Contacts of the strand formed by residues 386 - 391 (chain K) in PDB entry 6R90
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 SER 386 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379K SER* 2.7 44.3 + - - +
380K GLY 4.7 0.2 + - - -
384K GLU 4.3 4.9 + - - -
385K GLY* 1.3 75.6 - - - -
387K LEU* 1.3 64.6 + - - +
388K ARG* 3.0 32.1 + - - -
714K THR* 4.3 6.1 - - - -
715K VAL 3.3 18.6 - - - -
716K PRO* 4.0 3.6 - - - -
717K LEU* 3.5 16.0 - - - +
719K GLU 4.3 0.2 + - - -
721K PRO* 3.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376K VAL* 4.8 11.2 - - + -
377K THR 3.3 13.9 - - - +
378K CYS* 4.5 8.7 - - - -
386K SER* 1.3 79.0 - - - +
388K ARG* 1.3 65.1 + - - +
389K ILE* 4.3 7.2 - - + -
713K ARG 4.1 0.2 - - - +
714K THR* 3.8 1.2 - - - -
715K VAL* 2.9 41.8 + - + +
717K LEU* 3.5 32.7 - - + +
721K PRO* 4.7 0.9 - - + -
724K ILE* 4.7 5.8 - - + -
733K PHE* 6.1 1.6 - - + -
735K VAL* 4.4 28.9 - - + -
794K ILE* 4.4 25.4 - - + -
799K PHE* 4.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 388 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329K GLY* 5.4 1.8 - - - -
330K ASP* 2.9 41.0 + - - +
354K THR* 4.3 9.9 - - - +
355K ASN* 3.0 26.2 + - - +
356K LEU* 4.3 22.2 - - + +
375K LEU 3.7 0.9 - - - +
376K VAL* 3.5 3.6 - - - +
377K THR* 2.9 43.2 + - - +
379K SER* 3.3 24.2 + - - +
384K GLU 5.1 5.1 + - - -
386K SER* 3.0 22.1 + - - -
387K LEU* 1.3 74.7 - - - +
389K ILE* 1.3 63.1 + - - +
390K ILE* 4.1 4.0 + - + -
712K ILE* 4.5 9.6 - - + +
713K ARG 3.6 2.5 - - - +
714K THR* 3.6 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367K LEU* 4.4 15.3 - - + -
374K GLN* 3.9 21.5 - - + +
375K LEU 3.3 8.7 - - - +
376K VAL* 4.4 10.3 - - + -
387K LEU* 4.2 5.8 - - + +
388K ARG* 1.3 83.1 - - - +
390K ILE* 1.3 62.2 + - - +
391K ARG* 5.7 1.4 - - + +
711K HIS* 3.6 1.9 + - - +
712K ILE* 3.3 4.3 - - - -
713K ARG* 2.9 55.6 + - + +
715K VAL* 3.7 27.8 - - + -
799K PHE* 3.7 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356K LEU* 4.4 14.6 - - + -
374K GLN* 3.6 2.6 - - - +
375K LEU* 2.9 41.7 + - + +
377K THR* 4.0 27.1 - - + +
388K ARG* 4.7 1.3 - - + +
389K ILE* 1.3 79.0 - - - +
391K ARG* 1.3 66.9 + - - +
710K LEU* 4.0 29.4 - - + -
711K HIS 3.5 6.1 - - - +
712K ILE* 4.1 22.2 - - + -
1012K LEU* 4.7 15.3 - - + +
1037K ILE* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 391 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368K GLU* 4.0 19.0 + - - -
372K GLN* 4.8 10.6 - - + +
373K GLY 5.1 1.6 - - - +
374K GLN* 3.5 43.3 + - + +
389K ILE* 5.7 1.3 - - + +
390K ILE* 1.3 76.1 - - - +
392K ASN* 1.3 73.2 + - - +
393K GLY 3.4 26.1 + - - -
710K LEU* 3.5 5.9 - - - -
711K HIS* 2.9 67.5 + - + +
1012K LEU* 6.0 2.0 - - - -
----------------------------------------------------------
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