Contacts of the strand formed by residues 254 - 260 (chain B) in PDB entry 4I6J
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 HIS 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515A LEU* 3.3 37.1 - - + +
204B LYS* 4.3 16.4 + - - -
227B ARG 3.2 2.7 + - - +
228B GLU* 2.9 63.8 + - + +
229B LEU 3.1 3.7 + - - -
252B LEU* 3.5 5.8 - - - +
253B GLU* 1.3 83.1 - - + +
255B LEU* 1.3 73.7 + - - +
256B ARG* 3.8 20.4 + - + +
287B VAL* 4.1 1.4 - - - +
288B ASN* 3.6 9.9 - - + -
290B VAL* 3.9 14.2 - - + +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 3.5 39.5 - - + +
231B LEU* 5.3 1.1 - - + -
236B LEU* 5.0 3.4 - - + -
240B LEU* 6.0 0.2 - - + -
241B LEU* 4.2 14.8 - - + -
244B LEU* 5.0 3.6 - - + -
252B LEU* 4.1 14.1 - - + -
254B HIS* 1.3 76.9 - - - +
256B ARG* 1.3 58.5 + - - +
257B ILE* 4.0 22.9 - - + -
277B TRP* 4.4 3.1 - - + -
280B PHE* 3.4 33.0 - - + -
287B VAL* 4.7 0.4 - - + +
288B ASN 3.0 11.3 + - - +
289B LEU* 3.6 22.0 - - + +
290B VAL 3.1 23.6 + - - +
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Residues in contact with ARG 256 (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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496A ARG* 5.6 1.4 - - - +
499A ILE* 5.5 0.6 - - - +
500A GLU* 3.5 25.1 + - - +
503A LYS* 3.6 10.1 - - - +
229B LEU 2.8 11.2 + - - +
230B ALA* 3.2 25.0 - - + -
231B LEU 3.0 26.8 + - - +
254B HIS* 3.8 21.2 - - + +
255B LEU* 1.3 74.8 - - - +
257B ILE* 1.3 76.0 + - - +
258B ASP* 2.2 43.7 + - - +
290B VAL* 3.3 24.8 - - + +
292B TYR* 3.0 42.8 - - - -
294B PHE* 5.4 0.2 - - - -
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Residues in contact with ILE 257 (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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231B LEU* 3.5 15.9 - - + -
233B TYR* 3.7 41.5 - - + +
236B LEU* 3.9 31.2 - - + -
255B LEU* 4.0 21.1 - - + -
256B ARG* 1.3 86.9 - - - +
258B ASP* 1.3 68.4 + - - +
259B VAL* 4.3 5.5 - - + +
277B TRP* 5.2 0.9 - - + -
289B LEU* 4.4 11.2 - - + -
290B VAL 2.9 13.5 + - - +
291B MET* 3.5 13.8 - - + +
292B TYR 3.0 25.6 + - - +
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Residues in contact with ASP 258 (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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496A ARG* 3.9 21.3 + - + +
206B SER* 3.6 25.6 + - - -
231B LEU 3.1 10.3 + - - +
232B ASN* 3.5 10.8 + - - +
233B TYR* 2.6 33.3 + - - +
256B ARG* 2.2 42.4 + - - +
257B ILE* 1.3 74.3 - - - +
259B VAL* 1.3 59.0 + - - +
260B VAL* 4.0 15.7 - - + -
292B TYR* 3.7 8.8 - - - +
294B PHE* 5.2 0.4 - - + -
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Residues in contact with VAL 259 (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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233B TYR* 4.1 18.4 - - + -
257B ILE* 4.3 11.0 - - + +
258B ASP* 1.3 75.6 - - - +
260B VAL* 1.3 59.4 + - - +
269B PHE* 4.3 11.7 - - + -
291B MET* 5.6 2.7 - - + -
292B TYR 2.9 16.6 + - - +
293B PHE* 3.8 31.2 - - + -
294B PHE* 2.7 32.2 + - - -
295B LEU* 3.5 18.6 - - + +
303B PHE* 3.5 28.3 - - + -
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Residues in contact with VAL 260 (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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492A ALA* 3.9 10.5 - - + +
493A GLU* 3.8 36.6 - - + +
496A ARG* 3.9 27.4 - - + -
232B ASN* 3.7 20.2 + - - +
258B ASP* 4.0 2.8 + - + -
259B VAL* 1.3 83.6 - - - +
261B SER* 1.3 64.0 + - - +
262B GLU* 2.9 41.2 + - + +
269B PHE* 3.2 16.3 - - - -
294B PHE* 4.3 6.1 - - + -
295B LEU* 4.0 0.9 - - - -
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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