Contacts of the strand formed by residues 363 - 372 (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 GLY 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A PRO* 1.3 73.0 - - - +
364A GLU* 1.3 61.8 + - - +
418A PRO* 3.0 10.6 - - - +
419A VAL* 2.8 40.5 + - - +
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Residues in contact with GLU 364 (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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361A PRO* 4.6 9.2 - - - +
362A PRO 3.9 2.5 + - - +
363A GLY* 1.3 76.4 - - - +
365A LEU* 1.3 61.3 + - - +
366A THR 4.5 0.2 + - - -
416A THR* 3.4 29.8 - - + +
417A VAL* 3.4 13.9 + - - -
418A PRO* 4.2 6.6 - - + +
419A VAL* 4.4 2.2 - - - -
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Residues in contact with LEU 365 (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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353A GLN* 5.9 1.3 - - + +
354A PRO* 4.4 12.3 - - + -
360A VAL* 4.0 29.8 - - + -
361A PRO* 5.6 0.7 - - + +
364A GLU* 1.3 75.6 - - - +
366A THR* 1.3 70.3 + - - +
367A VAL* 4.0 22.4 - - + -
386A LEU* 5.2 0.7 - - + -
415A LEU 3.7 0.5 - - - +
416A THR* 3.3 2.2 - - - -
417A VAL* 2.7 43.8 + - + +
419A VAL* 3.9 17.7 - - + -
425A LEU* 3.9 27.6 - - + -
427A ILE* 4.1 10.3 - - + -
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Residues in contact with THR 366 (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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353A GLN* 3.1 31.0 - - - +
364A GLU 4.3 0.2 - - - -
365A LEU* 1.3 82.5 - - - +
367A VAL* 1.3 63.4 + - - +
368A LYS* 3.9 21.8 - - + -
414A GLU* 4.5 15.7 - - + +
415A LEU 3.5 4.5 - - - +
416A THR* 2.9 25.0 + - - +
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Residues in contact with VAL 367 (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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351A VAL* 3.7 12.1 - - + -
353A GLN 3.4 11.4 - - - +
354A PRO* 4.5 1.1 - - + -
365A LEU* 4.0 24.5 - - + -
366A THR* 1.3 74.2 - - - +
368A LYS* 1.3 63.2 + - - +
384A VAL* 4.4 9.9 - - + -
386A LEU* 4.5 11.0 - - + -
413A TRP* 3.7 26.2 - - + -
414A GLU* 3.2 3.3 - - - +
415A LEU* 2.8 39.4 + - + +
417A VAL* 4.7 6.3 - - + -
427A ILE* 3.8 24.2 - - + -
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Residues in contact with LYS 368 (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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125A ALA* 4.1 14.4 + - + -
126A GLU* 3.0 36.7 + - - +
351A VAL* 3.5 5.2 - - - +
352A THR* 2.7 34.5 + - - +
353A GLN* 2.9 41.8 + - + +
366A THR* 3.9 17.3 - - + -
367A VAL* 1.3 79.9 - - - +
369A GLY* 1.3 53.8 + - - +
413A TRP* 3.5 14.8 - - - +
414A GLU* 3.8 25.0 + - + -
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Residues in contact with GLY 369 (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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125A ALA* 3.5 12.8 - - - +
350A ALA 3.2 13.7 - - - -
352A THR* 3.6 11.7 - - - -
368A LYS* 1.3 79.7 - - - +
370A TYR* 1.3 60.5 + - - -
412A LEU* 3.5 4.7 - - - +
413A TRP* 3.0 40.2 + - - +
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Residues in contact with TYR 370 (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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124A LEU* 4.0 11.9 - - + -
125A ALA* 4.7 0.9 - - + -
188A ASN* 3.1 15.6 + - - -
189A ARG* 4.5 3.3 - - - -
206A ILE* 2.7 32.1 + - + +
209A ILE* 3.7 32.1 - - + -
348A GLN* 4.3 8.3 - - + -
349A SER* 3.3 7.5 - - - -
350A ALA* 3.1 53.1 + - + +
352A THR* 4.0 16.4 - - + -
369A GLY* 1.3 74.1 - - - -
371A ALA* 1.3 67.0 + - - +
372A TRP* 5.1 0.7 - - + -
410A TRP* 3.8 29.6 - + + -
411A ALA 3.6 6.1 - - - +
412A LEU* 3.8 10.3 - - + -
413A TRP* 3.0 12.8 + - - -
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Residues in contact with ALA 371 (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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348A GLN 3.2 12.6 - - - +
349A SER* 3.9 5.8 - - - +
370A TYR* 1.3 77.8 - - - +
372A TRP* 1.3 64.9 + - - +
379A VAL* 3.7 16.4 - - + -
382A VAL* 3.7 30.3 - - + -
410A TRP* 3.3 3.2 - - - +
411A ALA 2.9 33.8 + - - +
413A TRP* 4.1 0.2 - - + -
431A ALA* 4.0 3.6 - - + -
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Residues in contact with TRP 372 (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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182A THR* 3.6 28.0 - - + -
184A GLN* 3.4 32.5 - - + -
209A ILE* 4.7 10.1 - - + -
293A GLY* 3.9 24.5 - - - -
294A VAL 4.7 3.6 - - - -
345A LEU* 3.7 30.5 - - + -
346A PRO 4.6 3.4 - - - -
347A VAL* 3.6 1.4 - - - +
348A GLN* 2.8 36.5 + - + +
370A TYR* 5.1 0.9 - - + -
371A ALA* 1.3 76.4 - - - +
373A SER* 1.3 78.9 + - - +
374A GLY* 3.5 21.5 - - - -
379A VAL* 3.6 11.7 - - - +
407A ALA 5.0 1.1 - - - -
408A TRP 3.0 21.6 + - - -
409A ALA 3.7 5.4 - - - -
410A TRP* 3.6 31.0 - - + +
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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