Contacts of the strand formed by residues 379 - 385 (chain A) in PDB entry 1SOX
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 VAL 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A VAL* 5.5 1.6 - - + -
371A ALA* 3.7 13.0 - - + +
372A TRP* 3.6 38.1 - - - +
373A SER* 4.5 2.7 - - - +
378A GLU* 1.3 82.4 - - - +
380A VAL* 1.3 61.3 + - - +
381A ARG 3.7 21.3 - - - +
382A VAL* 3.8 19.3 - - + -
397A LEU* 3.5 18.8 - - + +
411A ALA* 4.2 14.9 - - + +
431A ALA* 4.3 6.5 - - + -
432A VAL 3.6 6.1 - - - +
433A ASP* 4.3 0.9 - - - +
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Residues in contact with VAL 380 (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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378A GLU* 3.9 18.2 - - - +
379A VAL* 1.3 75.7 - - - +
381A ARG* 1.3 66.0 + - + +
397A LEU* 4.0 8.3 - - - +
432A VAL* 2.8 31.8 + - + +
433A ASP 3.6 9.6 - - - +
434A SER* 3.7 28.5 - - - +
436A TYR* 4.7 7.9 - - + -
338B THR 4.8 8.8 - - - +
340B PRO* 3.8 34.4 - - + +
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Residues in contact with ARG 381 (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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379A VAL* 3.5 4.3 - - - +
380A VAL* 1.3 89.8 - - + +
382A VAL* 1.3 67.3 + - - +
383A ASP* 2.7 39.4 + - - +
394A VAL* 3.8 25.4 - - + -
397A LEU* 4.3 5.8 - - - -
430A LYS* 4.4 3.0 - - - +
431A ALA* 3.4 2.6 - - - -
432A VAL* 2.9 55.3 + - + +
436A TYR* 5.1 3.4 - - - -
324B GLY 3.9 9.3 + - - -
325B PHE* 3.5 23.8 + - - +
326B SER* 3.4 28.5 - - - +
327B PRO* 4.2 2.6 - - - +
446B ILE* 6.3 0.4 - - - +
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Residues in contact with VAL 382 (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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349A SER* 5.3 0.7 - - - +
371A ALA* 3.7 27.8 - - + -
379A VAL* 3.8 3.4 - - + -
381A ARG* 1.3 81.4 - - - +
383A ASP* 1.3 71.0 + - - +
384A VAL* 4.2 6.5 - - + -
394A VAL* 3.7 4.0 - - - +
395A ALA* 2.9 32.9 + - + +
397A LEU* 3.6 27.6 - - + +
413A TRP* 3.8 32.5 - - + +
429A CYS* 4.3 6.3 - - + -
430A LYS 3.4 10.5 - - - +
431A ALA* 4.2 3.1 - - + -
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Residues in contact with ASP 383 (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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381A ARG* 2.7 43.8 + - - +
382A VAL* 1.3 73.5 - - - +
384A VAL* 1.3 61.0 + - - +
392A TRP* 3.6 22.2 - - + -
393A LYS 3.5 3.8 - - - -
394A VAL* 3.9 2.9 - - - +
429A CYS* 3.2 5.2 - - - +
430A LYS* 2.8 61.7 + - + +
432A VAL* 4.9 1.5 - - - +
326B SER* 3.0 20.7 + - - -
327B PRO* 3.6 5.1 - - - +
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Residues in contact with VAL 384 (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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367A VAL* 4.4 22.7 - - + -
382A VAL* 4.2 3.4 - - + -
383A ASP* 1.3 78.8 - - - +
385A SER* 1.3 67.0 + - - +
386A LEU* 4.8 7.7 - - + +
392A TRP* 3.5 3.4 - - - -
393A LYS* 2.8 37.0 + - - +
395A ALA* 3.9 20.2 - - + -
413A TRP* 3.7 29.2 - - + -
415A LEU* 3.6 22.2 - - + +
427A ILE* 4.6 4.0 - - + -
428A VAL 3.2 9.0 - - - +
429A CYS* 4.6 1.3 - - + -
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Residues in contact with SER 385 (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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384A VAL* 1.3 74.2 - - - +
386A LEU* 1.3 64.8 + - - +
387A ASP* 2.7 28.9 + - - -
389A GLY* 2.9 25.2 + - - -
391A THR 2.8 15.8 + - - -
392A TRP* 3.6 17.2 - - - -
426A GLU 4.0 0.4 - - - -
427A ILE* 3.2 6.2 - - - +
428A VAL* 2.8 33.1 + - - +
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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