Contacts of the strand formed by residues 387 - 393 (chain A) in PDB entry 6N8Q
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 ILE 387 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 3.4 43.7 - - + +
383A HIS* 4.9 1.4 - - - +
385A SER 4.2 0.4 - - - -
386A ALA* 1.3 74.2 - - - +
388A THR* 1.3 62.8 + - - +
389A CYS 3.8 20.9 - - - +
390A SER* 4.1 10.8 - - - +
440A THR* 4.5 8.3 - - + -
441A GLY 3.5 5.8 - - - +
442A HIS* 4.0 8.3 - - + -
900A SER* 6.2 1.1 - - - -
912A LEU* 4.3 23.1 - - + -
915A PRO 4.2 12.9 + - - +
918A PHE* 4.2 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ALA* 3.4 3.3 + - + +
387A ILE* 1.3 77.9 - - - +
389A CYS* 1.3 59.6 + - - +
441A GLY 2.6 25.4 + - - -
442A HIS 3.2 6.1 + - - +
443A GLU* 3.9 31.0 - - + +
506A GLY* 4.8 5.4 - - - -
507A ILE 2.7 24.4 + - - +
508A GLN* 4.8 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 3.8 5.3 - - - +
388A THR* 1.3 79.0 - - - +
390A SER* 1.3 68.6 + - - +
440A THR* 3.4 3.5 - - - -
441A GLY* 2.7 29.7 + - - +
507A ILE* 3.3 36.6 - - - +
508A GLN 3.2 25.8 - - - +
509A LYS* 3.9 2.2 - - - -
510A ILE* 3.7 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 4.1 7.4 - - - +
389A CYS* 1.3 81.8 + - - +
391A HIS* 1.3 67.8 + - - +
438A LEU* 4.5 6.5 - - - -
439A LEU 3.2 9.9 - - - -
440A THR* 4.3 2.2 - - - +
510A ILE* 5.2 0.7 + - - -
900A SER* 4.5 9.8 + - - -
902A VAL* 4.4 29.1 - - - +
918A PHE* 3.8 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 1.3 79.1 + - - +
392A HIS* 1.3 62.8 + - - +
393A VAL* 3.9 22.8 - - + +
438A LEU* 3.8 2.6 - - - +
439A LEU* 2.7 47.6 + - + +
510A ILE* 3.0 49.8 + - + +
511A PHE* 3.8 14.9 - + - -
512A LEU 3.8 21.6 + - - -
902A VAL* 4.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A HIS* 1.3 78.6 + - - +
393A VAL* 1.3 74.3 + - - +
394A SER* 3.0 29.2 + - - -
436A ASP* 3.8 23.8 + - + +
437A LEU 3.4 13.6 + - - -
438A LEU* 4.1 10.8 - - + -
452A ALA* 4.2 7.0 + - + +
902A VAL* 4.6 11.8 - - + +
903A PHE 3.9 16.8 - - - +
904A THR* 3.6 24.9 - - + +
905A LYS 5.0 0.4 + - - -
908A GLN* 6.0 0.4 + - - -
910A PHE* 3.6 29.5 - + - -
920A ARG* 5.9 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A HIS* 3.9 26.5 - - + +
392A HIS* 1.3 79.3 + - - +
394A SER* 1.3 62.7 + - - +
396A ILE* 3.7 24.7 - - + +
436A ASP* 3.8 0.5 - - - -
437A LEU* 2.9 40.5 + - + +
439A LEU* 5.0 3.1 - - + -
512A LEU* 4.1 28.7 - - + +
514A LYS* 4.0 25.8 - - + -
791A GLU* 6.1 0.9 - - - +
----------------------------------------------------------
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