Contacts of the strand formed by residues 363 - 372 (chain B) in PDB entry 1SNX
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 363 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359B ASP* 4.6 9.0 - - + -
360B PRO 3.7 21.1 - - - +
361B SER* 3.1 13.2 + - - +
362B GLU* 1.3 81.1 - - - +
364B THR* 1.3 60.0 + - - +
365B PHE* 3.8 22.0 + - + -
381B TYR 3.0 10.3 - - - +
382B TRP* 3.5 29.8 - - + +
388B VAL* 5.9 0.2 - - + -
390B ILE* 3.3 36.8 - - + -
425B CYS* 5.0 12.1 - - + -
432B CYS* 5.0 0.7 - - - -
434B VAL* 3.4 24.0 - - + -
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Residues in contact with THR 364 (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 GLU 4.2 4.5 + - - -
363B LEU* 1.3 73.2 + - - +
365B PHE* 1.3 68.1 + - - +
366B VAL* 3.1 11.1 + - + +
380B GLY* 3.3 1.4 - - - -
381B TYR* 2.5 41.6 + - - +
384B ASN* 5.2 6.2 + - - +
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Residues in contact with PHE 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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361B SER* 4.7 8.7 - - - -
363B LEU* 4.0 23.1 - - + -
364B THR* 1.3 75.8 - - - +
366B VAL* 1.3 62.2 + - - +
378B HIS* 3.3 48.5 - + + +
379B LEU 3.9 2.5 - - - -
380B GLY* 4.2 1.8 - - - -
390B ILE* 3.4 39.0 - - + -
392B THR* 4.1 10.8 - - + -
430B PRO* 5.7 4.7 - - + -
432B CYS* 4.2 10.8 - - - -
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Residues in contact with VAL 366 (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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364B THR* 3.4 16.4 - - + +
365B PHE* 1.3 74.9 - - - +
367B GLN* 1.3 79.4 + - + +
379B LEU* 2.6 36.7 + - + +
380B GLY* 4.0 5.8 - - - -
381B TYR* 4.1 19.3 - - + -
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Residues in contact with GLN 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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366B VAL* 1.3 96.7 + - + +
368B GLU* 1.3 68.7 + - - +
369B ILE* 5.8 1.3 - - + -
378B HIS* 2.6 40.8 + - - -
379B LEU* 3.4 18.8 + - + +
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Residues in contact with GLU 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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367B GLN* 1.3 86.9 + - - +
369B ILE* 1.3 75.1 + - - +
370B GLY 3.8 18.5 + - - +
371B SER* 4.0 13.0 - - - -
376B LEU* 3.4 32.9 - - - +
377B VAL 3.3 11.4 - - - +
378B HIS* 3.5 25.1 + - + +
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Residues in contact with ILE 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 GLN* 5.8 1.3 - - + -
368B GLU* 1.3 85.6 - - - +
370B GLY* 1.3 59.2 + - - +
377B VAL* 2.9 46.5 + - + +
379B LEU* 3.9 22.2 - - + +
389B ALA* 5.1 1.1 - - + -
437B PHE* 3.6 32.3 - - + -
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Residues in contact with GLY 370 (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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368B GLU* 3.8 6.6 + - - +
369B ILE* 1.3 75.6 - - - +
371B SER* 1.3 61.0 + - - -
375B GLY 3.8 1.5 - - - +
376B LEU* 3.6 3.1 - - - -
377B VAL* 3.0 35.2 + - - +
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Residues in contact with SER 371 (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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368B GLU* 4.0 7.4 - - - -
370B GLY* 1.3 75.9 - - - -
372B GLY* 1.3 59.4 + - - +
375B GLY 4.6 4.7 - - - -
376B LEU* 3.7 19.7 - - - -
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Residues in contact with GLY 372 (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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371B SER* 1.3 81.7 + - - +
373B GLN* 1.3 60.6 + - - -
374B PHE* 3.3 7.3 + - - -
375B GLY 3.8 7.7 + - - -
376B LEU* 4.0 13.9 - - - +
394B ARG* 5.4 2.4 - - - +
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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