Contacts of the strand formed by residues 362 - 369 (chain B) in PDB entry 1LJ1
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 ILE 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B PHE* 4.0 23.8 - - + -
323B VAL* 4.0 17.7 - - + +
326B LEU* 4.0 25.1 - - + -
327B ASP* 4.7 11.3 + - + +
330B LEU* 3.6 28.4 - - + +
359B MET 4.0 8.3 - - - +
360B GLN 3.4 6.1 + - - +
361B TYR* 1.3 78.8 - - - +
363B PHE* 1.3 64.4 + - - +
364B ALA* 3.5 3.8 + - - +
503B VAL* 3.9 21.8 - - + -
505B HIS 3.9 7.9 - - - +
506B THR* 4.3 11.4 - - + -
507B MET* 3.7 5.1 - - - +
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Residues in contact with PHE 363 (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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362B ILE* 1.3 72.9 - - - +
364B ALA* 1.3 65.8 + - - +
365B HIS* 3.8 18.6 - + + -
366B PRO* 4.8 0.4 - - + -
378B GLU* 5.7 2.7 - - - -
402B ALA* 3.5 28.0 - - + -
503B VAL* 3.9 1.7 - - - -
504B HIS* 3.0 47.9 + + - -
505B HIS* 3.0 26.6 + - + +
507B MET* 3.5 15.9 - - + +
543B ASN* 5.3 2.0 - - - -
544B ARG* 3.6 66.2 - - + -
546B GLY* 5.0 4.9 - - - -
1801B FUM 4.3 8.3 - - + -
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Residues in contact with ALA 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 4.0 29.8 - - + -
333B PHE* 5.5 0.4 - - + -
362B ILE 3.5 5.1 + - - +
363B PHE* 1.3 76.9 - - - +
365B HIS* 1.3 61.9 + - - +
366B PRO* 3.7 3.8 - - - +
402B ALA* 3.8 8.5 - - - +
403B ASP* 4.9 2.7 + - - +
406B SER* 3.0 28.5 + - - +
410B LEU* 6.5 0.2 - - + -
501B PRO* 4.8 6.7 - - + -
502B GLY 3.3 11.0 - - - +
503B VAL* 4.6 1.1 - - - +
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Residues in contact with HIS 365 (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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336B THR* 4.7 6.1 - - + -
363B PHE* 3.7 14.2 + + + -
364B ALA* 1.3 71.5 - - - +
366B PRO* 1.3 68.3 - - + +
367B THR* 3.1 47.6 + - - -
368B LEU* 4.5 1.3 + - + +
375B MET* 3.5 27.4 - - + +
376B VAL 3.4 10.5 - - - -
378B GLU* 4.5 2.0 - - + +
381B ARG* 4.2 12.1 - - - -
406B SER* 3.5 0.4 - - - -
500B THR 4.2 0.3 - - - +
501B PRO* 3.0 1.0 - - - +
502B GLY 2.7 35.3 + - - +
504B HIS* 3.7 32.8 - + + +
1801B FUM 2.8 26.6 + - + +
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Residues in contact with PRO 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PHE* 4.8 0.4 - - + -
364B ALA 3.7 2.9 - - - +
365B HIS* 1.3 92.5 - - + +
367B THR* 1.3 56.8 + - + +
381B ARG* 3.5 28.5 - - - +
387B LEU* 6.1 0.4 - - + -
402B ALA* 4.1 16.4 - - + +
405B ALA* 4.0 17.0 - - + -
406B SER* 3.2 27.6 - - - +
409B ILE* 3.4 29.2 - - + +
500B THR* 3.2 21.3 + - - -
501B PRO* 3.3 4.9 - - + -
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Residues in contact with THR 367 (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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365B HIS* 3.1 18.3 + - - -
366B PRO* 1.3 86.7 - - + +
368B LEU* 1.3 59.8 + - - +
375B MET* 4.9 0.2 - - - -
376B VAL* 2.8 50.1 + - - +
377B THR 4.6 1.0 + - - -
381B ARG* 3.8 29.0 + - - +
387B LEU* 4.7 2.7 - - + -
409B ILE* 4.5 4.3 - - + -
419B LEU* 4.6 12.1 - - + +
499B VAL* 3.7 31.6 - - + -
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Residues in contact with LEU 368 (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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334B ILE* 3.7 46.2 - - + -
335B SER 4.4 0.7 - - - -
336B THR* 3.8 32.3 - - + +
365B HIS* 4.5 2.6 + - + +
367B THR* 1.3 73.1 - - - +
369B SER* 1.3 74.7 + - - +
370B VAL* 3.3 1.1 + - - -
373B GLY* 4.1 11.4 - - - +
374B VAL 3.6 15.3 - - - +
375B MET* 4.3 2.7 - - - +
499B VAL* 3.2 4.8 - - - -
500B THR* 2.9 49.6 + - + +
501B PRO 4.8 4.0 - - - +
502B GLY* 4.2 14.6 - - - +
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Residues in contact with SER 369 (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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367B THR 3.8 1.8 + - - -
368B LEU* 1.3 74.6 - - - +
370B VAL* 1.3 60.2 + - - +
371B LYS* 3.3 4.5 + - - +
372B GLY* 2.8 25.2 + - - -
373B GLY* 3.0 23.4 + - - -
374B VAL* 3.0 20.9 + - - -
376B VAL* 3.8 18.8 - - - +
440B VAL* 3.4 23.5 - - - +
497B ILE* 4.6 2.1 - - - +
498B GLU 3.6 10.1 + - - -
499B VAL* 4.5 0.4 - - - -
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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