Contacts of the strand formed by residues 257 - 267 (chain B) in PDB entry 1JEY
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 LEU 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A MET* 4.5 8.3 - - + -
465A ILE* 4.6 13.0 - - + -
522A VAL* 4.0 20.4 - - + -
525A PHE* 4.1 32.5 - - + -
526A LYS* 4.7 9.6 - - + +
530A TYR* 4.7 8.1 - - + -
251B LEU 3.9 0.7 - - - +
252B THR* 3.4 6.3 - - - +
253B ILE* 3.0 68.5 + - + +
254B GLY 4.9 0.5 - - - +
255B SER 3.6 1.5 - - - -
256B ASN* 1.3 80.0 - - - +
258B SER* 1.3 72.2 + - - +
259B ILE* 4.8 8.1 - - + -
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Residues in contact with SER 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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526A LYS* 5.7 0.4 - - - +
530A TYR* 2.9 25.5 + - - -
250B ARG* 3.3 29.6 - - - +
251B LEU 3.6 4.0 - - - -
252B THR* 4.5 9.0 - - - +
256B ASN 4.1 2.0 + - - -
257B LEU* 1.3 75.7 - - - +
259B ILE* 1.3 68.0 + - - +
260B ARG* 5.5 0.7 - - - +
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Residues in contact with ILE 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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462A MET* 4.9 13.5 - - + -
525A PHE* 5.0 2.5 - - + -
530A TYR* 3.5 13.0 - - - +
250B ARG* 3.3 3.3 - - - -
251B LEU* 2.7 56.9 + - + +
253B ILE* 5.3 1.1 - - + -
257B LEU* 4.8 11.4 - - + -
258B SER* 1.3 82.1 + - - +
260B ARG* 1.3 74.3 + - - +
261B ILE* 3.3 11.8 + - + +
373B ALA* 4.0 19.5 - - - +
376B ALA* 4.0 24.9 - - + +
377B LEU* 4.4 14.6 - - + +
380B LEU* 5.2 3.4 - - + -
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Residues in contact with ARG 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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530A TYR* 5.1 0.2 + - - -
534A TYR* 4.1 13.5 + - + +
249B CYS 3.7 5.8 - - - +
250B ARG* 3.6 42.9 - - + +
258B SER* 4.3 1.3 - - - +
259B ILE* 1.3 72.7 - - - +
261B ILE* 1.3 62.8 + - - +
366B ALA* 3.6 2.1 - - - -
367B ALA* 3.1 41.6 + - + +
368B ARG 4.8 4.9 + - - -
370B ASP* 3.4 26.1 + - - +
373B ALA* 3.5 19.3 - - + +
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Residues in contact with ILE 261 (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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247B TRP* 4.9 5.8 - - + -
248B PRO* 3.7 3.3 - - - +
249B CYS* 2.9 47.8 + - + +
250B ARG 4.2 0.7 - - - -
251B LEU* 3.8 30.1 - - + +
259B ILE* 3.4 17.9 - - + +
260B ARG* 1.3 80.4 - - - +
262B ALA* 1.3 63.2 + - - +
340B PHE* 3.9 24.5 - - + -
364B VAL* 3.7 25.4 - - + -
365B PHE 3.1 14.1 - - - +
367B ALA* 3.6 8.5 - - - +
377B LEU* 4.6 10.5 - - + -
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Residues in contact with ALA 262 (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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246B HIS* 4.0 20.6 - - + -
247B TRP 3.3 6.1 - - - -
261B ILE* 1.3 77.6 - - - +
263B ALA* 1.3 60.7 + - - +
264B TYR* 3.6 29.4 - - + +
364B VAL* 4.6 1.1 - - - -
365B PHE* 2.8 30.7 + - - +
366B ALA 4.4 3.4 - - - +
367B ALA* 4.1 13.4 - - - +
368B ARG* 4.8 3.6 - - + +
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Residues in contact with ALA 263 (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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245B ILE 3.9 1.0 - - - +
246B HIS* 3.5 5.9 - - - -
247B TRP* 2.8 63.9 + - + +
261B ILE* 4.3 0.4 - - + -
262B ALA* 1.3 73.2 - - - +
264B TYR* 1.3 64.3 + - - +
362B LEU* 4.5 16.8 - - + -
363B LYS 3.2 9.6 - - - +
364B VAL* 4.2 16.6 - - + +
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Residues in contact with TYR 264 (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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446A MET* 4.0 31.4 - - + -
447A PRO* 5.7 10.3 - - + -
244B SER* 4.3 19.5 - - - +
245B ILE 4.0 9.9 - - - +
246B HIS* 3.4 36.3 - - + +
262B ALA* 3.6 23.2 - - + +
263B ALA* 1.3 73.9 - - - +
265B LYS* 1.3 65.4 + - - +
266B SER 3.5 0.2 + - - -
362B LEU* 3.4 5.4 - - - -
363B LYS* 2.9 30.3 + - - +
365B PHE* 3.5 37.9 - + + -
368B ARG* 4.2 22.5 + - - +
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Residues in contact with LYS 265 (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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444A ARG* 3.2 38.4 - - - +
446A MET* 3.9 4.8 - - - +
244B SER* 4.3 8.8 + - - +
245B ILE 5.1 0.8 + - - +
264B TYR* 1.3 71.8 - - - +
266B SER* 1.3 59.7 + - - +
267B ILE 3.6 7.6 - - - +
268B LEU* 4.0 27.4 - - + +
360B GLN* 3.4 19.8 + - + +
361B VAL 3.5 7.9 - - - +
362B LEU* 3.5 19.3 - - + -
395B TYR* 5.7 1.3 - - - -
397B TYR* 5.3 4.5 - - - -
23D T 3.5 34.9 + - - +
24D A 2.8 38.3 + - - -
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Residues in contact with SER 266 (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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359A HIS 5.3 1.6 - - - -
443A LYS* 3.6 0.2 - - - -
444A ARG* 2.8 30.6 + - - +
446A MET* 3.8 10.9 - - - +
264B TYR 3.5 2.2 + - - -
265B LYS* 1.3 73.3 - - - +
267B ILE* 1.3 75.6 + - - +
361B VAL* 3.0 17.9 + - - -
363B LYS* 2.7 52.3 + - - +
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Residues in contact with ILE 267 (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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359A HIS 3.6 22.0 - - - +
360A HIS* 4.2 16.4 - - + +
361A TYR 3.1 28.5 - - - +
362A LEU* 3.7 24.5 - - + -
438A PRO* 4.3 10.3 - - + -
442A ASP 3.4 5.8 - - - +
443A LYS* 4.1 23.8 - - + -
265B LYS* 4.6 1.0 - - - +
266B SER* 1.3 90.2 + - - +
268B LEU* 1.3 66.8 + - - +
360B GLN* 3.3 9.3 - - - +
361B VAL* 3.2 31.6 + - + +
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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