Contacts of the strand formed by residues 455 - 460 (chain A) in PDB entry 4L28
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 ILE 455 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A PRO* 5.0 1.1 - - + -
448A VAL 3.8 10.1 - - - +
449A VAL* 3.9 22.9 - - + -
453A GLY 4.5 7.4 - - - +
454A VAL* 1.3 83.0 - - - +
456A LEU* 1.3 64.5 + - - +
457A GLY 3.8 9.2 - - - +
487A PHE* 3.5 34.1 - - + -
489A GLN* 4.1 21.3 - - + +
510A LEU* 3.8 17.5 - - + -
512A VAL* 4.7 8.7 - - + -
528A GLN 4.7 17.0 - - - +
530A VAL* 4.3 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PRO* 3.7 34.8 - - + -
448A VAL* 2.7 22.6 + - + +
450A ASP* 4.0 14.6 - - + +
454A VAL* 3.7 31.0 - - + +
455A ILE* 1.3 79.1 - - - +
457A GLY* 1.3 55.2 + - - +
483A ILE* 3.8 13.1 - - + +
485A LYS* 3.6 18.5 - - - +
487A PHE* 3.9 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A PRO* 3.4 2.1 - - - +
448A VAL* 2.9 26.9 + - - +
455A ILE* 3.6 6.2 - - - +
456A LEU* 1.3 81.8 - - - +
458A MET* 1.3 75.8 + - - +
483A ILE* 3.8 4.6 - - - +
484A TYR 3.3 12.1 - - - -
487A PHE* 3.8 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN* 5.1 4.0 - - - +
446A ALA 3.8 6.7 - - - +
447A PRO* 3.6 26.7 - - + -
448A VAL* 4.1 1.3 - - - +
457A GLY* 1.3 85.4 - - - +
459A VAL* 1.3 72.3 + - - +
460A THR* 4.9 1.6 - - + -
483A ILE* 3.8 3.2 - - - +
484A TYR* 2.7 43.3 + - + +
486A GLN 5.9 0.2 - - - +
487A PHE* 5.2 3.4 - - + -
508A PHE* 3.7 43.5 - - + -
510A LEU* 3.4 38.4 - - + -
533A VAL* 4.0 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL* 5.8 1.8 - - + -
434A THR* 5.3 4.0 - - + -
438A LEU* 4.9 2.1 - - + +
445A GLN* 3.4 3.1 - - - +
446A ALA* 2.9 39.5 + - + +
448A VAL* 3.7 10.8 - - + -
458A MET* 1.3 80.9 - - - +
460A THR* 1.3 69.2 + - - +
463A ASN* 6.3 0.2 - - - +
464A MET* 3.4 40.8 - - + -
479A VAL* 3.5 27.4 - - + +
482A VAL* 4.4 7.6 - - + +
483A ILE* 3.7 17.7 - - - +
484A TYR* 4.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 5.1 0.7 - - - -
444A ASN 3.8 6.5 - - - -
445A GLN* 4.0 20.6 - - + +
458A MET* 4.9 0.4 - - + -
459A VAL* 1.3 82.1 - - - +
461A LEU* 1.3 65.0 + - - +
462A GLY 4.2 2.2 - - - -
463A ASN* 3.2 17.3 + - - +
464A MET* 3.2 23.2 + - - +
484A TYR* 3.6 16.2 + - + -
508A PHE* 4.1 8.1 - - + -
201C GLU* 2.9 45.4 + - + +
----------------------------------------------------------
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