Contacts of the strand formed by residues 376 - 385 (chain B) in PDB entry 1K8F
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 376 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B CYS 3.0 5.9 + - - +
357B VAL* 2.9 25.6 - - + +
358B ASN 2.8 18.2 + - - -
375B CYS* 1.3 73.5 - - - +
377B LYS* 1.3 100.8 + - + +
378B LEU 3.1 2.7 + - - -
395B LYS* 3.3 28.4 - - + +
396B ASP* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B VAL* 5.5 0.9 - - + -
358B ASN* 3.1 39.4 - - + +
359B THR 3.3 5.4 + - - +
376B LYS* 1.3 108.3 - - + +
378B LEU* 1.3 59.3 + - - +
395B LYS 3.0 12.3 + - - -
396B ASP* 3.2 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ILE* 3.5 28.3 - - + -
356B CYS* 3.5 22.9 - - + +
359B THR* 3.4 17.7 - - + +
361B LEU* 5.6 4.9 - - + +
372B VAL* 3.8 33.9 - - + -
375B CYS* 3.8 18.2 - - + -
376B LYS 4.0 1.3 - - - +
377B LYS* 1.3 77.6 - - - +
379B GLY* 1.3 63.8 + - - +
380B LEU* 4.0 18.2 - - + -
395B LYS 4.6 0.2 + - - -
396B ASP 3.3 5.2 + - - +
397B VAL* 3.4 11.1 - - + +
398B LYS* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B THR 2.8 14.4 + - - +
360B THR* 3.2 13.9 + - - +
361B LEU* 2.7 33.8 + - - +
377B LYS 4.0 0.2 + - - -
378B LEU* 1.3 77.0 - - - +
380B LEU* 1.3 53.9 + - - -
381B VAL* 4.9 1.1 - - - +
398B LYS* 3.7 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ILE* 4.4 1.8 - - + -
361B LEU* 3.3 32.1 - - + +
363B ILE* 4.0 15.5 - - + -
370B ILE* 3.9 30.7 - - + -
372B VAL* 4.1 15.7 - - + -
378B LEU* 4.0 15.0 - - + -
379B GLY* 1.3 73.2 - - - +
381B VAL* 1.3 81.3 + - - +
382B PHE* 4.3 5.6 - - + +
389B VAL* 4.9 2.5 - - + -
398B LYS* 2.8 24.3 + - - +
399B VAL* 3.5 20.9 - - + -
400B GLN 3.0 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B THR* 5.6 5.2 - - + -
361B LEU 3.1 14.5 + - - +
362B GLN* 3.1 31.6 - - + +
363B ILE 3.0 22.3 + - - -
379B GLY 4.9 1.8 - - - +
380B LEU* 1.3 81.2 - - - +
382B PHE* 1.3 62.1 + - - +
383B ASP* 5.6 0.4 - - - +
398B LYS* 4.6 9.2 - - - +
400B GLN* 3.3 23.6 - - + +
402B MET* 4.4 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ILE* 3.4 17.0 - - + +
365B GLY 5.6 0.4 - - - +
367B ILE* 6.3 0.7 - - + -
370B ILE* 3.7 23.1 - - + -
380B LEU* 4.3 5.4 - - + -
381B VAL* 1.3 75.5 - - - +
383B ASP* 1.3 72.1 + - - +
384B ASP 4.1 2.2 - - - +
385B VAL* 3.4 32.8 - - + -
389B VAL* 3.6 20.4 - - + -
399B VAL* 3.5 32.1 - - + -
400B GLN 2.9 20.5 + - - +
401B VAL* 3.3 30.5 - - + -
402B MET* 3.0 28.3 + - - +
405B VAL* 3.9 11.9 - - + -
408B ILE* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLN* 4.9 7.6 - - - +
363B ILE 3.4 8.1 + - - +
364B LYS* 3.9 7.2 - - - +
365B GLY* 3.2 33.9 + - - +
381B VAL* 5.6 0.5 - - - +
382B PHE* 1.3 82.4 - - - +
384B ASP* 1.3 71.1 + - - +
401B VAL* 3.9 4.0 - - - +
402B MET* 3.7 23.0 + - + +
403B GLY* 2.8 28.0 + - - +
404B LYS 3.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B GLY 3.5 3.6 + - - +
366B LYS* 3.4 39.3 + - + +
367B ILE* 3.3 20.3 + - - +
382B PHE* 4.2 2.2 - - - +
383B ASP* 1.3 92.9 - - - +
385B VAL* 1.3 68.8 + - - +
403B GLY* 4.1 5.9 - - - -
404B LYS* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 4.7 3.9 + - - -
367B ILE* 3.3 9.0 - - + +
368B ASN 3.3 17.0 - - - +
369B SER* 3.9 1.3 - - - -
370B ILE* 3.9 17.5 - - + -
382B PHE* 3.4 30.9 - - + -
384B ASP* 1.3 79.4 - - - +
386B VAL* 1.3 65.3 + - - +
387B GLY 3.4 20.9 - - - +
388B ILE 3.8 14.4 - - - +
389B VAL* 3.8 11.0 - - + -
404B LYS* 3.1 10.9 + - - +
405B VAL* 4.0 6.7 - - + -
406B PRO* 3.4 15.2 - - - +
----------------------------------------------------------
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