Contacts of the helix formed by residues 386 - 398 (chain C) in PDB entry 3K6G
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 GLY 386 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C TYR* 3.5 23.5 - - - -
382C VAL* 2.7 26.2 + - - -
385C PHE* 1.3 77.3 - - - +
387C ALA* 1.3 65.1 + - - -
388C GLN* 3.3 3.7 + - - -
389C ASN 3.3 1.0 + - - -
390C VAL* 3.2 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C VAL* 3.8 23.5 - - + +
386C GLY* 1.3 70.8 - - - -
388C GLN* 1.3 65.2 + - + +
390C VAL* 3.4 6.6 + - - +
391C ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLY 3.3 1.0 - - - -
387C ALA* 1.3 77.0 - - + +
389C ASN* 1.3 66.9 + - - +
391C ALA* 3.4 6.4 + - - +
392C ARG* 3.0 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C SER* 5.1 0.7 + - - -
342C GLU* 4.4 1.7 - - - +
355C ARG* 3.3 22.6 + - - +
357C ASP* 3.0 21.6 + - - +
359C TYR* 3.3 17.0 - - - +
360C PRO 5.5 0.2 + - - -
362C TRP* 3.7 13.3 + - - +
385C PHE* 2.8 36.5 + - + +
386C GLY 3.3 2.6 + - - -
388C GLN* 1.3 78.9 - - - +
390C VAL* 1.3 56.1 + - - +
392C ARG* 3.3 25.0 + - - +
393C ARG* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C TRP* 4.1 9.6 - - + -
370C LEU* 3.9 20.0 - - + -
378C ARG* 4.1 18.4 - - - +
381C LEU* 3.6 34.5 - - + +
382C VAL* 4.0 9.2 - - + +
385C PHE* 4.1 7.2 - - + -
386C GLY 3.2 14.5 + - - +
387C ALA* 3.7 9.0 - - - +
388C GLN 3.2 0.2 - - - -
389C ASN* 1.3 74.3 - - - +
391C ALA* 1.3 66.5 + - - +
393C ARG* 3.0 3.8 + - - +
394C ILE* 3.0 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C ALA 3.1 16.1 + - - +
388C GLN* 3.7 6.5 - - - +
390C VAL* 1.3 77.9 - - - +
392C ARG* 1.3 64.1 + - + +
394C ILE* 3.3 11.6 + - - +
395C GLU* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C SER* 4.6 11.7 - - - -
342C GLU* 3.3 30.5 + - + -
355C ARG* 4.8 2.2 - - - +
357C ASP* 5.2 1.8 + - - -
388C GLN* 3.0 56.1 + - - +
389C ASN* 3.3 23.4 + - - +
391C ALA* 1.3 77.0 - - + +
393C ARG* 1.3 58.2 + - - +
395C GLU* 3.5 6.7 + - - +
396C PHE* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C LEU 2.7 30.5 + - - -
338C LYS* 4.1 4.8 - - - +
340C SER* 3.0 29.5 + - - +
362C TRP* 3.4 47.0 - - + +
367C ASP* 2.8 37.0 + - - +
370C LEU* 3.6 19.5 - - + -
389C ASN 2.9 18.1 + - - +
390C VAL 3.0 4.2 + - - +
392C ARG* 1.3 75.2 - - - +
394C ILE* 1.3 66.2 + - - +
396C PHE* 3.6 10.7 - - - +
397C ARG* 3.0 47.0 + - - +
309F ASP* 4.7 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LEU* 3.9 22.2 - - + -
371C GLN* 5.5 6.4 + - - +
378C ARG* 3.8 31.9 - - - +
390C VAL* 3.0 27.1 + - + +
391C ALA* 3.3 11.2 + - - +
393C ARG* 1.3 74.2 - - - +
395C GLU* 1.3 62.5 + - - +
397C ARG* 3.5 2.3 + - - +
398C LYS* 3.1 57.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ALA 3.1 15.7 + - - +
392C ARG* 3.7 6.7 - - - +
394C ILE* 1.3 79.9 - - - +
396C PHE* 1.3 63.3 + - - +
398C LYS* 3.3 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C PHE 4.3 3.1 - - - -
337C LEU* 3.7 25.4 - - + -
340C SER* 3.4 33.0 - - - +
341C GLY* 3.6 9.6 - - - -
392C ARG 2.9 18.6 + - - +
393C ARG* 3.6 20.6 - - - +
395C GLU* 1.3 80.8 - - - +
397C ARG* 1.3 66.4 + - + +
398C LYS 3.7 3.1 + - - +
282F THR* 5.0 3.4 - - + -
283F ILE 3.5 12.3 - - - -
284F GLY* 4.6 2.0 - - - -
285F MSE 3.3 77.9 + - + +
288F LEU* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ARG* 3.7 14.3 - - - +
367C ASP* 3.5 37.7 + - - +
370C LEU* 5.1 4.3 - - + -
371C GLN* 5.2 13.0 - - - +
393C ARG* 3.0 38.7 + - - +
394C ILE* 3.9 2.0 - - - +
396C PHE* 1.3 85.6 - - + +
398C LYS* 1.3 65.9 + - - +
285F MSE 2.9 30.1 - - + +
309F ASP* 2.8 43.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ILE* 3.1 43.6 + - + +
395C GLU* 3.3 26.3 + - - +
396C PHE 4.4 3.1 - - - +
397C ARG* 1.3 82.8 - - - +
----------------------------------------------------------
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