Contacts of the strand formed by residues 425 - 433 (chain E) in PDB entry 5IXM
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 MET 425 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417E GLU* 3.9 13.5 - - - +
418E TYR 3.3 13.9 - - - +
419E ARG* 4.1 13.2 - - + +
423E ASP 5.5 0.4 - - - -
424E ARG* 1.3 76.5 - - - +
426E ILE* 1.3 76.9 + - - +
427E GLN* 3.7 7.9 - - + +
460E THR* 3.3 42.2 - - + +
461E ALA* 3.2 8.2 - - - +
462E SER* 2.9 40.5 + - - +
463E TRP* 3.7 4.1 - - - -
545E LEU* 4.9 7.9 - - - -
552E TYR* 3.4 38.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 426 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416E MET* 5.0 3.1 - - + +
417E GLU* 3.3 3.5 - - - +
418E TYR* 2.9 42.1 + - + +
425E MET* 1.3 81.5 - - - +
427E GLN* 1.3 64.5 + - - +
428E LEU* 4.1 20.2 - - + -
459E THR* 6.5 0.4 - - - -
460E THR 3.5 8.5 - - - +
461E ALA* 4.6 9.2 - - + -
463E TRP* 3.5 31.2 - - + -
603G C8E 4.3 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 427 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415E ILE* 3.6 29.5 - - + +
416E MET 3.3 11.0 - - - +
417E GLU* 2.9 25.7 - - + +
425E MET* 3.8 11.9 - - + -
426E ILE* 1.3 78.4 - - - +
428E LEU* 1.3 66.7 + - - +
429E ASN* 4.2 13.4 + - - +
458E GLY 3.8 0.2 - - - +
459E THR* 3.2 6.4 - - - -
460E THR* 2.9 42.3 + - - +
476E TYR* 4.5 9.1 + - - -
552E TYR* 3.4 24.9 - - - +
553E GLN 3.7 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415E ILE* 3.3 3.5 - - - +
416E MET* 2.9 61.8 + - + +
426E ILE* 4.1 14.6 - - + -
427E GLN* 1.3 80.1 - - - +
429E ASN* 1.3 65.2 + - - +
458E GLY 3.4 3.1 - - - +
459E THR* 4.0 21.1 - - + -
222G ILE* 3.9 27.6 - - + -
263G VAL* 4.3 14.8 - - + -
603G C8E 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 429 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414E ALA 3.2 13.5 - - - +
415E ILE* 3.9 15.5 - - + +
427E GLN* 4.2 11.4 + - - +
428E LEU* 1.3 78.6 - - - +
430E TYR* 1.3 64.0 + - - +
431E ARG* 4.1 17.8 - - + +
456E GLN* 4.6 3.6 + - - +
457E VAL* 3.6 5.2 - - - +
458E GLY* 2.9 54.6 + - - +
460E THR* 5.3 0.6 + - - -
476E TYR* 3.6 26.4 + - - -
67F VAL 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 430 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413E ASN* 3.1 7.3 - - - +
414E ALA* 2.9 38.3 + - + +
429E ASN* 1.3 75.1 - - - +
431E ARG* 1.3 74.7 + - - +
432E TYR* 3.7 24.1 - - + +
455E SER* 2.8 30.5 + - - -
456E GLN 3.2 23.8 - - - -
457E VAL* 3.7 21.3 - - + -
603E C8E 3.6 35.7 - - + +
215G LEU* 3.5 27.8 - - + -
602G C8E 3.5 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 431 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E GLN* 5.9 0.4 - - - +
411E LEU* 5.8 1.0 - - - +
412E GLY 3.8 5.0 + - - +
413E ASN* 4.0 27.9 + - + +
429E ASN* 4.1 14.6 - - + +
430E TYR* 1.3 83.8 - - - +
432E TYR* 1.3 60.0 + - - +
454E ILE* 3.7 10.6 - - + +
455E SER* 3.3 4.2 - - - -
456E GLN* 2.9 39.5 + - + +
67F VAL* 3.6 42.7 - - - +
68F SER* 4.3 1.3 - - - -
77F GLU* 2.5 40.3 + - - +
79F GLN* 5.2 4.9 + - - -
105F THR* 3.2 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 432 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E LEU* 3.7 38.5 + - + +
410E THR 4.1 4.9 - - - -
411E LEU* 3.5 6.4 - - - +
412E GLY 2.8 42.6 + - - +
430E TYR* 3.7 28.3 - - + +
431E ARG* 1.3 75.0 - - - +
433E ALA* 1.3 65.8 + - - +
434E SER* 3.5 34.7 + - - -
435E PRO* 4.3 6.1 - - + +
454E ILE* 3.1 24.7 - - - -
455E SER* 4.4 2.9 - - - -
480E LYS* 4.9 14.8 - - - -
603E C8E 4.1 29.8 - - + +
77F GLU* 4.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410E THR 3.4 6.1 - - - +
411E LEU* 3.6 6.7 - - + -
432E TYR* 1.3 81.1 - - - +
434E SER* 1.3 64.9 + - - +
435E PRO* 4.1 0.7 - - - +
437E TYR* 5.1 0.7 - - + -
438E ILE* 4.3 6.1 - - + -
453E GLY* 3.3 2.9 - - - -
454E ILE* 2.9 45.7 + - + +
77F GLU* 4.3 1.8 - - - +
107F PHE* 3.5 33.7 - - + -
----------------------------------------------------------
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