Contacts of the helix formed by residues 384 - 398 (chain C) in PDB entry 6E7P
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 ASP 384 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B TYR* 2.6 39.7 + - - -
487B SER* 3.6 19.1 + - - -
489B LEU* 5.3 5.8 - - + +
490B VAL* 3.6 18.6 - - + +
382C SER* 3.1 1.4 - - - +
383C TYR* 1.3 85.2 - - - +
385C VAL* 1.3 66.1 + - + +
386C CYS 3.4 0.7 - - - -
387C SER* 2.6 22.1 + - - -
388C ILE* 3.0 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B LEU* 4.8 14.8 - - + -
371C MET* 4.8 16.2 - - + -
382C SER* 3.5 20.5 + - - +
384C ASP* 1.3 79.7 - - + +
386C CYS* 1.3 62.1 + - - +
387C SER 3.3 0.5 + - - -
388C ILE* 4.4 4.2 - - - +
389C LEU* 3.3 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 4.3 16.8 - - + -
368C GLY 4.8 2.6 - - - +
371C MET* 3.7 40.2 - - + +
372C LYS* 4.6 6.1 - - + +
380C LEU* 5.9 2.0 - - + -
382C SER 3.2 23.5 + - - +
383C TYR* 3.8 25.1 - - - -
385C VAL* 1.3 78.1 - - - +
387C SER* 1.3 61.9 + - - +
389C LEU* 4.4 4.7 - - - +
390C LEU* 3.3 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ILE* 3.7 37.2 - - - +
446B VAL* 4.0 9.7 + - - +
83C PHE* 4.9 7.6 - - - -
87C ASN* 5.9 2.7 - - - -
383C TYR 3.4 13.8 + - - -
384C ASP* 2.6 29.3 + - - -
386C CYS* 1.3 81.6 - - - +
388C ILE* 1.3 68.9 + - - +
389C LEU 3.3 1.3 - - - -
390C LEU* 3.5 2.2 + - - -
391C GLY* 3.2 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B VAL* 4.1 25.1 - - + -
489B LEU* 3.8 35.2 - - + +
490B VAL* 5.0 7.9 - - + -
493B PHE* 4.0 31.4 - - + -
384C ASP* 3.0 17.5 + - - +
385C VAL* 4.5 3.1 - - - +
387C SER* 1.3 83.5 + - - +
389C LEU* 1.3 62.5 + - + +
392C THR* 2.7 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C LEU* 4.1 38.0 - - + +
367C SER* 4.0 22.7 - - - +
368C GLY* 4.1 22.2 - - - +
371C MET* 5.5 5.4 - - + -
385C VAL* 3.3 32.7 + - + +
386C CYS* 4.6 2.7 - - - +
387C SER 3.3 0.6 - - - -
388C ILE* 1.3 82.3 - - + +
390C LEU* 1.3 62.8 + - - +
393C SER* 3.2 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ILE* 5.6 2.9 - - + -
76C VAL* 6.0 3.1 - - + -
79C GLN* 4.9 10.3 - - + +
80C LEU* 4.5 12.8 - - + -
83C PHE* 4.3 26.9 - - + -
365C THR* 4.5 8.3 - - + +
368C GLY* 4.1 8.1 - - - +
369C THR* 3.8 33.9 - - + +
372C LYS* 4.5 20.9 - - + -
386C CYS 3.3 21.0 + - - +
387C SER* 3.5 4.6 + - - +
388C ILE 3.3 0.4 - - - -
389C LEU* 1.3 75.6 - - - +
391C GLY* 1.3 62.1 + - - +
393C SER* 2.5 23.7 + - - +
394C THR* 3.0 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B PHE 5.1 0.4 - - - -
442B CYS* 3.6 29.4 - - - +
445B ILE* 5.2 4.0 - - - +
446B VAL* 5.1 1.6 - - - -
80C LEU* 4.5 10.5 - - - +
387C SER 3.2 15.9 + - - -
388C ILE 4.0 0.7 - - - -
390C LEU* 1.3 74.8 - - - +
392C THR* 1.3 54.7 + - - +
394C THR* 3.1 2.6 + - - -
395C LEU* 2.7 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B CYS* 4.0 2.4 - - - -
493B PHE* 3.9 17.5 - - + -
364C LEU* 4.2 19.7 - - + -
388C ILE* 2.7 34.4 + - - +
391C GLY* 1.3 72.7 - - - +
393C SER* 1.3 64.6 + - - +
395C LEU* 3.7 14.9 + - + +
396C LEU* 3.2 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 4.4 6.6 - - - +
361C SER* 4.4 15.6 - - - +
364C LEU* 4.5 6.1 - - - +
365C THR* 3.3 29.0 + - - -
389C LEU 3.2 15.4 + - - -
390C LEU* 2.5 28.1 + - - +
392C THR* 1.3 76.8 - - - +
394C THR* 1.3 56.9 + - - +
396C LEU* 2.8 5.4 + - - +
397C VAL* 2.5 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B GLY* 4.7 2.6 - - - +
441B PHE* 4.2 18.6 - - + -
76C VAL* 3.7 16.2 - - + +
77C THR* 4.4 9.6 - - - +
80C LEU* 3.3 27.0 - - + +
390C LEU 3.0 15.9 + - - -
391C GLY* 3.1 4.3 + - - -
393C SER* 1.3 83.0 + - - +
395C LEU* 1.3 62.2 + - - +
397C VAL* 4.2 7.6 - - + +
398C TRP* 3.2 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 5.1 0.4 - - + +
438B GLY* 3.5 33.2 + - - +
439B TYR* 3.7 41.7 - - + +
442B CYS* 3.8 22.6 - - + +
493B PHE* 5.5 2.9 - - + -
497B TYR* 5.0 3.4 - - + -
391C GLY 2.7 21.2 + - - +
392C THR* 3.8 14.6 - - + +
394C THR* 1.3 73.0 - - - +
396C LEU* 1.3 57.8 + - + +
398C TRP* 4.7 1.4 - - - +
399C VAL* 3.4 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C LEU* 3.3 62.4 - - + +
358C LEU* 5.5 0.2 - - - +
360C THR* 4.4 15.0 - - + -
361C SER* 3.7 21.5 - - - +
364C LEU* 6.4 1.6 - - + -
392C THR* 3.2 23.8 + - + +
393C SER* 2.8 3.4 + - - +
395C LEU* 1.3 76.6 - - + +
397C VAL* 1.3 64.1 + - - +
398C TRP 3.5 0.2 - - - -
399C VAL* 3.3 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLN* 5.0 6.1 - - - +
72C LYS* 4.7 26.9 - - + +
73C ILE* 3.7 27.7 - - + +
76C VAL* 5.0 12.1 - - + -
357C LEU* 5.6 0.2 - - - -
358C LEU* 5.4 6.8 - - + +
361C SER* 3.8 24.7 - - - +
365C THR* 5.0 3.4 - - - +
393C SER* 2.5 36.1 + - - +
394C THR* 4.2 7.6 - - + +
396C LEU* 1.3 71.7 - - - +
398C TRP* 1.3 62.7 + - + +
400C GLY* 2.9 22.2 + - - -
401C VAL 4.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 3.3 52.5 - - + +
437B LEU* 4.9 22.0 - - + -
438B GLY* 4.5 12.3 - - - -
441B PHE* 4.4 22.6 - + - -
73C ILE* 4.1 26.6 + - + +
77C THR* 3.1 30.1 + - + -
394C THR* 3.2 38.4 + - + +
395C LEU 4.7 0.7 - - - +
397C VAL* 1.3 85.1 - - + +
399C VAL* 1.3 60.6 + - + +
400C GLY 3.3 0.7 + - - -
401C VAL* 3.3 22.4 + - + +
----------------------------------------------------------
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