Contacts of the strand formed by residues 285 - 291 (chain D) in PDB entry 1CCW
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 PHE 285 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D LEU* 5.6 0.2 - - + -
53D VAL* 3.8 46.7 - - + -
56D LYS* 3.8 24.9 - - + -
246D LYS 2.8 14.3 + - - +
247D ASN* 3.4 15.6 + - + +
248D ILE 3.0 25.5 + - - +
283D ASP 3.9 1.2 + - - -
284D VAL* 1.3 70.9 - - - +
286D VAL* 1.3 63.0 + - - +
287D THR* 3.8 27.3 + - + -
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Residues in contact with VAL 286 (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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56D LYS* 3.7 13.3 - - - -
248D ILE* 3.3 10.3 - - + +
250D VAL* 4.2 10.1 - - + +
269D GLU* 3.9 12.6 - - + +
272D THR* 4.1 20.4 - - + -
273D ASN* 3.5 34.1 + - - +
276D LEU* 3.6 27.4 - - + -
284D VAL* 3.6 10.4 + - + +
285D PHE* 1.3 80.0 - - - +
287D THR* 1.3 78.2 + - - +
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Residues in contact with THR 287 (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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52D LEU* 3.9 19.4 - - + +
56D LYS* 3.9 10.3 - - + +
247D ASN* 4.9 1.5 + - - +
248D ILE 3.0 6.1 + - - +
249D THR* 2.7 29.4 + - - +
250D VAL* 3.0 30.0 + - - +
269D GLU* 4.6 0.4 - - - -
285D PHE* 3.8 24.9 - - + -
286D VAL* 1.3 79.0 - - - +
288D THR* 1.3 65.0 + - - +
321D THR* 3.3 30.3 - - + +
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Residues in contact with THR 288 (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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56D LYS* 5.3 0.2 + - - -
249D THR* 3.6 4.5 - - - +
250D VAL* 3.3 12.6 - - + +
265D LEU* 3.9 27.7 - - + +
268D LEU* 5.3 0.4 - - + -
269D GLU* 3.7 41.5 + - + +
287D THR* 1.3 78.1 - - - +
289D VAL* 1.3 59.4 + - - +
319D GLY 4.1 2.6 + - - -
320D ALA* 3.4 10.6 - - - -
321D THR* 3.0 25.9 + - - -
322D LYS* 3.0 24.4 + - - +
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Residues in contact with VAL 289 (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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214D GLU* 3.5 22.0 - - - +
249D THR* 3.7 15.5 - - + -
250D VAL 3.0 9.4 + - - +
251D GLY* 3.2 20.9 - - - +
252D TYR 3.0 26.2 + - - +
265D LEU* 4.0 6.7 - - - +
288D THR* 1.3 74.5 - - - +
290D PHE* 1.3 63.3 + - - +
291D HIS* 3.8 7.4 + - + -
322D LYS* 3.3 22.0 - - - +
324D ILE* 3.6 37.9 - - + -
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Residues in contact with PHE 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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252D TYR* 3.5 29.8 - + - -
254D GLU* 3.7 34.5 - - + -
261D ASP* 3.9 13.0 - - + -
265D LEU* 4.5 15.7 - - + -
289D VAL* 1.3 72.0 - - - +
291D HIS* 1.3 68.5 + - - +
292D GLN* 4.3 2.5 - - - -
311D ALA* 3.5 20.6 - - - -
314D ILE* 3.5 28.3 - - + -
315D ALA* 3.7 31.2 - - + -
318D ALA* 5.3 1.3 - - + -
320D ALA* 3.9 12.9 - - + +
322D LYS 2.9 5.8 + - - +
323D VAL* 3.1 10.2 - - + +
324D ILE 3.0 22.2 + - - -
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Residues in contact with HIS 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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66D ARG* 3.5 23.1 - - - -
149D ARG* 3.6 16.6 + - - -
214D GLU* 3.8 16.1 + - - -
216D PHE* 4.0 2.6 - + - -
217D GLY 4.4 5.6 - - - -
218D PRO* 3.3 43.7 - - + +
251D GLY* 4.6 1.3 - - - -
252D TYR 2.9 20.9 + - - +
253D GLY* 4.0 0.6 - - - -
254D GLU* 3.1 24.9 + - - +
289D VAL* 3.8 17.9 + - + +
290D PHE* 1.3 78.2 - - - +
292D GLN* 1.3 65.8 - - - +
294D MET* 3.9 13.4 - - + +
324D ILE* 3.8 13.2 - - + -
900D TAR 3.7 6.2 + - - -
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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