Contacts of the strand formed by residues 389 - 395 (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 LYS 389 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380E ALA* 3.7 11.0 - - + -
381E PHE 3.8 2.9 - - - +
382E TYR* 3.5 39.2 + - + +
387E GLY 3.7 1.0 + - - +
388E TYR* 1.3 71.9 - - - +
390E MET* 1.3 65.3 + - - +
413E VAL* 3.9 2.9 - - - +
414E MET* 2.9 61.8 + - + +
415E LYS 3.8 18.5 + - - +
416E GLY* 3.8 19.9 - - - -
417E PRO* 4.6 4.2 - - + +
419E ASP* 5.1 0.4 + - - -
462E ASP* 5.1 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 390 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352E GLY* 4.8 0.2 - - - -
381E PHE* 3.0 59.7 + - + +
382E TYR 3.6 4.9 - - - -
383E THR* 3.6 44.9 - - + +
388E TYR* 3.8 9.2 - - + +
389E LYS* 1.3 79.1 - - - +
391E CYS* 1.3 58.3 + - - +
411E PHE* 3.5 37.0 - - + -
412E VAL 3.2 12.3 - - - +
413E VAL* 4.8 3.1 - - + -
414E MET* 2.9 18.4 - - - +
426E PHE* 4.1 9.6 - - + -
496E VAL* 3.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 391 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E PHE* 4.1 4.9 - - - -
378E SER* 3.6 14.8 - - - +
379E PRO 3.6 17.9 - - - +
381E PHE* 4.1 5.8 - - - -
390E MET* 1.3 76.2 - - - +
392E LEU* 1.3 78.8 + - - +
411E PHE* 4.2 1.6 - - - -
412E VAL* 2.8 50.0 + - - -
414E MET* 3.7 23.1 - - + -
463E MET* 4.1 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E PHE* 4.4 12.1 - - + -
356E TRP* 4.2 17.0 - - + -
376E ILE 4.5 0.2 - - - -
377E PHE* 3.3 4.0 - - - -
378E SER* 2.8 41.3 + - - +
381E PHE* 4.5 8.7 - - + -
391E CYS* 1.3 84.8 - - - +
393E ARG* 1.3 62.0 + - - +
409E LEU* 4.2 7.2 - - + -
410E PHE 3.4 13.0 - - - +
411E PHE* 4.1 14.8 - - + -
412E VAL* 4.4 2.5 - - - -
432E LEU* 4.0 20.4 - - + -
492E ILE* 4.2 24.2 - - + +
494E ALA* 3.9 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375E ALA* 3.6 29.9 + - + +
376E ILE 3.3 14.8 - - - +
377E PHE* 3.4 49.7 - - + -
392E LEU* 1.3 75.4 - - - +
394E ILE* 1.3 61.2 + - - +
395E TYR* 4.0 7.0 + - + -
409E LEU* 3.8 2.2 - - - -
410E PHE* 2.8 42.7 + - + +
412E VAL* 4.1 9.2 - - + +
466E ALA* 4.6 6.1 - - + -
253M GLU* 2.9 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 394 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E TRP* 3.6 26.9 - - + -
358E ILE* 4.2 17.7 - - + -
375E ALA* 3.2 3.3 - - - -
376E ILE* 3.0 40.4 + - + +
393E ARG* 1.3 76.3 - - - +
395E TYR* 1.3 64.7 + - - +
396E LEU* 3.8 22.5 + - + -
407E LEU* 3.2 37.2 - - + -
408E SER 3.2 15.3 - - - +
409E LEU* 4.4 8.7 - - + -
490E ILE* 4.9 1.1 - - + -
492E ILE* 4.5 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 395 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374E PRO* 3.2 29.4 - - + +
375E ALA* 3.8 18.6 - - + -
393E ARG* 4.0 10.9 + - + -
394E ILE* 1.3 77.5 - - - +
396E LEU* 1.3 57.4 + - - +
397E ASN 3.0 4.5 - - - +
398E GLY* 2.9 43.5 + - - +
399E ASP* 3.4 22.7 - - + -
407E LEU* 3.7 0.3 - - - -
408E SER* 2.8 25.2 + - - +
410E PHE* 3.6 33.2 - + - -
253M GLU* 2.6 28.6 + - + +
255M NH2 3.5 14.9 + - - -
----------------------------------------------------------
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