Contacts of the strand formed by residues 342 - 347 (chain D) in PDB entry 1KHU
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 GLU 342 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D TYR 3.6 1.6 - - - +
338D TYR* 3.7 4.5 - - - -
339D VAL 3.1 31.5 + - - +
340D GLY 3.3 7.2 - - - +
341D GLY* 1.3 85.9 - - - +
343D VAL* 1.3 64.9 + - - +
344D TYR* 2.4 39.5 + - + -
381D LYS* 3.0 28.2 + - + -
383D PHE* 3.2 14.6 - - - +
384D ASN* 3.1 21.9 - - - +
385D ASN* 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D TRP* 3.8 23.1 - - + -
337D TYR 3.2 7.2 - - - +
338D TYR* 3.7 23.6 - - + -
342D GLU* 1.3 78.4 - - - +
344D TYR* 1.3 61.5 + - - +
381D LYS* 3.6 4.9 - - - +
382D ILE* 3.0 48.2 + - + -
383D PHE* 3.0 33.4 + - + -
385D ASN* 5.7 0.7 - - - +
412D ILE* 4.5 3.6 - - + -
440D LEU* 4.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D TRP* 5.8 0.2 - - - -
335D HIS 4.3 0.4 - - - -
336D LEU* 3.6 6.4 - - - +
337D TYR* 2.9 55.3 + + + +
339D VAL* 4.0 17.0 - - + -
342D GLU* 2.4 45.6 + - + -
343D VAL* 1.3 75.1 - - - +
345D ALA* 1.3 62.7 + - - +
346D GLU* 6.3 0.2 - - + -
379D SER* 4.5 12.6 - - - +
380D LEU 3.3 9.2 - - - +
381D LYS* 3.5 37.2 + - + -
382D ILE* 4.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D VAL* 4.3 3.6 - - + -
335D HIS 3.3 6.1 - - - +
336D LEU* 4.3 2.2 - - + -
344D TYR* 1.3 75.7 - - - +
346D GLU* 1.3 61.5 + - - +
347D CYS 4.3 0.3 + - - -
374D ILE* 4.0 20.0 - - + +
378D CYS 4.2 0.2 - - - +
379D SER* 3.4 5.5 - - - -
380D LEU* 2.8 29.0 + - - +
382D ILE* 3.7 31.2 - - + -
414D MET* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D VAL* 3.2 4.8 - - - +
335D HIS* 2.8 62.7 + - + +
344D TYR* 6.3 0.4 - - + -
345D ALA* 1.3 74.3 - - - +
347D CYS* 1.3 62.1 + - - +
348D LEU* 2.8 26.1 + - + +
377D GLY* 4.9 7.5 - - - +
378D CYS 3.5 14.4 - - - +
379D SER* 4.4 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D GLY 4.0 2.7 - - - -
334D VAL* 4.6 0.4 - - - -
346D GLU* 1.3 71.3 - - - +
348D LEU* 1.3 61.0 + - - +
349D SER* 3.9 8.3 - - - -
351D SER 3.0 28.5 - - - -
353D ILE* 4.0 22.7 - - + -
374D ILE* 3.6 28.3 - - + +
375D PRO 3.4 17.0 - - - +
376D SER* 3.9 8.7 - - - -
377D GLY* 2.9 31.4 + - - +
378D CYS 3.2 7.3 + - - -
----------------------------------------------------------
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