Contacts of the strand formed by residues 285 - 291 (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 PHE 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LEU 5.3 0.2 - - - -
53B VAL* 3.9 46.4 - - + -
56B LYS* 3.9 24.2 - - + -
246B LYS 2.8 14.1 + - - +
247B ASN* 3.5 16.6 + - + +
248B ILE 3.0 24.9 + - - +
283B ASP 4.0 1.4 + - - +
284B VAL* 1.3 70.8 - - - +
286B VAL* 1.3 63.5 + - - +
287B THR* 3.7 27.8 + - + -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LYS* 3.8 12.8 - - - -
248B ILE* 3.3 9.6 - - + +
250B VAL* 4.1 10.1 - - + -
269B GLU* 3.8 11.7 - - + +
272B THR* 4.1 21.1 - - + -
273B ASN* 3.5 35.0 + - - +
276B LEU* 3.7 27.1 - - + -
284B VAL* 3.6 10.4 + - + +
285B PHE* 1.3 80.0 - - - +
287B THR* 1.3 79.4 + - - +
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.9 18.7 - - + +
56B LYS* 3.7 27.1 - - + +
247B ASN* 4.8 1.5 + - - +
248B ILE 2.9 6.3 + - - -
249B THR* 2.7 29.1 + - - -
250B VAL* 2.9 30.3 + - - +
269B GLU* 4.7 0.2 - - - -
285B PHE* 3.7 15.5 - - + -
286B VAL* 1.3 80.2 - - - +
288B THR* 1.3 66.0 + - - +
321B THR* 3.3 21.8 - - + +
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Residues in contact with THR 288 (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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56B LYS* 5.3 0.2 + - - -
249B THR* 3.6 3.7 - - - +
250B VAL* 3.2 12.6 - - + +
265B LEU* 3.9 29.3 - - + +
268B LEU* 5.3 0.4 - - + -
269B GLU* 3.7 40.9 + - + +
287B THR* 1.3 81.4 - - - +
289B VAL* 1.3 61.4 + - - +
319B GLY 4.0 2.9 + - - -
320B ALA* 3.4 10.4 - - - -
321B THR* 3.0 28.5 + - - -
322B LYS* 3.0 24.4 + - - +
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Residues in contact with VAL 289 (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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214B GLU* 3.5 21.3 - - - +
249B THR* 3.6 19.3 - - + -
250B VAL 3.0 6.3 + - - -
251B GLY* 3.2 19.3 - - - +
252B TYR 3.1 26.0 + - - +
265B LEU* 4.0 6.7 - - - +
288B THR* 1.3 76.4 - - - +
290B PHE* 1.3 63.5 + - - +
291B HIS* 4.0 5.6 - - - +
322B LYS* 3.2 30.5 - - - +
324B ILE* 3.6 31.6 - - + -
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Residues in contact with PHE 290 (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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252B TYR* 3.5 31.6 - + - -
254B GLU* 3.6 33.2 - - + -
261B ASP* 3.8 12.6 - - + -
265B LEU* 4.4 14.8 - - + -
289B VAL* 1.3 72.9 - - - +
291B HIS* 1.3 67.6 + - - +
292B GLN* 4.3 1.8 - - - -
311B ALA* 3.5 21.3 - - - -
314B ILE* 3.5 29.4 - - + -
315B ALA* 3.6 30.3 - - + -
318B ALA* 5.3 0.9 - - + -
320B ALA* 4.0 11.8 - - + +
322B LYS 2.9 6.0 + - - +
323B VAL* 3.2 10.0 - - + +
324B ILE 3.0 22.0 + - - -
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Residues in contact with HIS 291 (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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66B ARG* 3.0 19.2 + - - -
149B ARG* 3.5 26.7 - - - -
214B GLU* 3.9 11.3 + - - -
216B PHE* 4.1 3.1 - + - -
217B GLY 4.5 3.8 + - - -
218B PRO* 3.3 43.5 - - + +
252B TYR 2.9 19.0 + - - +
253B GLY* 3.9 0.6 - - - -
254B GLU* 3.0 24.9 + - - +
289B VAL* 4.0 15.9 - - + +
290B PHE* 1.3 78.1 - - - +
292B GLN* 1.3 66.5 + - - +
294B MET* 3.9 13.0 - - + +
324B ILE* 3.7 12.2 - - + +
900B TAR 3.6 9.4 - - - -
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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