Contacts of the strand formed by residues 554 - 559 (chain D) in PDB entry 3K0J
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 GLN 554 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513D TYR* 2.4 41.1 + - + +
514D ILE 3.4 6.3 - - - -
515D ASN* 3.9 6.5 + - + -
517D LEU* 5.0 2.3 - - - +
526D LEU* 5.5 2.4 - - - +
545D VAL* 4.4 6.9 - - - +
551D MET* 3.1 52.7 - - + +
552D ARG 3.4 5.3 - - - +
553D GLY* 1.3 88.5 + - - +
555D ALA* 1.3 66.0 + - - +
556D PHE* 5.9 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 555 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513D TYR* 3.4 5.9 - - - -
514D ILE* 2.8 32.5 + - + +
517D LEU* 4.2 10.1 - - + -
526D LEU* 5.7 0.9 - - + -
530D LEU* 3.8 21.5 - - + -
544D LEU 3.5 14.1 - - - +
545D VAL* 3.6 14.6 - - + -
551D MET* 4.0 5.2 - - - -
554D GLN* 1.3 78.9 - - - +
556D PHE* 1.3 66.7 + - - +
557D VAL* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 556 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511D THR* 4.3 17.9 - - + -
512D ILE 3.2 7.0 - - - +
513D TYR* 3.1 49.8 - + + -
543D ILE* 3.2 8.5 - - - +
544D LEU* 2.9 45.4 + - + -
551D MET* 4.2 20.4 - - + -
554D GLN* 5.4 0.9 - - + -
555D ALA* 1.3 79.7 - - - +
557D VAL* 1.3 64.2 + - - +
558D ILE* 4.1 5.2 - - + -
587D ALA* 4.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 557 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511D THR* 3.5 1.4 - - - -
512D ILE* 2.8 47.6 + - + +
514D ILE* 4.3 6.3 - - + -
530D LEU* 4.8 5.2 - - + -
534D PHE* 3.7 34.8 - - + -
540D ILE* 3.9 21.8 - - + -
542D ASP 3.6 2.2 - - - -
543D ILE* 3.9 15.9 - - + -
555D ALA 5.6 0.4 - - - -
556D PHE* 1.3 78.5 - - - +
558D ILE* 1.3 62.9 + - - +
559D PHE* 3.6 29.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 558 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510D HIS* 4.0 12.6 - - + -
511D THR* 3.5 33.7 - - + +
540D ILE* 3.5 3.1 - - - -
541D LEU* 2.7 43.8 + - + -
542D ASP* 2.7 40.7 + - + +
544D LEU* 5.9 6.3 - - + +
556D PHE* 5.2 5.6 - - + +
557D VAL* 1.3 72.1 - - - +
559D PHE* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 559 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510D HIS* 2.8 39.3 + - - +
512D ILE* 3.5 27.4 - - + -
534D PHE* 3.8 19.3 - - + -
537D PHE* 3.8 22.4 - - + -
538D GLY 4.7 0.2 - - - -
539D GLN 3.8 14.4 - - - -
540D ILE* 4.2 10.8 - - + -
541D LEU* 3.6 7.9 - - - +
557D VAL* 3.6 24.0 - - + -
558D ILE* 1.3 75.4 - - - +
560D LYS* 1.3 60.0 + - - +
561D GLU 3.3 16.4 - - - +
564D SER* 3.7 14.8 - - - -
565D ALA* 3.3 25.8 - - + -
568D ALA* 3.8 18.4 - - + -
----------------------------------------------------------
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