Contacts of the strand formed by residues 289 - 298 (chain D) in PDB entry 6Q0W
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 ARG 289 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259D PHE* 3.5 55.2 - - - +
260D ASN* 4.9 10.0 - - - +
283D MET* 3.9 9.4 - - - +
284D ASP* 2.8 33.3 + - + +
287D THR* 2.9 22.7 + - + +
288D GLY* 1.3 74.4 - - - +
290D SER* 1.3 62.9 + - - +
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Residues in contact with SER 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D LEU* 5.7 0.3 - - - +
258D HIS 4.8 1.9 + - - -
259D PHE* 3.2 44.5 + - - +
261D ILE 3.9 8.2 + - - -
281D LEU* 3.4 35.6 - - - +
282D MET 3.8 5.4 - - - -
283D MET* 4.0 13.4 - - - +
284D ASP* 5.6 0.2 - - - -
289D ARG* 1.3 77.4 - - - +
291D LYS* 1.3 59.6 + - - +
292D GLY* 3.3 12.0 + - - -
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Residues in contact with LYS 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D PHE* 4.1 13.5 - - - -
282D MET* 2.8 30.9 + - + +
283D MET 3.4 26.7 + - - +
284D ASP* 3.8 20.0 - - + +
285D SER 5.4 0.2 - - - +
290D SER* 1.3 70.9 - - - +
292D GLY* 1.3 57.2 + - - +
293D TYR* 3.5 42.0 + - + -
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Residues in contact with GLY 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D SER* 3.5 9.0 + - - -
257D LEU* 3.1 55.6 + - - +
258D HIS 5.2 1.1 - - - -
259D PHE* 5.2 3.4 - - - -
281D LEU* 4.9 0.2 - - - -
290D SER* 3.3 14.8 + - - -
291D LYS* 1.3 77.6 - - - +
293D TYR* 1.3 58.5 + - - +
319D ARG* 5.3 1.6 - - - -
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Residues in contact with TYR 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D TYR* 3.5 39.7 - + - +
254D VAL 3.3 9.2 - - - +
255D GLY* 4.3 2.0 - - - -
256D SER 5.4 0.2 - - - +
257D LEU* 4.3 1.8 - - - -
281D LEU* 3.5 10.9 - - - +
282D MET* 3.0 49.4 + - + +
291D LYS* 3.7 45.1 + - + +
292D GLY* 1.3 79.4 - - - +
294D GLY* 1.3 59.2 + - - +
295D PHE* 4.4 12.3 - + - -
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Residues in contact with GLY 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D TYR* 3.8 5.7 - - - -
254D VAL* 2.9 40.6 + - - +
266D LEU* 6.0 0.2 - - - -
280D GLN 3.3 13.5 - - - -
281D LEU* 4.2 5.2 - - - -
282D MET* 4.3 2.2 - - - -
293D TYR* 1.3 78.6 - - - +
295D PHE* 1.3 73.5 + - - -
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Residues in contact with PHE 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ARG* 4.0 34.5 - - - +
252D LEU 3.4 17.0 - - - +
253D TYR* 3.6 31.9 - + + -
254D VAL* 4.3 0.8 - - - +
278D SER 3.8 1.9 - - - +
279D ILE* 3.4 3.2 - - - +
280D GLN* 2.9 43.6 + - + +
282D MET* 3.6 30.5 - - + -
293D TYR* 4.4 12.8 - + - -
294D GLY* 1.3 77.9 - - - -
296D ILE* 1.3 63.8 + - - +
297D THR* 4.8 1.1 + - - +
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Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ARG* 3.6 0.2 - - - -
252D LEU* 2.8 43.7 + - + +
254D VAL* 3.7 28.0 - - + -
266D LEU* 4.4 12.1 - - + +
270D PHE* 3.6 38.4 - - + -
276D ILE* 3.7 26.5 - - + -
278D SER 3.6 2.9 - - - -
279D ILE* 3.8 23.1 - - + -
295D PHE* 1.3 73.2 - - - +
297D THR* 1.3 62.4 + - - +
298D PHE* 3.8 27.1 + - + -
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Residues in contact with THR 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ARG 5.1 1.3 - - - +
250D MET 3.5 17.5 - - - +
251D ARG* 3.3 36.8 + - + +
276D ILE* 3.3 4.2 - - - +
277D GLU* 2.8 48.3 + - + +
278D SER* 2.8 32.5 + - - +
295D PHE 4.8 1.0 + - - -
296D ILE* 1.3 72.3 + - - +
298D PHE* 1.3 58.8 + - - +
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Residues in contact with PHE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ARG 3.2 4.2 + - - -
250D MET 2.8 28.7 + - - +
252D LEU* 3.7 25.8 - - + -
270D PHE* 3.3 35.4 - + + -
273D PHE* 4.0 4.0 - - + -
274D GLY* 3.6 30.5 - - - -
275D ARG 3.5 15.0 - - - -
276D ILE* 3.9 6.5 - - + +
277D GLU* 4.4 0.8 - - - +
296D ILE* 3.8 18.8 - - + -
297D THR* 1.3 73.5 - - - +
299D SER* 1.3 62.1 + - - +
300D ASP 3.3 16.8 - - - +
303D CYS* 4.1 9.4 - - + -
304D ALA* 3.7 18.6 - - + -
307D ALA* 3.7 20.0 - - + -
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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