Contacts of the strand formed by residues 448 - 455 (chain B) in PDB entry 1KEK
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 PHE 448 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLN* 5.4 4.5 - - - +
182B LYS* 4.7 21.5 - - + -
446B ASP 4.5 7.2 - - - -
447B LEU* 1.3 79.8 - - - +
449B ALA* 1.3 59.4 + - - +
470B PHE* 3.2 5.2 - - - -
471B GLY 2.7 33.1 + - - +
472B GLU 3.4 21.3 - - - -
473B LYS 3.2 26.2 - - - +
474B PRO* 3.6 33.9 - - + -
475B ILE* 3.8 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 5.3 0.2 - - + -
181B GLN* 3.2 11.1 + - - +
182B LYS* 3.2 34.8 + - + +
438B ILE* 4.0 25.1 - - + +
441B ILE* 5.4 0.2 - - + -
442B GLY* 5.0 7.6 - - - -
447B LEU 4.2 1.1 + - - +
448B PHE* 1.3 77.3 - - - +
450B GLN* 1.3 61.2 - - - +
469B ARG 3.4 4.5 - - - -
470B PHE* 3.6 26.5 - - + -
475B ILE* 3.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 3.9 5.5 - - - +
179B GLU* 3.1 34.5 + - + +
180B ILE 3.1 7.9 - - - +
181B GLN* 3.7 18.2 + - - +
438B ILE* 4.3 6.6 - - - +
449B ALA* 1.3 78.3 - - - +
451B GLY* 1.3 63.5 + - - +
452B TYR* 5.7 1.1 - - - -
467B HIS 3.8 2.8 - - - +
468B LEU* 3.3 7.3 - - - +
469B ARG* 2.7 71.4 + - + +
475B ILE* 3.8 17.4 + - + +
476B GLN 5.3 0.2 - - - -
477B SER 3.0 26.5 + - - +
478B THR* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B HIS 4.2 0.3 - - - +
179B GLU* 3.5 4.5 - - - +
180B ILE* 2.8 36.4 + - - +
438B ILE* 3.8 19.1 - - - +
450B GLN* 1.3 78.2 - - - +
452B TYR* 1.3 63.6 - - - +
453B PHE* 4.2 8.5 - - - -
467B HIS 3.4 6.3 - - - -
468B LEU* 3.9 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 5.1 4.9 - - - -
174B PHE* 3.4 48.4 - + + +
175B ARG* 3.5 41.7 + - - +
178B HIS* 4.6 6.5 - - + -
179B GLU* 4.3 10.8 - - - -
367B SER* 4.8 8.1 + - - -
450B GLN* 5.7 1.8 - - - -
451B GLY* 1.3 76.2 - - - +
453B PHE* 1.3 85.6 + - - +
454B SER* 4.6 6.1 - - - -
466B SER* 3.7 0.3 - - - -
467B HIS* 2.8 42.9 + - + +
480B LEU* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE* 5.6 5.2 - - - -
178B HIS* 5.0 7.1 + - - +
180B ILE* 4.2 12.6 - - + -
431B VAL* 3.9 20.2 - - + -
434B ASN* 3.8 19.7 - - + -
435B LYS* 3.9 38.6 - - + -
438B ILE* 4.6 4.9 - - + -
451B GLY 4.2 4.5 - - - -
452B TYR* 1.3 100.7 + - - +
454B SER* 1.3 61.4 + - - +
455B TYR* 3.6 32.6 - - + +
464B THR* 4.7 0.9 - - + -
465B ILE 3.7 2.2 - - - +
466B SER* 3.3 34.1 - - - -
468B LEU* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B TYR* 4.6 10.7 - - - -
453B PHE* 1.3 73.1 - - - +
455B TYR* 1.3 63.3 + - - +
463B ILE 4.1 0.2 - - - +
464B THR* 3.3 6.9 - - - +
465B ILE* 2.8 48.3 + - - +
467B HIS* 4.5 13.9 - - - -
480B LEU* 5.3 5.5 - - - +
649B GLN* 5.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ASN* 5.6 4.7 + - - +
1198A ASP 5.9 0.7 - - - -
1199A ASP* 3.5 27.1 - - - +
1200A THR 3.9 4.5 - - - -
1201A PRO* 3.7 37.9 - - + +
1204A ALA* 3.6 28.9 - - + +
1208A SER* 4.5 5.4 + - - -
1209A GLY* 5.8 0.5 - - - -
124B PHE* 5.8 1.2 - - - -
174B PHE* 6.0 1.3 - + - -
178B HIS* 6.2 1.8 - + - -
431B VAL* 3.5 26.8 - - + +
435B LYS* 4.5 3.5 + - - -
453B PHE* 3.6 32.7 - - + +
454B SER* 1.3 76.3 + - - +
456B ASP* 1.3 62.2 + - - +
463B ILE* 3.7 6.5 - - - -
464B THR* 3.7 22.0 - - + +
----------------------------------------------------------
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