR* 1.3 69.2 + - - +
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Residues in contact with THR 296 (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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226K PHE* 3.6 17.5 - - - +
239K TYR* 5.3 2.7 - - + -
241K ASN* 6.2 0.7 - - + +
244K LYS* 4.1 25.8 - - + -
287K LYS* 3.6 5.2 - - - -
288K GLU* 2.9 44.9 + - - +
290K GLN* 2.6 27.0 + - - -
294K THR* 5.1 3.8 - - - +
295K VAL* 1.3 76.0 + - - +
297K LEU* 1.3 69.1 + - + +
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Residues in contact with LEU 297 (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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226K PHE* 3.3 19.5 - - + +
230K ILE* 5.2 1.1 - - + -
239K TYR* 3.9 44.4 - - + -
244K LYS* 3.0 16.3 - - - -
246K LEU* 4.5 5.8 - - + +
285K LEU* 3.4 37.2 - - + -
286K GLU 3.4 7.4 - - - +
288K GLU* 2.7 18.3 - - - +
296K THR* 1.3 75.6 - - - +
298K LYS* 1.3 57.3 + - - +
299K ASP 3.4 24.5 - - - +
300K LEU* 3.7 27.4 - - + -
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Residues in contact with LYS 298 (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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244K LYS* 4.9 1.8 + - - +
246K LEU* 3.0 16.5 - - - +
286K GLU* 2.6 44.9 + - + +
287K LYS 3.5 21.0 + - - +
288K GLU* 3.6 26.5 - - + +
296K THR 3.5 1.2 + - - -
297K LEU* 1.3 73.6 - - - +
299K ASP* 1.3 62.4 + - + +
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Residues in contact with ASP 299 (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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246K LEU* 3.7 21.6 - - - +
248K ILE* 4.8 3.5 - - - +
285K LEU* 3.8 0.2 - - - -
286K GLU* 3.0 48.4 + - + +
297K LEU* 3.4 10.9 - - - +
298K LYS* 1.3 82.7 - - + +
300K LEU* 1.3 84.2 + - - +
301K ARG* 4.4 12.7 + - - +
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Residues in contact with LEU 300 (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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230K ILE* 4.5 14.8 - - + -
237K ILE* 4.4 23.1 - - + +
238K THR 5.4 0.4 - - - -
239K TYR* 4.7 11.4 - - + +
246K LEU* 4.6 10.4 - - + +
248K ILE* 3.9 33.7 - - + +
283K LEU* 4.1 15.3 - - + -
284K LEU 3.4 14.1 - - - +
285K LEU* 3.6 30.5 - - + -
297K LEU* 3.7 23.6 - - + -
299K ASP* 1.3 89.5 + - - +
301K ARG* 1.3 61.7 + - - +
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Residues in contact with ARG 301 (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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248K ILE* 5.2 1.3 - - - -
282K MET 3.9 0.2 - - - +
283K LEU* 3.5 3.3 - - - +
284K LEU* 2.7 61.8 + - + +
286K GLU* 4.6 18.2 + - - +
299K ASP* 4.4 12.8 + - - +
300K LEU* 1.3 75.0 - - - +
302K VAL* 1.3 75.4 + - - +
303K GLU* 4.3 21.5 - - + -
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Residues in contact with VAL 302 (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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237K ILE* 4.7 11.2 - - + -
248K ILE* 4.6 13.7 - - + +
250K PRO* 4.9 14.3 - - + +
252K ILE* 4.8 12.4 - - + +
253K ILE* 5.2 4.0 - - + -
273K LEU* 5.1 4.5 - - + -
281K PHE* 3.9 31.4 - - + -
282K MET 3.2 11.2 - - - +
283K LEU* 3.6 25.6 - - + -
301K ARG* 1.3 81.3 - - - +
303K GLU* 1.3 71.8 + - - +
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Residues in contact with GLU 303 (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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281K PHE* 3.7 0.3 - - - -
282K MET* 2.8 50.7 + - + +
284K LEU* 5.2 9.5 - - + +
301K ARG* 4.3 23.3 - - + +
302K VAL* 1.3 83.4 - - - +
304K LEU* 1.3 65.8 - - - +
305K LEU* 3.3 3.6 + - + +
346K TYR* 6.2 3.1 - - + -
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Residues in contact with LEU 304 (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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252K ILE* 4.4 16.6 - - + -
279K ARG* 4.2 32.5 - - - +
280K LEU 4.6 2.9 - - - +
281K PHE* 4.2 17.6 - - + -
302K VAL* 4.4 0.4 - - - +
303K GLU* 1.3 72.1 - - - +
305K LEU* 1.3 63.7 + - - +
306K GLY* 3.6 25.4 - - - +
344K GLY 4.8 10.5 - - - +
345K SER* 5.4 1.8 - - - -
346K TYR* 3.9 17.0 - - - -
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Residues in contact with LEU 305 (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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272K LEU* 4.1 20.6 - - + -
280K LEU* 2.9 21.7 + - + +
281K PHE 3.7 8.1 - - - +
282K MET* 3.5 55.2 - - + +
303K GLU* 3.3 5.6 + - + +
304K LEU* 1.3 76.4 - - - +
306K GLY* 1.3 59.1 + - - +
336K LEU* 4.5 14.6 - - + -
337K ASN 6.1 0.2 - - - +
345K SER* 3.3 4.0 + - - -
346K TYR* 2.8 50.2 + - + -
347K VAL* 3.5 14.7 - - + +
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Residues in contact with GLY 306 (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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279K ARG* 3.5 8.0 - - - +
280K LEU* 2.9 28.0 + - - +
304K LEU* 3.6 17.1 - - - +
305K LEU* 1.3 80.8 - - - +
307K GLU* 1.3 61.2 + - - -
345K SER* 3.7 13.7 - - - -
347K VAL* 3.8 7.5 - - - +
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Residues in contact with GLU 307 (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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277K GLU 4.4 2.0 - - - +
278K GLY 3.6 9.0 - - - +
279K ARG* 4.3 6.3 - - + +
306K GLY* 1.3 73.9 - - - +
308K THR* 1.3 79.4 + - - +
332K GLN* 5.7 0.3 + - - -
345K SER* 4.7 1.0 + - - -
347K VAL* 4.2 13.9 - - - +
383K LYS* 2.9 35.2 + - - +
753K ARG* 4.5 9.7 + - - -
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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