Contacts of the helix formed by residues 355 - 365 (chain C) in PDB entry 6NYY
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 355 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LYS* 1.3 77.6 - - - +
356C LEU* 1.3 53.3 + - - +
357C LEU 3.2 1.1 - - - -
358C ALA* 3.1 7.7 + - - +
359C LYS* 2.8 40.8 + - - +
405C PHE* 4.5 2.6 - - + -
407C ASP* 3.6 24.1 + - - +
801C MG 2.2 30.6 - - - -
803C ANP 2.8 12.1 + - - -
439D ASP* 4.5 2.7 - - - +
440D GLY* 4.0 23.3 - - - -
441D PHE* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C VAL* 3.8 24.9 - - + -
309C ASP* 4.2 5.6 - - + +
310C VAL* 3.8 19.7 - - + -
353C GLY* 3.9 8.7 - - - -
355C THR* 1.3 80.0 - - - +
357C LEU* 1.3 57.1 + - - +
359C LYS* 3.0 22.6 + - + +
360C ALA* 2.9 27.4 + - - +
803C ANP 3.2 74.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C PHE* 4.3 14.8 - - + -
310C VAL* 3.8 20.1 - - + +
313C CYS* 4.6 5.6 - - - -
316C ALA 4.1 11.7 - - - +
317C LYS* 3.8 27.8 - - + +
320C ILE* 3.8 28.9 - - + +
346C LEU* 4.5 7.4 - - + -
353C GLY 3.3 18.6 + - - +
354C LYS* 4.4 4.9 - - - +
355C THR 3.2 0.2 - - - -
356C LEU* 1.3 78.7 - - - +
358C ALA* 1.3 58.6 + - - +
360C ALA* 3.7 1.4 + - - +
361C THR* 3.1 23.2 + - - -
475C ILE* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LEU* 5.0 2.6 - - + +
354C LYS 3.8 4.6 + - - +
355C THR 3.1 11.1 + - - +
357C LEU* 1.3 77.5 - - - +
359C LYS* 1.3 63.2 + - - +
360C ALA 3.2 0.7 - - - -
361C THR* 3.4 8.5 + - - -
362C ALA 3.4 15.6 + - - -
369C PHE* 3.8 7.5 - - + -
405C PHE* 3.6 38.1 - - + -
450C LEU* 5.0 6.5 - - + -
441D PHE* 3.3 21.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ILE* 3.6 23.7 - - + +
305C VAL* 3.6 11.8 - - + +
355C THR* 2.8 28.8 + - - +
356C LEU* 3.0 29.8 + - + +
358C ALA* 1.3 70.5 - - - +
360C ALA* 1.3 64.8 + - - +
362C ALA* 3.5 1.2 + - - +
363C GLY 3.4 15.8 + - - -
803C ANP 5.7 7.4 - - - -
342D LYS* 5.5 3.0 - - - +
439D ASP* 4.1 15.0 + - - -
440D GLY 3.3 32.3 + - - -
441D PHE* 3.6 25.6 - - + +
443D THR* 5.5 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C VAL* 3.3 12.8 - - + +
306C LYS 3.5 20.4 - - - +
307C PHE* 3.8 26.4 - - + -
310C VAL* 3.9 10.1 - - + -
356C LEU 2.9 14.1 + - - +
357C LEU* 3.9 4.5 - - - +
358C ALA 3.2 0.4 - - - -
359C LYS* 1.3 78.8 - - - +
361C THR* 1.3 60.9 + - - +
363C GLY 3.4 0.9 + - - -
364C GLU* 3.2 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C PHE* 3.9 10.7 - - - -
320C ILE* 3.3 21.0 - - + +
323C PHE* 5.8 0.9 - - + -
324C VAL* 3.8 22.4 - - + -
357C LEU 3.1 14.7 + - - -
358C ALA* 3.4 10.3 + - - -
359C LYS 3.3 0.8 - - - -
360C ALA* 1.3 75.4 - - - +
362C ALA* 1.3 59.8 + - - +
364C GLU 4.6 0.2 - - - +
365C ALA* 3.0 30.6 + - - +
369C PHE* 4.6 6.1 - - + -
403C ILE* 3.9 22.7 - - + -
450C LEU* 4.5 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LEU* 3.9 11.3 - - + +
303C ILE* 3.9 27.0 + - + -
358C ALA 3.4 6.1 + - - +
359C LYS 3.9 3.4 - - - +
360C ALA 3.3 0.2 - - - -
361C THR* 1.3 80.1 - - - +
363C GLY* 1.3 59.6 + - - +
364C GLU 3.5 0.7 + - - -
365C ALA 3.8 10.6 - - - +
367C VAL 5.6 0.5 - - - +
369C PHE* 3.6 42.6 - - + +
441D PHE* 4.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ILE* 3.4 28.6 - - - +
305C VAL 4.1 9.0 - - - -
306C LYS* 3.0 27.0 + - - -
359C LYS 3.4 8.2 + - - -
360C ALA 3.4 3.3 + - - -
361C THR 3.3 0.2 - - - -
362C ALA* 1.3 78.7 - - - +
364C GLU* 1.3 59.5 + - - +
365C ALA 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C LYS* 3.3 32.1 + - + +
307C PHE* 3.6 22.4 + - + +
324C VAL* 4.6 5.3 - - + +
328C LYS* 4.9 9.7 + - - +
360C ALA 3.2 17.0 + - - +
361C THR 4.4 0.2 - - - +
362C ALA 3.3 0.2 - - - -
363C GLY* 1.3 79.2 - - - +
365C ALA* 1.3 66.6 + - - +
366C ASN* 3.5 12.7 + - - +
778C ASP 5.3 0.5 - - - +
779C TRP* 3.2 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C VAL* 3.8 34.5 - - + +
327C LEU* 5.8 0.9 - - + -
361C THR* 3.0 20.8 + - + +
362C ALA* 3.8 13.0 - - - +
363C GLY 5.0 0.2 - - - -
364C GLU* 1.3 78.3 - - - +
366C ASN* 1.3 58.7 + - - +
367C VAL* 3.2 32.4 + - + +
369C PHE* 6.5 0.2 - - + -
403C ILE* 4.4 2.9 - - + -
----------------------------------------------------------
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