Contacts of the strand formed by residues 247 - 253 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA* 3.3 37.5 - - + +
52B LEU* 3.7 13.2 - - - +
53B VAL* 4.1 11.1 - - - +
205B GLU* 4.6 6.3 + - - +
210B HIS* 5.9 0.4 - - + -
211B ILE 4.2 7.8 + - - +
212B ASN* 2.8 35.1 + - - +
213B ARG 2.9 24.4 + - - -
245B VAL* 3.8 4.3 - - - +
246B LYS* 1.3 79.1 - - + +
248B ILE* 1.3 64.5 + - - +
285B PHE* 3.5 18.2 + - + +
287B THR* 4.8 1.6 + - - -
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASN* 3.8 0.7 - - - -
213B ARG* 3.3 11.4 - - + +
215B PRO* 3.9 17.9 - - + -
237B ALA* 3.7 36.3 - - + +
240B ALA* 4.3 5.8 - - + -
241B ALA* 4.4 5.2 - - + +
245B VAL* 3.6 25.8 - - + +
246B LYS 4.2 0.2 - - - -
247B ASN* 1.3 78.1 - - - +
249B THR* 1.3 67.1 + - - +
250B VAL* 3.9 13.1 + - + -
272B THR* 5.6 0.2 - - + -
276B LEU* 5.0 2.2 - - + -
284B VAL* 3.8 24.9 - - + -
285B PHE 3.0 7.3 + - - +
286B VAL* 3.3 11.7 - - + +
287B THR* 2.9 25.0 + - - +
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Residues in contact with THR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.3 11.5 - - + +
212B ASN* 3.0 17.0 + - - -
213B ARG 2.9 8.5 + - - -
214B GLU* 3.2 23.2 - - + +
215B PRO* 3.1 19.8 - - - +
248B ILE* 1.3 71.0 - - - +
250B VAL* 1.3 60.2 + - - +
251B GLY 4.0 0.2 + - - -
287B THR* 2.7 20.9 + - - +
288B THR 3.6 20.4 - - - +
289B VAL* 3.6 29.8 - - + -
322B LYS* 4.6 9.0 + - + -
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PRO* 4.6 6.3 - - + -
233B GLY* 3.9 23.8 - - - +
237B ALA* 4.1 8.5 - - + -
248B ILE* 3.9 7.5 + - + -
249B THR* 1.3 75.7 - - - +
251B GLY* 1.3 58.9 + - - +
268B LEU* 3.7 31.1 - - + +
269B GLU* 4.7 0.2 - - - -
272B THR* 3.9 28.7 - - + +
286B VAL* 4.1 12.8 - - + -
287B THR 2.9 17.2 + - - +
288B THR* 3.2 14.4 - - + -
289B VAL* 3.0 22.6 + - - -
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PRO* 4.1 8.6 + - - +
217B GLY* 3.3 26.4 - - - +
229B SER* 4.6 5.5 + - - +
230B ASN* 4.8 1.2 - - - +
233B GLY* 5.7 3.8 - - - -
249B THR 4.0 1.4 + - - -
250B VAL* 1.3 75.3 - - - +
252B TYR* 1.3 61.4 + - - +
268B LEU* 3.3 14.8 - - - +
289B VAL* 3.2 20.8 - - - +
291B HIS* 4.7 1.1 - - - -
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Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B GLY* 4.5 3.6 - - - -
218B PRO* 4.3 0.7 - - - -
224B VAL 5.3 1.1 - - - -
226B PRO* 3.6 24.8 - - + +
229B SER* 4.5 11.0 - - - -
230B ASN* 4.2 11.2 - - - +
251B GLY* 1.3 74.8 - - - +
253B GLY* 1.3 82.3 + - - +
255B CYS* 3.4 17.9 - - - +
260B GLN* 4.4 0.7 + - - +
261B ASP* 2.7 44.5 + - - -
264B ALA* 3.4 28.8 - - + +
265B LEU* 3.8 20.0 - - + -
268B LEU* 4.2 5.8 - - + -
289B VAL 3.1 4.6 + - - -
290B PHE* 3.5 21.2 - + - -
291B HIS* 2.9 29.8 + - - -
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Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B GLY 4.5 0.6 + - - -
218B PRO* 3.8 33.0 - - - +
229B SER* 5.0 1.0 + - - -
252B TYR* 1.3 95.6 - - - +
254B GLU* 1.3 69.5 + - - +
255B CYS* 4.1 4.7 - - - -
291B HIS* 3.9 4.9 - - - -
294B MET* 4.8 4.3 - - - -
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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