Contacts of the strand formed by residues 388 - 394 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B ILE* 6.0 0.3 - - - +
386B ALA* 3.4 4.1 - - - +
387B VAL* 1.3 86.4 - - + +
389B HIS* 1.3 63.0 + - - +
430B PRO* 4.4 1.7 - - - +
431B ILE* 3.3 11.9 - - + -
433B PHE* 4.1 11.4 - - - -
453B ASN* 5.5 0.3 - - - +
454B LEU 4.3 2.3 + - - -
455B ILE* 3.4 29.2 - - - +
456B PRO* 3.2 22.7 - - - +
387C VAL* 4.5 1.8 - - + -
388C THR* 3.5 31.9 - - + -
431C ILE* 3.9 21.5 - - + +
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Residues in contact with HIS 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 6.1 0.2 - - + -
377B GLY* 6.0 5.8 - - - -
388B THR* 1.3 76.5 - - - +
390B ALA* 1.3 62.0 + - - +
391B ILE* 3.7 20.1 + - + +
430B PRO* 4.2 11.9 - - + -
431B ILE 2.9 6.1 + - - -
432B ILE* 3.4 26.7 - - + +
433B PHE* 3.3 25.0 + - - -
456B PRO* 3.5 32.3 + - + +
457B CYS 4.8 0.2 - - - -
458B ASP* 3.2 40.7 + - - -
527B ASN* 4.8 5.2 - - - -
549B LYS* 3.6 22.6 + - - -
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Residues in contact with ALA 390 (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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389B HIS* 1.3 74.8 - - - +
391B ILE* 1.3 62.3 + - - +
392B LEU* 3.9 16.2 - - + -
433B PHE* 3.2 30.5 - - + +
448B ILE* 4.6 1.6 - - + -
455B ILE* 4.1 1.7 - - + +
456B PRO 2.9 8.6 + - - +
457B CYS* 3.5 25.3 - - - -
458B ASP* 2.9 30.5 + - - +
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Residues in contact with ILE 391 (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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389B HIS* 3.7 26.5 - - + +
390B ALA* 1.3 70.6 - - - +
392B LEU* 1.3 60.6 + - - +
393B PRO* 3.4 18.1 - - + +
401B LEU* 4.6 2.9 - - + -
402B PRO* 3.6 20.1 - - + +
405B LEU* 3.8 26.7 - - + -
432B ILE* 3.8 25.8 - - + -
433B PHE 2.9 11.5 + - - +
434B GLY* 3.4 20.1 - - - -
435B GLU 3.8 0.3 + - - -
458B ASP* 3.9 4.7 - - + +
460B ILE* 4.3 13.7 - - + -
546B TYR* 3.7 30.1 - - + +
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Residues in contact with LEU 392 (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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390B ALA* 4.1 13.5 - - + -
391B ILE* 1.3 81.0 - - - +
393B PRO* 1.3 62.3 - - - +
394B TYR* 3.4 13.9 - - + -
434B GLY* 4.2 2.2 - - - -
435B GLU 3.9 12.6 - - - +
444B PHE* 3.8 29.2 - - + -
445B TYR* 3.3 31.6 - - + +
448B ILE* 4.6 1.8 - - + -
457B CYS* 3.8 21.3 - - + -
458B ASP 2.8 15.2 + - - +
459B PHE* 3.5 29.6 - - + -
460B ILE* 3.2 18.9 + - - -
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Residues in contact with PRO 393 (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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391B ILE* 3.4 14.8 - - + +
392B LEU* 1.3 81.6 - - - +
394B TYR* 1.3 58.6 + - - +
395B ASP 3.0 9.1 + - - -
398B LEU* 3.5 50.0 - - + +
401B LEU* 4.3 11.0 - - + -
402B PRO* 3.9 15.3 - - + -
435B GLU 3.8 8.7 - - - +
436B ALA* 3.3 10.8 - - - +
437B GLY 3.0 19.2 + - - -
460B ILE* 3.5 11.0 - - + +
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Residues in contact with TYR 394 (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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392B LEU* 3.4 13.7 - - + -
393B PRO* 1.3 69.1 - - - +
395B ASP* 1.3 62.2 + - - +
437B GLY* 3.8 18.8 - - - -
438B THR* 4.0 6.1 - - + -
441B GLN* 2.6 33.7 + - - +
445B TYR* 3.0 34.4 + - - -
459B PHE* 3.5 23.4 - + - -
460B ILE 2.6 18.5 + - - +
461B GLY* 4.0 9.1 - - - -
462B ALA* 4.5 3.5 + - - +
473B HIS* 5.7 0.2 + - - -
476B PHE* 3.2 43.7 - + + -
477B MET* 4.8 1.8 - - - +
480B PHE* 3.6 47.6 - + + -
483B GLN* 3.7 1.2 - - - +
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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