Contacts of the strand formed by residues 459 - 466 (chain B) in PDB entry 4ICU
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 459 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LYS* 3.8 45.3 - - + +
450B ILE 3.5 9.0 - - - +
451B LYS* 4.7 6.7 - - + +
456B LEU* 5.7 0.7 - - - +
458B GLN* 1.3 79.8 + - - +
460B VAL* 1.3 61.7 + - - +
461B LEU 5.0 1.8 - - - +
494B GLU* 5.9 0.7 - - - -
496B PRO* 6.3 1.4 - - - +
520B GLY 5.7 1.2 + - - -
522B CYS* 4.0 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ILE 2.7 18.5 + - - +
452B TYR* 3.6 46.4 - - + +
456B LEU* 4.8 17.7 - - + -
458B GLN 3.8 13.2 - - - +
459B LYS* 1.3 73.0 - - - +
461B LEU* 1.3 72.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LYS* 3.4 3.5 - - - +
450B ILE* 2.6 52.4 + - + +
452B TYR* 3.4 25.4 - - - +
459B LYS* 3.8 2.1 - - - +
460B VAL* 1.3 93.6 + - + +
462B GLU* 1.3 65.7 + - - +
463B LYS* 3.7 39.9 - - + -
481B LEU* 4.1 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B THR* 3.5 24.2 - - + +
448B LEU 3.4 4.9 - - - +
449B LYS* 3.9 42.1 + - + +
461B LEU* 1.3 79.1 - - - +
463B LYS* 1.3 72.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU 3.4 2.3 - - - +
447B THR* 4.6 1.6 - - - -
448B LEU* 2.8 37.0 + - + +
450B ILE* 3.8 15.5 - - + +
461B LEU* 3.7 23.6 - - + -
462B GLU* 1.3 81.1 - - - +
464B GLN* 1.3 62.9 + - - +
465B LEU* 3.6 21.5 + - + +
477B LEU* 4.2 30.0 - - + +
481B LEU* 5.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B LEU* 3.6 45.5 + - + +
446B LEU 3.3 3.1 - - - +
447B THR* 3.3 30.0 + - + +
463B LYS* 1.3 72.9 - - - +
465B LEU* 1.3 67.5 + - - +
466B PRO* 4.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B LEU* 3.7 3.1 - - - -
446B LEU* 2.8 42.9 + - - +
448B LEU* 4.0 21.5 - - + -
450B ILE* 5.6 2.0 - - + -
463B LYS* 4.0 25.6 - - + +
464B GLN* 1.3 84.3 - - - +
466B PRO* 1.3 68.8 - - + +
469B MET* 3.9 18.8 - - - -
474B VAL* 4.2 24.9 - - + -
477B LEU* 4.0 22.7 - - + -
512B LEU* 3.8 18.2 - - + -
523B LEU* 4.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLN* 3.5 9.2 - - - +
445B LEU* 3.5 18.1 - - + -
464B GLN 4.2 3.1 - - - +
465B LEU* 1.3 85.7 - - + +
467B GLY* 1.3 60.1 + - - +
468B SER* 4.4 12.6 - - - +
469B MET* 3.0 42.6 + - + +
512B LEU* 3.7 4.2 - - - +
----------------------------------------------------------
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