Contacts of the strand formed by residues 279 - 285 (chain B) in PDB entry 1CK4
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 GLN 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B LEU* 5.8 1.6 - - - +
249B LYS* 6.1 2.6 - - - +
250B LYS 3.0 14.1 + - - +
251B VAL* 3.3 20.6 - - + +
252B MET 2.7 31.0 + - - +
277B ASN 3.7 3.4 + - - +
278B ILE* 1.3 70.9 - - - +
280B ARG* 1.3 54.4 + - - +
281B PHE* 3.3 18.2 - - + -
308B SER* 3.5 8.3 - - - +
314B HIS* 2.9 36.4 - - + -
335B ILE 4.8 3.3 + - - +
338B LEU 3.8 0.8 - - - -
339B GLU 3.3 27.5 + - - +
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Residues in contact with ARG 280 (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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230B ILE* 5.8 0.7 - - - -
252B MET* 3.2 11.9 - - + +
254B ILE* 4.1 14.6 - - + -
270B ILE* 3.9 29.1 - - - +
273B CYS* 3.7 17.5 - - - +
274B GLU* 2.6 48.9 + - - +
278B ILE* 2.9 34.3 + - + +
279B GLN* 1.3 74.3 - - - +
281B PHE* 1.3 63.2 + - - +
306B ILE* 2.7 32.6 + - - +
307B ALA* 3.4 7.5 + - - -
308B SER* 2.8 53.2 + - - +
309B GLU 5.2 0.4 - - - +
314B HIS* 3.5 5.9 - - - +
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Residues in contact with PHE 281 (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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251B VAL* 3.8 24.9 - - + -
252B MET 2.9 7.3 + - - +
253B VAL* 3.3 12.9 - - + -
254B ILE* 2.8 27.5 + - - +
279B GLN* 3.3 34.1 - - - -
280B ARG* 1.3 75.2 - - - +
282B SER* 1.3 60.2 + - - +
283B ILE* 4.2 5.5 - - + +
313B LYS 4.4 0.2 - - - -
314B HIS* 3.2 35.4 - + - +
316B PHE* 4.3 4.5 - + + -
331B LEU* 3.9 23.1 - - + -
334B ARG* 3.5 32.3 - - + -
335B ILE* 3.6 14.1 - - + -
338B LEU* 3.8 13.7 - - + -
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Residues in contact with SER 282 (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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254B ILE* 3.4 9.4 - - - -
280B ARG 4.1 1.0 + - - -
281B PHE* 1.3 74.8 - - - +
283B ILE* 1.3 63.6 + - - +
303B ILE* 2.6 40.9 + - - -
306B ILE* 4.2 18.4 - - - -
307B ALA* 3.6 10.3 - - - +
314B HIS 3.1 6.4 + - - +
315B PHE* 3.4 10.4 - - - -
316B PHE 2.9 24.3 + - - -
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Residues in contact with ILE 283 (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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168B PHE* 4.5 4.9 - - + -
253B VAL* 5.0 3.4 - - + -
254B ILE 2.7 22.8 + - - +
255B VAL* 4.4 13.7 - - + -
256B THR* 3.0 30.3 + - - +
281B PHE* 4.2 9.2 - - + +
282B SER* 1.3 83.4 - - - +
284B ALA* 1.3 63.4 + - - +
285B ILE* 4.5 5.8 - - + -
303B ILE* 4.1 3.1 - - - +
316B PHE* 3.5 15.0 - - + +
318B VAL* 3.7 27.1 - - + -
324B LEU* 4.0 16.4 - - + -
327B ILE* 3.9 18.8 - - + -
331B LEU* 4.5 17.5 - - + -
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Residues in contact with ALA 284 (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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256B THR 3.3 5.2 - - - -
283B ILE* 1.3 71.4 - - - +
285B ILE* 1.3 60.7 + - - +
286B LEU* 3.5 11.5 - - + +
299B PHE* 3.9 10.1 - - + -
300B VAL* 5.2 2.0 - - + -
303B ILE* 3.5 30.4 - - + +
315B PHE* 3.7 20.0 - - + -
316B PHE 2.9 6.5 + - - -
318B VAL* 2.9 28.6 + - - +
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Residues in contact with ILE 285 (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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159B ILE* 5.0 7.0 - - + -
165B VAL* 4.8 5.4 - - + -
255B VAL* 3.6 30.1 - - + -
256B THR 2.8 24.8 + - - +
257B ASP* 3.2 35.7 - - + +
283B ILE* 4.5 3.4 - - + -
284B ALA* 1.3 73.0 - - - +
286B LEU* 1.3 61.5 + - - +
287B GLY 3.5 12.6 + - - +
288B HIS 5.0 0.3 + - - -
289B TYR* 5.3 0.2 - - - -
299B PHE* 3.6 7.1 - - - -
318B VAL* 3.6 5.8 - - + -
320B ASP 4.1 3.1 - - - -
321B GLU* 3.9 33.7 - - + +
324B LEU* 4.1 32.5 - - + -
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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