Contacts of the strand formed by residues 379 - 385 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B VAL* 5.5 1.8 - - + -
371B ALA* 3.7 12.8 - - + +
372B TRP* 3.6 39.5 - - - +
373B SER* 4.3 3.6 - - - +
378B GLU* 1.3 82.7 - - - +
380B VAL* 1.3 60.5 - - - +
381B ARG 3.8 21.8 - - - +
382B VAL* 3.9 17.9 - - + -
397B LEU* 3.7 15.8 - - + +
401B LYS* 4.7 4.2 + - - -
410B TRP* 5.9 0.2 - - - -
411B ALA* 4.2 15.7 - - + +
431B ALA* 4.3 5.6 - - + -
432B VAL 3.5 7.6 - - - +
433B ASP* 4.3 0.9 - - - +
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Residues in contact with VAL 380 (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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338A THR 4.9 8.7 - - - +
340A PRO* 3.8 35.8 - - + +
912A GOL 5.2 4.9 + - - +
378B GLU* 3.6 24.5 - - + +
379B VAL* 1.3 76.8 - - - +
381B ARG* 1.3 67.5 + - + +
397B LEU* 3.9 10.7 - - - +
432B VAL* 2.8 27.8 + - + +
433B ASP 3.7 11.0 - - - +
434B SER* 3.8 20.6 - - - -
436B TYR* 4.6 6.7 - - + -
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Residues in contact with ARG 381 (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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324A GLY 4.0 8.3 + - - -
325A PHE* 3.5 24.3 + - - +
326A SER* 3.4 29.4 - - - +
327A PRO* 4.3 2.4 - - - +
445A PRO 5.6 0.2 + - - -
379B VAL* 3.5 3.9 - - - +
380B VAL* 1.3 89.3 - - + +
382B VAL* 1.3 68.2 + - - +
383B ASP* 2.8 38.2 + - - +
394B VAL* 3.9 23.8 - - + -
397B LEU* 4.2 6.1 - - - -
430B LYS* 4.4 3.0 - - - +
431B ALA* 3.4 3.1 - - - -
432B VAL* 2.9 55.4 + - + +
436B TYR* 5.0 3.4 - - - -
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Residues in contact with VAL 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B SER* 5.2 1.3 - - - +
371B ALA* 3.7 28.9 - - + -
379B VAL* 3.9 2.7 - - + -
381B ARG* 1.3 80.8 - - - +
383B ASP* 1.3 71.3 + - - +
384B VAL* 4.4 1.1 - - + -
394B VAL* 3.7 4.8 - - - +
395B ALA* 2.9 35.3 + - + +
397B LEU* 3.7 27.3 - - + +
413B TRP* 3.9 32.1 - - + +
429B CYS* 4.4 7.2 - - + -
430B LYS 3.4 11.0 - - - +
431B ALA* 4.1 3.6 - - + -
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Residues in contact with ASP 383 (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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326A SER* 2.8 21.4 + - - -
327A PRO* 3.7 5.0 - - - +
381B ARG* 2.8 42.2 + - - +
382B VAL* 1.3 74.4 - - - +
384B VAL* 1.3 59.3 + - - +
392B TRP* 3.7 22.1 - - + -
393B LYS 3.5 4.9 - - - +
394B VAL* 4.2 2.6 - - - +
428B VAL 3.9 0.2 - - - +
429B CYS* 3.3 5.7 - - - +
430B LYS* 2.6 60.1 + - + +
432B VAL* 5.0 1.7 - - - +
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Residues in contact with VAL 384 (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 VAL* 4.5 9.4 - - + -
382B VAL* 4.4 2.7 - - + -
383B ASP* 1.3 79.8 - - - +
385B SER* 1.3 70.2 + - - +
386B LEU* 4.5 8.9 - - + +
392B TRP* 3.7 2.9 - - - -
393B LYS* 2.7 40.2 + - - +
395B ALA* 3.8 20.6 - - + -
413B TRP* 3.6 29.4 - - + -
415B LEU* 3.7 24.0 - - + +
427B ILE* 4.3 14.1 - - + -
428B VAL 3.3 9.4 - - - +
429B CYS* 4.8 0.2 - - + -
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Residues in contact with SER 385 (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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384B VAL* 1.3 74.8 - - - +
386B LEU* 1.3 65.3 + - - +
387B ASP* 2.9 18.5 + - - -
389B GLY* 2.8 32.4 + - - -
391B THR 2.9 15.4 + - - -
392B TRP* 3.5 17.9 - - - -
426B GLU 4.1 0.4 - - - -
427B ILE* 3.1 6.6 - - - +
428B VAL* 2.8 32.4 + - - +
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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