Contacts of the strand formed by residues 388 - 394 (chain A) in PDB entry 2O2C
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 THR 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386A ALA* 3.4 4.8 - - - +
387A VAL* 1.3 92.6 - - + +
389A HIS* 1.3 62.7 + - - +
430A PRO* 4.4 2.2 - - - +
431A ILE* 3.3 22.7 - - + -
433A PHE* 4.2 14.7 - - + -
453A ASN* 5.6 1.4 - - + +
454A LEU 4.3 2.4 + - - -
455A ILE* 3.5 29.9 - - + +
456A PRO* 3.3 22.7 - - - +
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Residues in contact with HIS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 6.2 0.2 - - + -
377A GLY* 5.9 5.7 - - - -
388A THR* 1.3 77.0 - - - +
390A ALA* 1.3 61.2 + - - +
391A ILE* 3.7 19.8 + - + +
430A PRO* 4.2 11.2 - - + -
431A ILE 2.9 6.8 + - - +
432A ILE* 3.4 27.7 - - + +
433A PHE* 3.2 25.5 + - - +
456A PRO* 3.5 30.2 + - + +
458A ASP* 3.1 41.1 + - - -
527A ASN* 4.9 5.2 - - - -
549A LYS* 3.6 23.3 + - - -
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Residues in contact with ALA 390 (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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389A HIS* 1.3 75.8 - - - +
391A ILE* 1.3 61.8 + - - +
392A LEU* 3.8 15.5 - - + -
433A PHE* 3.2 31.4 - - + +
448A ILE* 4.7 1.6 - - + -
455A ILE* 4.1 3.2 - - + +
456A PRO 2.9 8.1 + - - +
457A CYS* 3.5 24.4 - - - -
458A ASP* 2.8 29.6 + - - +
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Residues in contact with ILE 391 (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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389A HIS* 3.7 27.4 - - + +
390A ALA* 1.3 71.6 - - - +
392A LEU* 1.3 60.5 + - - +
393A PRO* 3.4 18.7 - - + +
401A LEU* 4.5 4.5 - - + -
402A PRO* 3.7 17.2 - - + +
405A LEU* 3.8 31.6 - - + -
432A ILE* 3.8 26.0 - - + -
433A PHE 2.9 10.8 + - - +
434A GLY* 3.4 21.0 - - - -
458A ASP* 3.8 4.0 - - + +
460A ILE* 4.3 14.1 - - + -
546A TYR* 3.7 24.2 - - + +
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Residues in contact with LEU 392 (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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390A ALA* 4.1 10.5 - - + -
391A ILE* 1.3 82.1 - - - +
393A PRO* 1.4 63.9 - - - +
394A TYR* 3.4 13.8 - - + -
434A GLY* 4.2 3.4 - - - -
435A GLU 3.8 14.8 - - - +
444A PHE* 3.8 28.0 - - + -
445A TYR* 3.2 36.1 - - + +
448A ILE* 4.5 2.5 - - + -
457A CYS* 3.8 20.2 - - + -
458A ASP 2.8 16.5 + - - +
459A PHE* 3.5 26.5 - - + -
460A ILE* 3.2 17.4 + - - -
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Residues in contact with PRO 393 (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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391A ILE* 3.4 15.5 - - + +
392A LEU* 1.4 81.4 - - - +
394A TYR* 1.3 58.7 + - - +
395A ASP 3.1 7.7 + - - -
398A LEU* 3.5 50.9 - - + +
401A LEU* 4.4 8.1 - - + -
402A PRO* 4.0 14.4 - - + -
435A GLU 3.8 9.2 - - - +
436A ALA* 3.2 10.4 - - - +
437A GLY 2.9 20.1 + - - -
460A ILE* 3.6 14.6 - - + +
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Residues in contact with TYR 394 (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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392A LEU* 3.4 13.7 - - + -
393A PRO* 1.3 69.4 - - - +
395A ASP* 1.3 61.4 + - - +
437A GLY* 3.8 18.8 - - - -
438A THR* 4.0 6.3 - - + -
441A GLN* 2.9 29.7 + - - +
445A TYR* 3.0 34.2 + - - -
459A PHE* 3.4 25.5 - + - -
460A ILE 2.6 18.1 + - - +
461A GLY* 4.1 8.7 - - - -
462A ALA* 4.5 3.1 + - - +
473A HIS* 5.7 0.5 + - - -
476A PHE* 3.2 45.1 - + + -
477A MET* 4.8 2.4 - - - +
480A PHE* 3.5 49.1 - + + -
483A GLN* 3.7 2.1 - - - +
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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