Contacts of the helix formed by residues 384 - 389 (chain F) in PDB entry 1K9V
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 CYS 384 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F GLY 3.0 14.4 - - - +
383F VAL* 1.3 79.4 - - + +
385F LEU* 1.3 66.3 + - - +
387F MET* 2.9 19.6 + - - +
388F GLN* 3.5 2.9 + - - +
475F PHE 2.7 18.1 + - - -
476F GLN* 3.7 10.6 + - - -
477F PHE 3.8 11.4 - - - -
478F HIS* 2.9 52.7 - - - -
1001F ACY 3.0 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 385 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F PRO* 4.5 7.9 - - + -
349F PRO 5.5 0.2 - - - +
350F GLY* 3.1 16.8 + - - +
351F VAL* 3.9 6.7 - - - +
352F GLY* 3.5 43.1 - - - +
353F HIS 3.8 9.0 - - - +
354F PHE* 3.8 22.4 - - - +
357F GLY* 4.1 17.0 - - - +
384F CYS* 1.3 80.8 - - - +
386F GLY* 1.3 56.7 + - - +
388F GLN* 3.0 25.1 + - + +
389F LEU* 2.9 34.3 + - + +
396F GLU* 4.8 0.2 - - - +
1001F ACY 3.4 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 386 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348F ILE* 3.1 33.1 - - - +
349F PRO 3.8 10.1 + - - -
382F GLY* 3.7 8.4 - - - -
383F VAL 2.9 5.9 + - - -
385F LEU* 1.3 78.1 - - - +
387F MET* 1.3 61.5 + - - +
389F LEU* 3.4 15.3 + - - +
390F LEU* 3.5 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 387 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F GLY* 3.6 24.7 - - - +
384F CYS 2.9 13.0 + - - +
386F GLY* 1.3 77.6 - - - +
388F GLN* 1.3 61.3 + - + +
390F LEU* 3.1 22.0 - - - +
391F PHE* 3.6 6.0 - - + -
445F ALA* 4.0 24.2 - - + -
464F PRO 3.4 24.0 - - - +
465F SER 3.8 2.2 - - - +
467F VAL* 4.0 18.4 - - + -
474F GLY* 3.4 27.6 - - - +
475F PHE 3.7 5.4 - - - +
476F GLN* 3.2 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 388 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354F PHE* 3.3 22.6 - - + -
384F CYS 3.5 1.5 + - - +
385F LEU* 3.0 21.6 + - + +
387F MET* 1.3 77.2 - - + +
389F LEU* 1.3 58.0 + - - +
390F LEU 2.9 10.1 + - - -
391F PHE* 2.9 20.4 + - - +
394F SER* 5.1 0.3 + - - -
396F GLU* 4.5 6.9 - - - +
410F VAL* 3.7 36.9 - - + +
443F TYR* 3.1 35.5 + - - +
444F ARG 5.1 2.7 - - - -
445F ALA* 5.2 2.5 - - + +
476F GLN* 3.2 28.5 + - - +
1001F ACY 3.8 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348F ILE* 4.4 6.1 - - + -
349F PRO 5.1 3.4 - - - +
354F PHE* 3.6 38.8 - - + +
357F GLY* 4.0 18.2 - - - +
358F MET* 3.5 22.4 - - + +
361F LEU* 3.9 25.6 - - + -
385F LEU* 2.9 23.9 + - + +
386F GLY* 3.6 18.4 - - - +
387F MET 3.3 0.4 - - - -
388F GLN* 1.3 76.6 - - - +
390F LEU* 1.3 58.9 + - - +
391F PHE 3.2 1.6 - - - +
403F LEU* 2.8 44.8 + - + +
----------------------------------------------------------
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