Contacts of the strand formed by residues 284 - 289 (chain B) in PDB entry 5KJH
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 ARG 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B ASP* 3.4 28.7 + - - +
254B ALA 6.0 0.4 - - - +
255B ASN* 5.1 3.2 + - - -
268B LYS* 3.5 3.5 - - - +
269B PHE* 2.8 39.5 + - + +
281B ASN* 5.5 2.2 - - - +
283B GLY* 1.4 76.2 - - - +
285B ARG* 1.3 60.4 + - - +
286B PHE* 3.4 37.4 - - + -
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Residues in contact with ARG 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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254B ALA* 3.3 54.9 + - + +
258B ARG* 3.8 8.5 - - - +
266B ASP* 2.8 51.6 + - + -
267B VAL 3.3 11.9 - - - +
268B LYS* 4.0 18.9 - - + +
284B ARG* 1.3 73.6 + - - +
286B PHE* 1.3 71.4 + - - +
287B GLN* 4.4 7.7 - - - +
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Residues in contact with PHE 286 (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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79A ASN* 5.1 6.5 - - + -
251B ALA* 4.1 16.8 - - + -
252B ILE 3.5 14.6 - - - +
253B ASP* 3.3 25.6 - - - -
254B ALA 4.6 1.3 - - - +
266B ASP* 3.3 6.4 - - - +
267B VAL 2.8 31.4 + - - +
269B PHE* 3.7 27.1 - + + -
284B ARG* 3.4 55.4 - - + -
285B ARG* 1.3 77.3 - - - +
287B GLN* 1.3 63.1 + - - +
288B TYR* 3.7 23.9 - - + +
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Residues in contact with GLN 287 (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 ALA* 3.6 0.9 - - - -
252B ILE* 2.7 55.7 + - + +
253B ASP 3.1 20.3 + - - +
254B ALA* 3.2 15.0 + - - +
256B ARG* 3.1 20.2 + - - +
257B PRO 4.4 0.2 - - - +
258B ARG* 2.9 42.3 - - - +
259B PRO* 4.3 2.4 - - - +
264B THR* 3.6 12.1 - - + +
265B MET 3.8 4.0 - - - -
266B ASP* 3.5 17.5 - - - +
285B ARG* 4.4 7.2 - - - +
286B PHE* 1.3 74.1 - - - +
288B TYR* 1.3 64.1 + - - +
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Residues in contact with TYR 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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82A GLU* 5.5 0.7 - - - -
83A ILE* 3.5 42.0 + - + +
86A LEU* 3.9 18.4 - - + -
249B SER* 4.6 0.6 + - - -
250B LYS* 3.7 10.1 - - + -
251B ALA* 3.4 43.4 - - + +
252B ILE* 5.0 0.2 - - - -
264B THR* 3.3 8.0 - - - +
265B MET 2.8 43.2 + - - +
267B VAL* 3.8 28.7 - - + -
269B PHE* 3.3 23.9 - - - -
286B PHE* 3.7 21.7 - - + +
287B GLN* 1.3 74.8 - - - +
289B PRO* 1.3 68.8 - - + +
290B VAL* 3.9 1.6 - - - +
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Residues in contact with PRO 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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86A LEU* 4.0 16.5 - - - +
250B LYS* 3.3 48.3 + - + +
252B ILE* 4.1 17.2 - - + -
259B PRO* 5.5 0.7 - - + -
262B VAL* 4.3 22.2 - - + -
263B PRO 3.6 6.7 - - - +
264B THR* 4.6 3.8 - - - +
288B TYR* 1.3 87.4 - - + +
290B VAL* 1.3 59.8 + - - +
291B VAL* 4.3 0.6 + - - -
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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