Contacts of the strand formed by residues 247 - 253 (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 ASN 247 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D ALA* 3.3 33.3 - - + +
52D LEU* 3.7 12.6 - - - +
53D VAL* 4.1 11.8 - - - +
205D GLU* 4.6 5.9 + - - +
210D HIS* 6.0 0.4 - - + -
211D ILE 3.9 14.0 + - - +
212D ASN* 2.8 34.9 + - - +
213D ARG 2.9 24.4 + - - -
245D VAL* 3.8 2.3 - - - +
246D LYS* 1.3 80.7 - - - +
248D ILE* 1.3 64.6 + - - +
285D PHE* 3.4 17.1 + - + +
287D THR* 4.9 1.6 + - - -
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Residues in contact with ILE 248 (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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212D ASN* 3.8 0.7 - - - -
213D ARG* 3.2 11.2 - - + +
215D PRO* 4.0 17.0 - - + -
237D ALA* 3.6 37.0 - - + +
240D ALA* 4.3 6.7 - - + -
241D ALA* 4.5 5.4 - - + +
245D VAL* 3.6 25.6 - - + +
246D LYS 4.1 0.2 - - - -
247D ASN* 1.3 78.7 - - - +
249D THR* 1.3 68.5 + - - +
250D VAL* 4.0 13.6 + - + -
276D LEU* 5.0 1.8 - - + -
284D VAL* 3.8 25.8 - - + -
285D PHE 3.0 7.6 + - - +
286D VAL* 3.3 11.1 - - + +
287D THR* 3.0 24.1 + - - +
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Residues in contact with THR 249 (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* 3.4 11.3 - - + +
212D ASN* 2.9 19.8 + - - -
213D ARG 2.9 9.6 + - - -
214D GLU* 3.3 19.0 - - + +
215D PRO* 3.2 18.7 - - - +
248D ILE* 1.3 73.0 - - - +
250D VAL* 1.3 59.8 + - - +
287D THR* 2.7 22.1 + - - +
288D THR 3.6 31.2 - - - +
289D VAL* 3.7 17.5 - - + +
322D LYS* 4.7 9.0 + - - -
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Residues in contact with VAL 250 (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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215D PRO* 4.6 7.2 - - + -
233D GLY* 3.9 22.7 - - - +
237D ALA* 4.1 13.9 - - + -
248D ILE* 4.0 8.0 - - + -
249D THR* 1.3 75.2 - - - +
251D GLY* 1.3 58.7 + - - +
268D LEU* 3.6 32.6 - - + +
269D GLU* 4.7 0.2 - - - -
272D THR* 3.8 25.4 - - + +
286D VAL* 4.2 11.2 - - + -
287D THR 3.0 16.6 + - - +
288D THR* 3.3 14.5 - - + -
289D VAL* 3.0 21.7 + - - +
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Residues in contact with GLY 251 (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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215D PRO* 4.0 8.8 + - - +
217D GLY* 3.3 27.4 - - - +
229D SER* 4.6 5.4 + - - +
230D ASN* 4.9 1.2 - - - +
233D GLY* 5.7 3.8 - - - -
249D THR 4.0 1.2 + - - -
250D VAL* 1.3 75.5 - - - +
252D TYR* 1.3 60.0 + - - +
268D LEU* 3.3 15.5 - - - +
289D VAL* 3.2 22.3 - - - +
291D HIS* 4.6 1.1 - - - -
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Residues in contact with TYR 252 (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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217D GLY* 4.5 2.9 - - - -
218D PRO* 4.3 0.9 - - - -
224D VAL 5.2 1.1 - - - -
226D PRO* 3.6 25.5 - - + +
229D SER* 4.4 11.2 - - - -
230D ASN* 4.2 11.2 - - - +
251D GLY* 1.3 75.1 - - - +
253D GLY* 1.3 83.5 + - - +
254D GLU 4.0 0.3 + - - -
255D CYS* 3.4 17.4 - - - +
260D GLN* 4.4 0.5 + - - +
261D ASP* 2.6 42.6 + - + -
264D ALA* 3.4 30.8 - - + +
265D LEU* 3.9 18.2 - - + -
268D LEU* 4.2 6.5 - - + -
289D VAL 3.0 5.1 + - - -
290D PHE* 3.5 20.9 - + - -
291D HIS* 2.9 30.9 + - - -
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Residues in contact with GLY 253 (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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217D GLY 4.5 0.4 - - - -
218D PRO* 3.8 31.9 - - - +
229D SER* 5.0 1.0 + - - -
252D TYR* 1.3 96.7 - - - +
254D GLU* 1.3 69.2 + - - -
255D CYS* 3.3 4.7 + - - -
291D HIS* 4.0 5.4 - - - -
294D MET* 4.9 4.7 - - - -
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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