Contacts of the strand formed by residues 264 - 270 (chain A) 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 THR 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ARG* 3.5 22.6 + - - +
259A ALA 4.6 4.0 + - - +
262A GLU* 3.3 26.8 + - + +
263A ASP* 1.3 83.2 - - - +
265A ILE* 1.4 63.7 + - - +
266A VAL* 3.8 14.8 + - - +
317A GLN* 4.2 24.1 + - + +
318A PHE 3.2 9.0 - - - +
320A THR* 3.7 7.4 - - - +
510A LEU* 3.6 28.5 - - + -
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 3.9 24.7 - - + -
257A SER 3.7 5.2 - - - +
258A ARG* 4.3 7.4 - - + -
264A THR* 1.4 74.9 - - - +
266A VAL* 1.3 60.9 + - - +
317A GLN* 3.5 2.1 - - - -
318A PHE* 2.8 46.7 + - + -
320A THR* 3.8 20.0 - - + +
331A PHE* 3.8 53.6 - - + -
343A LEU* 4.3 15.7 - - + -
345A PHE* 3.8 16.8 - - + -
355A TRP* 4.6 5.4 - - + -
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ILE* 4.0 4.5 - - + -
241A HIS* 3.6 25.1 - - + +
255A ILE 3.6 1.4 - - - +
256A LEU* 3.3 7.3 - - - -
257A SER 2.8 36.6 + - - +
262A GLU* 4.9 1.8 - - - +
264A THR* 3.8 18.2 - - - +
265A ILE* 1.3 72.1 - - - +
267A LEU* 1.3 67.6 + - - +
268A TRP* 3.6 20.4 - - + -
314A ARG* 3.6 40.2 - - + +
316A ALA 3.7 4.0 - - - +
317A GLN* 4.0 10.5 - - + +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 4.6 9.4 - - + -
254A LEU* 3.8 26.7 - - + -
255A ILE 3.3 13.7 - - - +
256A LEU* 3.9 24.5 - - + -
265A ILE 3.8 1.8 + - - -
266A VAL* 1.3 72.7 - - - +
268A TRP* 1.3 54.9 + - - +
315A LEU* 2.8 41.7 + - + -
316A ALA* 2.8 28.3 + - + +
318A PHE* 4.2 15.3 - - + -
357A LEU* 6.1 0.4 - - + -
221B VAL* 4.2 19.3 - - + -
225B LEU* 3.8 26.7 - - + -
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Residues in contact with TRP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 5.9 0.2 - - + -
211A ILE* 4.0 24.2 - - + -
235A PHE* 3.7 22.0 - + - -
240A ILE* 3.6 48.0 - - + +
254A LEU* 3.8 4.9 - - - +
255A ILE* 2.9 66.4 + - + +
257A SER* 2.9 21.8 + - - -
266A VAL* 3.6 21.1 - - + -
267A LEU* 1.3 74.9 - - - +
269A ARG* 1.3 81.9 + - - +
270A ILE* 3.7 22.0 - - + -
312A PHE* 3.9 10.5 - - + -
313A THR 3.3 14.8 - - - +
314A ARG* 3.9 9.4 - - - -
315A LEU* 3.9 6.7 - - - +
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Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ASP 5.4 1.3 - - - +
254A LEU* 3.9 21.3 - - + +
255A ILE* 4.8 3.4 - - - +
268A TRP* 1.3 81.5 - - - +
270A ILE* 1.3 68.4 + - - +
271A GLU* 2.9 35.6 + - - +
272A GLY 5.8 0.9 - - - +
312A PHE* 3.1 6.9 - - - +
313A THR* 3.0 42.8 + - - +
315A LEU* 4.0 6.9 - - + +
220B LEU* 3.5 33.0 - - - +
224B LEU* 3.8 29.9 - - - +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 5.3 0.9 - - + -
213A LEU* 3.6 28.9 - - + -
235A PHE* 3.6 43.3 - - + -
253A ASP 5.3 2.2 + - - -
255A ILE* 3.5 29.9 - - + +
268A TRP* 3.7 13.5 - - + -
269A ARG* 1.3 80.2 - - - +
271A GLU* 1.3 71.3 + - - +
272A GLY 3.4 0.7 + - - -
273A PHE* 3.3 38.1 + - + +
297A SER* 4.1 1.1 - - - +
299A PHE* 3.9 12.6 - - + -
311A MET 3.7 5.4 - - - +
312A PHE* 4.4 0.7 - - - +
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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