Contacts of the strand formed by residues 406 - 414 (chain E) in PDB entry 1D00
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 HIS 406 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E ASN* 3.4 3.6 - - - -
398E GLY* 2.9 29.9 + - - -
402E GLY* 2.7 13.5 + - - +
405E THR* 1.3 109.3 + - - +
407E LEU* 1.3 62.6 + - - +
470E PRO 3.6 18.2 - - - +
471E LEU* 3.4 49.1 + - + +
473E CYS 3.3 5.2 - - - +
474E PRO* 3.8 29.2 - - + +
475E VAL* 3.9 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361E PHE* 5.5 0.4 - - + -
394E ILE* 3.2 40.4 - - + -
395E TYR 3.7 5.8 - - - +
396E LEU* 4.5 21.5 - - + +
406E HIS* 1.3 72.5 - - - +
408E SER* 1.3 62.5 + - - +
409E LEU* 4.3 1.8 - - + +
434E LEU* 4.5 17.0 - - + -
472E PHE* 3.4 25.3 + - + +
473E CYS* 2.7 34.7 + - + +
474E PRO 5.7 0.2 - - - -
475E VAL* 4.4 5.3 - - + +
478E MET* 4.4 26.5 - - + -
490E ILE* 4.8 6.1 - - + -
492E ILE* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 408 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E ARG 4.0 0.5 - - - +
394E ILE* 3.2 5.7 - - - +
395E TYR* 2.8 41.3 + - - +
398E GLY* 3.4 3.5 - - - -
399E ASP* 3.0 30.8 + - - -
406E HIS 3.6 1.0 + - - -
407E LEU* 1.3 73.2 - - - +
409E LEU* 1.3 60.3 + - - +
410E PHE* 3.5 21.3 - - - -
469E CYS 3.7 4.3 - - - -
470E PRO* 2.6 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E TRP* 5.3 0.9 - - + -
392E LEU* 4.2 18.4 - - + -
393E ARG 3.8 8.1 - - - +
394E ILE* 4.4 15.9 - - + -
407E LEU* 3.9 2.8 + - + -
408E SER* 1.3 73.0 - - - +
410E PHE* 1.3 88.0 + - - +
432E LEU* 4.0 29.8 - - + +
468E GLY* 3.8 0.7 - - - -
469E CYS* 2.9 36.6 + - - +
472E PHE* 3.9 37.0 - - + +
492E ILE* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 410 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392E LEU* 3.4 6.7 - - - +
393E ARG* 2.8 42.9 + - + +
395E TYR* 3.6 26.0 - + - -
399E ASP* 3.4 22.2 - - + -
408E SER* 3.5 27.6 - - - -
409E LEU* 1.3 83.1 - - - +
411E PHE* 1.3 59.1 + - - +
432E LEU* 4.8 2.0 - - - -
466E ALA* 3.5 21.5 - - + -
467E SER* 3.7 5.6 - - - +
468E GLY* 3.4 20.6 - - - -
470E PRO* 4.2 22.0 - - + -
251M VAL 3.5 14.1 - - - -
252M GLN 3.8 2.5 - - - -
253M GLU* 3.4 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 411 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381E PHE* 4.6 4.3 - + - -
390E MET* 3.5 48.9 - - + -
391E CYS 4.0 2.2 - - - -
392E LEU* 4.1 15.7 - - + -
410E PHE* 1.3 73.4 - - - +
412E VAL* 1.3 63.0 + - - +
413E VAL* 3.6 24.0 - - + -
426E PHE* 3.7 25.1 - + - -
430E VAL* 4.0 24.2 - - + -
432E LEU* 4.9 2.4 - - + +
447E PHE* 3.9 14.1 - + + -
456E PHE* 4.1 16.1 - + - -
465E ILE 4.8 0.3 - - - +
466E ALA* 3.4 4.9 - - - -
467E SER* 2.9 35.8 + - - +
468E GLY* 4.5 0.8 - - - -
494E ALA* 6.1 0.4 - - + -
496E VAL* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 412 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E PHE* 4.5 6.1 - - + -
390E MET* 3.2 8.7 - - - +
391E CYS* 2.8 63.2 + - - +
393E ARG* 4.1 19.3 - - + +
411E PHE* 1.3 83.9 - - - +
413E VAL* 1.3 73.6 + - - +
414E MET* 3.6 2.0 + - + -
463E MET* 4.0 17.5 - - + -
464E ASN 3.9 16.4 - - - +
465E ILE 5.5 0.4 - - - -
466E ALA* 3.6 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 413 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E TYR* 5.4 1.1 - - + -
389E LYS 4.0 6.7 - - - +
390E MET* 4.6 2.5 - - + +
411E PHE* 3.6 25.3 - - + -
412E VAL* 1.3 75.6 - - - +
414E MET* 1.3 62.2 + - - +
424E TRP* 3.9 23.3 - - + -
426E PHE* 4.3 14.8 - - + -
455E SER 3.5 17.5 + - - +
456E PHE* 4.1 11.9 - - + -
457E GLN 4.7 0.2 - - - +
459E PRO* 3.8 11.2 - - + -
464E ASN* 3.1 49.7 + - - +
465E ILE 5.7 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 414 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380E ALA* 3.1 25.4 - - + -
389E LYS* 2.9 45.1 + - + +
390E MET 2.9 35.0 - - - +
391E CYS* 3.7 17.0 - - + +
412E VAL* 4.2 9.9 - - + +
413E VAL* 1.3 78.3 - - - +
415E LYS* 1.3 60.4 + - - +
416E GLY* 2.9 10.2 + - - -
419E ASP* 3.9 1.7 - - - +
424E TRP* 5.1 1.2 - - - -
459E PRO* 3.7 11.3 - - - +
462E ASP* 3.4 17.7 - - - +
463E MET* 3.9 20.9 - - + -
----------------------------------------------------------
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