Contacts of the strand formed by residues 456 - 463 (chain A) in PDB entry 2IUK
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 ALA 456 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TYR 4.1 1.3 - - - +
436A GLN* 3.0 23.0 + - - +
439A PHE* 3.7 21.8 - - + -
440A ILE* 3.5 35.2 - - + +
443A LEU* 3.5 6.9 - - + +
455A TYR* 1.3 70.5 - - - +
457A THR* 1.3 59.9 + - - +
475A GLU 4.0 1.4 - - - +
477A SER 2.8 22.7 + - - +
515A ASN* 3.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LEU 3.8 2.1 + - - +
435A TYR* 3.0 34.3 + - - +
436A GLN 3.6 0.7 + - - -
455A TYR* 4.1 7.0 - - + +
456A ALA* 1.3 73.7 - - - +
458A ARG* 1.3 66.3 + - - +
459A THR* 4.7 0.2 + - - -
475A GLU 3.3 6.1 - - - -
476A LEU* 3.3 30.3 - - + -
511A HIS 4.0 4.0 - - - -
512A VAL* 3.5 44.5 + - - +
515A ASN* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PRO* 4.5 2.4 + - - -
392A LYS 3.6 21.6 + - - -
393A SER* 5.1 0.2 - - - -
403A GLN 2.8 24.0 + - - -
404A THR 3.3 2.8 + - - -
405A SER* 3.1 33.2 - - - +
407A ILE* 4.4 6.4 - - + +
432A ILE* 4.4 11.0 - - + -
433A LEU 3.5 5.6 - - - +
434A ASP* 3.1 26.0 + - - +
436A GLN* 2.7 46.0 + - + +
457A THR* 1.3 80.4 - - - +
459A THR* 1.3 60.6 + - - +
460A ILE* 4.2 0.8 + - + -
473A ALA 3.8 1.0 - - - +
474A ILE* 3.3 2.6 - - - -
475A GLU* 2.7 69.6 + - + +
477A SER* 5.0 0.4 + - - -
490A SER* 5.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 3.7 32.3 - - + -
432A ILE* 3.4 5.6 - - - +
433A LEU* 3.0 44.5 + - + +
458A ARG* 1.3 74.5 + - - +
460A ILE* 1.3 68.7 + - - +
461A LEU* 3.8 12.4 + - + +
471A PRO* 4.9 2.2 - - + -
473A ALA 3.5 2.9 - - - -
474A ILE* 3.8 11.1 - - + +
512A VAL* 3.3 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 3.8 22.2 - - + -
389A PHE* 4.4 3.4 - - + -
391A PRO* 3.9 18.8 - - + -
407A ILE* 3.9 21.8 - - + -
412A LEU* 3.8 26.2 - - + -
430A LEU* 3.7 27.6 - - + -
431A PHE 3.6 8.7 - - - +
432A ILE* 4.1 11.4 - - + -
458A ARG* 5.8 0.4 - - + -
459A THR* 1.3 74.4 - - - +
461A LEU* 1.3 62.3 + - - +
471A PRO* 3.5 5.0 - - - +
472A LEU* 3.0 36.5 + - + -
473A ALA 3.0 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 5.0 1.8 - - + -
371A ALA* 3.8 33.4 - - + -
374A VAL* 4.0 21.1 - - + -
383A ILE* 3.8 28.9 - - + -
429A ARG 3.8 0.3 - - - +
430A LEU* 3.8 4.7 - - - +
431A PHE* 3.0 38.5 + - + +
432A ILE* 4.6 6.3 - - - -
433A LEU* 4.6 4.0 - - + +
459A THR* 4.2 18.2 - - + +
460A ILE* 1.3 79.7 - - - +
462A PHE* 1.3 61.8 + - - +
469A LEU* 3.9 17.7 - - + -
470A LYS 3.3 3.1 - - - +
471A PRO* 4.1 14.6 - - + -
472A LEU* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASN 4.7 0.9 - - - -
416A MET* 3.6 62.4 - - + -
419A VAL* 4.1 6.3 - - + -
424A ALA* 3.7 13.5 - - + -
429A ARG* 3.5 46.4 - - + -
430A LEU* 4.1 7.2 - - + -
461A LEU* 1.3 74.8 - - - +
463A LEU* 1.3 67.9 + - - +
464A LYS* 3.6 15.5 + - + -
468A THR 3.3 1.2 - - - +
469A LEU* 3.1 10.3 - - - -
470A LYS* 2.8 35.7 + - + +
472A LEU* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A THR 5.7 0.2 - - - +
428A GLN 4.1 11.9 - - - +
429A ARG* 2.9 47.3 + - + +
431A PHE* 3.7 16.2 - - + -
462A PHE* 1.3 76.1 - - - +
464A LYS* 1.3 64.7 + - - +
467A GLY* 4.2 16.6 - - - +
468A THR 3.4 9.6 - - - +
469A LEU* 4.2 6.0 - - + +
630A VAL 3.6 22.7 - - - +
631A ILE* 4.0 31.0 - - + -
----------------------------------------------------------
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