Contacts of the strand formed by residues 405 - 412 (chain A) in PDB entry 2JED
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 PHE 405 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A HIS* 4.0 4.9 - + - -
396A LEU* 3.8 24.2 - - + -
397A ALA 3.2 9.9 - - - -
398A GLU* 3.7 34.3 - - + -
403A ASN* 3.7 18.6 - - + -
404A GLN* 1.3 74.7 - - - +
406A PHE* 1.3 70.1 + - - +
459A GLU* 5.8 0.2 - - - -
460A TYR* 4.0 20.6 + - + +
658A PRO* 3.6 30.5 - - + -
659A PHE* 3.7 39.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A PHE* 4.0 17.0 - + - -
395A PHE 3.7 0.7 - - - +
396A LEU* 3.8 8.5 - - - +
397A ALA* 2.7 32.2 + - + +
399A PHE* 3.9 15.3 - + + -
404A GLN* 3.5 45.1 - - + -
405A PHE* 1.3 78.5 - - - +
407A ALA* 1.3 61.6 + - - +
408A ILE* 4.7 4.9 - - + -
445A PHE* 3.5 44.2 - + + -
457A VAL* 3.8 19.7 - - + -
458A MET 3.4 6.3 - - - +
459A GLU* 5.2 0.2 - - - -
460A TYR* 3.7 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 4.3 7.0 - - + -
394A VAL* 3.9 14.8 - - + -
395A PHE 3.3 6.3 - - - +
406A PHE* 1.3 73.9 - - - +
408A ILE* 1.3 62.1 + - - +
409A LYS 4.1 0.7 - - - -
458A MET* 2.7 38.8 + - + +
459A GLU 3.8 7.2 - - - +
460A TYR* 3.9 3.9 - - + +
1701A LG8 3.6 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ILE* 3.9 15.7 - - + -
380A PHE* 3.8 26.5 - - + -
382A LEU* 4.6 1.8 - - + -
393A LYS 3.5 1.0 - - - +
394A VAL* 3.2 4.9 - - - -
395A PHE* 2.9 47.3 + - + +
397A ALA* 3.7 26.0 - - + -
406A PHE* 4.7 1.6 - - + -
407A ALA* 1.3 78.7 - - - +
409A LYS* 1.3 72.2 + - - +
410A ALA* 3.7 2.7 + - + +
455A PHE* 4.0 24.9 - - + -
456A PHE 3.3 6.7 - - - +
457A VAL* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER 5.3 0.2 + - - -
391A PHE* 2.6 44.1 + - - +
393A LYS 3.2 7.4 - - - +
394A VAL* 4.2 6.2 - - + +
407A ALA 4.1 0.8 + - - -
408A ILE* 1.3 74.0 - - - +
410A ALA* 1.3 63.2 + - - +
411A LEU* 4.0 16.9 - - - +
428A GLU* 3.2 33.6 + - - +
432A LEU* 5.7 0.2 - - + -
455A PHE* 3.4 5.5 - - - -
456A PHE* 2.9 72.5 + - + +
458A MET* 4.9 1.9 - - + +
522A ASP* 5.6 0.2 + - - -
1701A LG8 3.9 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLY* 4.2 0.7 - - - -
393A LYS* 2.8 33.9 + - + +
395A PHE* 3.9 19.3 - - + -
408A ILE* 3.7 0.6 + - + -
409A LYS* 1.3 74.9 - - - +
411A LEU* 1.3 67.6 + - - +
453A ASN* 6.0 0.2 - - - +
454A LEU 3.4 4.3 - - - -
455A PHE* 3.8 12.3 - - + -
675A LEU* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PHE 4.2 0.9 - - - +
392A GLY* 4.0 21.3 - - - +
409A LYS* 4.0 29.6 - - - +
410A ALA* 1.3 82.3 - - - +
412A LYS* 1.3 63.6 + - - +
416A VAL* 3.9 20.0 - - + -
425A THR* 3.7 37.7 - - + +
428A GLU* 5.5 0.4 - - - +
453A ASN* 3.3 7.6 - - - +
454A LEU* 2.8 41.9 + - + -
456A PHE* 4.1 7.6 - - + -
675A LEU* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 1.3 73.4 - - - +
413A LYS* 1.3 60.2 + - - +
414A ASP* 3.4 11.4 - - - +
415A VAL* 3.2 23.2 + - + +
416A VAL* 3.0 29.8 + - - +
452A GLU* 3.1 28.4 + - - +
453A ASN* 2.9 27.3 + - - +
675A LEU* 5.0 8.3 - - + +
676A SEP 3.0 41.2 + - - +
677A PHE 4.4 2.2 - - - +
678A ALA* 3.5 22.6 - - - +
----------------------------------------------------------
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