Contacts of the strand formed by residues 411 - 416 (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 THR 411 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D GLN 4.6 3.1 - - - +
357D SER* 5.2 1.9 - - - -
358D ARG 5.3 2.1 + - - -
407D THR* 4.2 11.7 - - + +
408D LYS* 3.5 21.9 + - - +
409D MET 3.3 2.3 - - - +
410D CYS* 1.3 83.8 - - + +
412D ILE* 1.3 65.5 + - - +
413D ARG* 4.4 4.3 + - - +
437D GLU* 4.3 17.3 + - - +
438D ILE 3.0 6.7 - - - -
439D HIS* 3.3 40.6 - - + +
444D LEU* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 412 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D VAL* 4.5 1.6 - - + -
355D VAL* 3.5 30.5 - - + -
356D GLN 3.7 6.3 - - - +
357D SER* 3.3 26.9 - - - +
382D ILE* 3.6 35.9 - - + +
383D PHE* 4.2 9.0 - - + -
409D MET 5.0 2.0 - - - +
411D THR* 1.3 80.5 - - - +
413D ARG* 1.3 66.9 + - - +
414D MET* 4.6 5.6 - - + -
437D GLU* 3.5 0.7 - - - -
438D ILE* 2.7 51.6 + - + +
440D LEU* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 413 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D VAL* 3.5 2.1 - - - +
356D GLN* 2.8 48.9 + - + +
411D THR* 4.4 5.5 + - - +
412D ILE* 1.3 82.2 - - - +
414D MET* 1.3 64.6 + - - +
420D TRP* 4.2 5.8 - - + -
428D ASP* 5.9 0.6 + - - -
429D VAL* 3.8 34.9 - - + +
430D THR* 5.4 3.4 - - - +
435D TRP* 4.3 14.6 - - + -
436D ILE 3.3 6.5 - - - +
437D GLU* 2.8 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 414 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D VAL* 4.0 30.3 - - - -
336D LEU* 3.8 24.5 - - + -
345D ALA* 4.1 4.7 - - + -
353D ILE* 4.2 9.2 - - + -
354D PHE 2.8 17.9 - - - +
355D VAL* 3.3 35.7 - - + -
382D ILE* 4.1 14.6 - - + -
412D ILE* 4.6 1.8 - - + -
413D ARG* 1.3 76.6 - - - +
415D SER* 1.3 60.3 + - - +
416D PHE* 5.3 3.0 - - + -
420D TRP* 4.5 3.3 - - - -
429D VAL* 5.1 0.4 - - - +
435D TRP* 3.3 3.8 - - - +
436D ILE* 2.9 51.4 + - + +
438D ILE* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 415 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D ILE* 3.4 6.3 - - - +
354D PHE* 2.8 34.8 + - - +
414D MET* 1.3 74.2 - - - +
416D PHE* 1.3 64.0 + - - +
417D VAL 3.8 0.2 + - - -
418D LYS 2.5 28.0 + - - -
420D TRP* 3.7 18.7 - - - -
432D THR* 3.5 22.6 - - - +
434D CYS 3.4 12.1 - - - -
435D TRP* 3.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D TYR* 4.8 1.1 - + - -
296D VAL* 3.8 33.0 - - + -
311D LEU* 3.8 20.6 - - + -
326D THR* 3.7 8.5 - - - +
330D ILE* 3.6 49.1 - - + -
333D GLY* 4.1 4.3 - - - -
334D VAL* 4.1 9.0 - - + -
349D SER* 5.7 1.3 - - - -
353D ILE* 3.7 31.2 - - + -
414D MET* 5.3 2.2 - - + -
415D SER* 1.3 74.3 + - - +
417D VAL* 1.3 63.3 + - + +
418D LYS* 2.8 17.5 + - - +
432D THR* 5.8 0.2 - - - -
434D CYS* 2.9 30.1 + - + +
435D TRP* 4.7 1.3 - - - -
436D ILE* 4.1 22.2 - - + -
----------------------------------------------------------
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