Contacts of the strand formed by residues 380 - 388 (chain A) in PDB entry 5O67
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 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ASN* 3.7 40.3 + - + +
372A THR* 4.7 0.7 - - + -
373A ILE 3.3 24.7 - - - +
374A ALA 4.3 0.7 - - - +
375A ALA 4.5 0.2 - - - +
378A ASN 4.5 0.5 + - - -
379A LEU* 1.3 81.4 + - - +
381A ILE* 1.3 65.5 + - - +
382A VAL* 4.3 8.7 - - + -
401A LYS 3.3 0.9 - - - +
402A PHE* 3.3 25.8 - - - -
403A PRO* 3.3 28.0 + - - +
405A TYR* 4.2 9.0 - - - -
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Residues in contact with ILE 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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373A ILE* 2.8 59.9 + - + +
375A ALA* 3.7 27.4 - - + -
379A LEU* 4.9 4.3 - - + -
380A THR* 1.3 71.7 - - - +
382A VAL* 1.3 67.1 + - - +
383A PRO* 3.6 18.7 - - + +
400A LEU* 4.5 13.9 - - + -
401A LYS 3.6 2.5 - - - +
402A PHE* 3.8 29.6 - - + -
505C C8E 6.5 0.7 - - + -
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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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98A GLU* 3.7 37.0 - - + +
371A MET 3.5 14.4 - - - +
372A THR* 3.8 13.0 - - - +
380A THR* 4.3 9.4 - - + -
381A ILE* 1.3 80.8 - - - +
383A PRO* 1.4 62.2 - - - +
384A ASN* 5.0 2.1 - - + +
399A SER* 4.0 2.1 + - - +
400A LEU* 3.6 5.0 + - - -
401A LYS* 3.0 50.7 + - + +
403A PRO* 4.3 18.4 - - + -
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Residues in contact with PRO 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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370A GLY* 3.5 1.1 - - - -
371A MET* 3.2 56.5 + - + +
373A ILE* 4.8 5.2 - - + -
381A ILE* 3.6 15.7 - - + +
382A VAL* 1.4 87.3 - - - +
384A ASN* 1.3 64.6 + - - +
398A PHE* 4.1 14.1 - - + -
399A SER 3.6 7.6 - - - +
400A LEU* 3.6 16.5 - - + -
505C C8E 4.2 27.6 - - + -
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Residues in contact with ASN 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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98A GLU* 4.7 13.5 - - - +
334A SER* 5.6 1.0 + - - -
368A ASN* 3.7 20.9 + - - +
369A VAL 3.2 16.1 - - - +
370A GLY* 3.4 12.1 - - - -
382A VAL* 5.0 2.0 - - + +
383A PRO* 1.3 76.3 - - - +
385A LEU* 1.3 82.6 + - - +
386A ALA* 4.0 4.2 - - - +
397A THR 3.4 4.7 - - - +
398A PHE* 3.4 7.9 - - - -
399A SER* 3.0 48.6 + - - +
505C C8E 5.9 0.7 - - - -
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Residues in contact with LEU 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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367A PHE 4.1 0.6 - - - +
368A ASN* 3.3 1.0 - - - -
369A VAL* 2.8 40.9 + - + +
384A ASN* 1.3 80.2 + - - +
386A ALA* 1.3 62.4 + - - +
387A ILE* 4.2 7.4 - - + -
396A PHE* 4.4 14.6 - - + -
397A THR 3.5 9.4 - - - +
398A PHE* 4.1 18.0 - - + -
337C VAL* 3.7 35.9 - - + -
367C PHE* 4.0 19.7 - - + -
389C MET* 3.7 30.7 - - + -
505C C8E 4.2 12.7 - - + +
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Residues in contact with ALA 386 (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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366A TYR* 4.4 16.4 - - + -
367A PHE 3.5 5.4 - - - -
368A ASN* 3.1 20.4 - - - +
384A ASN* 4.2 4.7 - - - +
385A LEU* 1.3 74.4 - - - +
387A ILE* 1.3 62.2 + - - +
388A GLY 3.6 0.9 + - - -
394A PRO* 5.9 0.2 - - - +
396A PHE* 3.4 3.2 - - - -
397A THR* 2.9 49.0 + - + +
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Residues in contact with ILE 387 (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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366A TYR* 3.6 3.1 - - - -
367A PHE* 2.8 56.4 + - + +
369A VAL* 5.6 1.6 - - + -
385A LEU* 4.2 9.0 - - + -
386A ALA* 1.3 69.6 - - - +
388A GLY* 1.3 74.4 + - - +
389A MET* 3.3 4.6 + - + +
395A ASP 3.9 8.1 - - - +
387B ILE* 5.9 4.9 - - + -
367C PHE* 3.9 33.2 - - + -
387C ILE* 5.9 7.0 - - + -
389C MET* 3.3 44.6 - - + -
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Residues in contact with GLY 388 (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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365A GLY 3.8 9.4 - - - -
366A TYR* 4.5 3.9 - - - -
386A ALA 3.6 3.8 + - - -
387A ILE* 1.3 80.3 - - - +
389A MET* 1.3 62.3 + - - -
390A THR 3.5 4.2 - - - +
393A ALA* 4.0 8.1 - - - -
394A PRO 3.2 21.3 + - - -
395A ASP* 3.1 15.4 + - - +
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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