Contacts of the strand formed by residues 380 - 388 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASN* 3.3 41.0 + - + +
372B THR* 4.0 7.2 - - - +
373B ILE 3.4 11.7 - - - +
379B LEU* 1.3 87.1 + - - +
381B ILE* 1.3 67.3 + - - +
382B VAL* 3.9 15.5 - - + -
402B PHE* 3.5 3.3 - - - -
403B PRO* 3.1 37.9 + - + +
405B TYR* 4.0 15.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ILE* 2.8 54.7 + - + +
375B ALA* 4.4 19.3 - - + -
379B LEU* 4.8 5.2 - - + -
380B THR* 1.3 76.2 - - - +
382B VAL* 1.3 67.6 + - - +
383B PRO* 3.6 9.0 - - + +
400B LEU* 4.0 22.7 - - + -
401B LYS 3.6 3.1 - - - +
402B PHE* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 3.7 36.6 - - + +
371B MET 3.6 14.4 - - - +
372B THR* 3.7 16.4 - - - +
380B THR* 3.9 11.7 - - + -
381B ILE* 1.3 80.6 - - - +
383B PRO* 1.4 63.5 - - - +
384B ASN* 5.1 4.9 - - + +
399B SER 3.7 1.2 - - - +
400B LEU* 3.5 5.3 - - - -
401B LYS* 3.0 51.0 + - + +
403B PRO* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B GLY* 3.5 1.1 - - - -
371B MET* 3.2 53.1 + - + +
373B ILE* 4.6 10.8 - - + -
381B ILE* 3.6 12.8 - - + +
382B VAL* 1.4 87.7 - - - +
384B ASN* 1.3 64.1 + - - +
399B SER 3.4 7.4 - - - +
400B LEU* 4.0 15.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 5.7 4.3 - - - +
334B SER* 5.4 2.0 + - - -
368B ASN* 3.3 26.4 + - - +
369B VAL 2.9 29.7 + - - -
370B GLY* 3.7 5.0 - - - -
382B VAL* 5.1 5.8 - - + +
383B PRO* 1.3 77.6 - - - +
385B LEU* 1.3 64.2 + - - +
386B ALA* 4.3 3.5 + - - +
397B THR 3.4 4.9 - - - +
398B PHE* 3.6 2.5 - - - +
399B SER* 3.1 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL* 4.0 21.1 - - + -
367A PHE* 3.6 35.7 - - + -
389A MET* 4.1 16.8 - - - -
367B PHE 4.0 0.2 - - - +
368B ASN* 3.3 6.2 - - - +
369B VAL* 2.9 43.5 + - + +
384B ASN* 1.3 73.2 + - - +
386B ALA* 1.3 72.8 + - - +
387B ILE* 4.0 16.2 - - + -
396B PHE* 4.3 4.9 - - + -
397B THR 3.8 3.1 - - - +
398B PHE* 4.0 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TYR* 4.4 18.7 - - + -
367B PHE 3.6 5.4 - - - +
368B ASN* 3.4 19.1 - - - +
384B ASN* 4.4 4.3 - - - +
385B LEU* 1.3 73.1 - - - +
387B ILE* 1.3 62.6 + - - +
388B GLY 3.9 0.3 + - - -
396B PHE* 3.4 5.9 - - - +
397B THR* 3.1 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A PHE* 3.8 37.5 - - + -
387A ILE* 5.9 5.2 - - + -
389A MET* 3.9 26.2 - - + -
366B TYR* 3.4 4.4 - - - -
367B PHE* 2.9 58.6 + - + +
369B VAL* 5.5 0.9 - - + -
385B LEU* 4.0 19.1 - - + -
386B ALA* 1.3 73.9 - - - +
388B GLY* 1.3 73.9 + - - +
389B MET* 3.4 4.8 + - + +
395B ASP 4.0 6.5 - - - +
396B PHE* 4.7 0.9 - - - +
387C ILE* 6.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A MET 5.7 0.5 - - - +
365B GLY 3.8 6.5 - - - -
366B TYR* 4.4 2.8 - - - -
386B ALA 3.9 2.2 + - - -
387B ILE* 1.3 80.2 - - - +
389B MET* 1.3 61.6 + - - +
390B THR 3.6 3.1 - - - -
393B ALA* 3.9 9.4 - - - -
394B PRO 3.3 22.1 + - - -
395B ASP* 3.3 15.4 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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