Contacts of the helix formed by residues 268 - 277 (chain C) in PDB entry 7A62
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 SER 268 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.6 35.6 - - - +
126C TYR* 5.2 0.4 - - - -
131C LEU* 6.1 1.0 - - - +
171C GLU* 4.6 1.6 + - - -
266C GLN 4.5 0.7 + - - -
267C SER* 1.3 73.9 + - - +
269C VAL* 1.3 58.3 + - - +
270C PHE 3.6 0.7 - - - -
271C GLN* 3.9 4.3 - - - +
272C CYS* 2.9 30.5 + - - +
299C MET* 3.3 31.6 - - - +
300C PRO* 5.2 1.0 - - - +
303C HIS* 4.1 14.8 + - - +
307C LEU* 4.3 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 4.0 13.2 - - + -
170C VAL 5.8 0.4 - - - -
171C GLU* 3.4 32.1 - - - +
174C ALA* 3.8 33.7 - - + -
178C ILE* 4.6 0.9 - - + -
207C LEU* 5.2 4.7 - - + -
267C SER* 3.1 8.5 + - - +
268C SER* 1.3 75.5 - - - +
270C PHE* 1.3 84.1 + - + +
272C CYS* 3.2 9.9 + - - +
273C PHE* 3.0 35.0 - - + -
342C LEU* 6.0 1.1 - - + -
504C HEM 5.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C PHE* 4.9 3.4 - + - -
267C SER* 6.0 0.2 - - - -
269C VAL* 1.3 88.5 - - + +
271C GLN* 1.3 58.4 + - - +
273C PHE* 3.1 3.6 + - - +
274C ASP* 2.9 31.6 + - - +
339C LEU* 4.2 15.1 - - + +
342C LEU* 4.1 41.3 - - + -
343C ARG* 3.4 51.4 + - + +
346C HIS* 4.7 12.1 - + + -
504C HEM 3.3 63.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C GLY 5.6 1.6 + - - -
267C SER 4.9 4.3 + - - +
268C SER 3.8 7.4 + - - +
269C VAL 3.3 0.4 - - - -
270C PHE* 1.3 77.3 - - + +
272C CYS* 1.3 62.7 + - - +
274C ASP* 3.5 13.7 - - + +
275C VAL* 3.0 28.3 + - + +
281C GLN* 6.3 1.3 - - + -
282C THR* 4.9 3.2 - - - +
292C LEU* 3.1 47.6 + - + +
295C MET* 4.6 4.2 - - - +
296C ARG* 2.6 38.4 + - - +
299C MET* 3.7 23.4 - - + +
307C LEU* 4.1 11.7 - - + -
504C HEM 5.3 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 4.2 9.0 - - + -
178C ILE* 4.3 9.2 - - - -
181C ILE* 3.8 27.8 - - - -
268C SER 2.9 21.4 + - - +
269C VAL* 3.2 9.6 - - - +
270C PHE 3.2 0.2 - - - -
271C GLN* 1.3 77.4 - - - +
273C PHE* 1.3 73.1 + - + +
275C VAL* 3.5 0.3 + - - +
276C LEU* 3.1 23.9 + - - +
306C PHE* 4.1 16.6 - - - -
307C LEU* 3.7 13.2 - - + +
310C LEU* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ALA* 4.6 1.8 - - + -
177C ALA* 3.7 27.4 - - + -
178C ILE* 4.0 19.5 - - + -
181C ILE* 4.6 5.4 - - + -
203C ILE* 3.8 23.8 - - + -
207C LEU* 4.0 29.2 - - + -
269C VAL* 3.0 35.2 - - + -
270C PHE* 3.1 5.0 + - - +
272C CYS* 1.3 85.8 - - - +
274C ASP* 1.3 66.7 + - - +
275C VAL 3.2 0.2 - - - -
276C LEU* 4.0 20.9 - - + -
277C LEU* 3.0 34.5 + - + +
339C LEU* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C PHE 2.9 16.7 + - - +
271C GLN* 3.5 12.9 - - + +
273C PHE* 1.3 77.2 - - - +
275C VAL* 1.3 64.3 + - + +
278C GLY 3.1 2.6 + - - -
279C ILE* 2.8 50.2 + - - +
281C GLN* 3.2 31.1 + - + +
292C LEU* 5.6 0.9 - - - +
339C LEU* 3.5 8.8 - - - +
343C ARG* 2.6 39.5 + - - -
504C HEM 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C GLN 3.0 20.1 + - - +
272C CYS* 3.9 3.1 - - - +
274C ASP* 1.3 74.8 - - + +
276C LEU* 1.3 66.8 + - - +
278C GLY* 3.1 12.3 + - - +
279C ILE 4.7 2.9 - - - +
282C THR* 5.4 2.7 - - + -
296C ARG* 3.8 24.7 - - - +
307C LEU* 4.0 7.6 - - + +
310C LEU* 3.5 35.1 - - + +
311C GLU* 3.5 35.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ILE* 4.2 20.4 - - + -
184C VAL* 4.7 8.7 - - + -
185C PHE* 3.8 34.6 - - + -
200C LEU* 5.6 3.4 - - + -
203C ILE* 4.1 27.1 - - + -
272C CYS 3.1 18.7 + - - +
273C PHE* 3.8 22.4 - - + +
274C ASP 3.4 0.2 - - - -
275C VAL* 1.3 80.5 - - - +
277C LEU* 1.3 72.4 + - + +
278C GLY 3.4 0.5 + - - -
310C LEU* 4.5 7.6 - - + -
316C VAL* 3.5 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LEU* 4.8 7.0 - - + -
207C LEU* 6.1 0.7 - - + -
273C PHE* 3.0 24.3 + - + +
276C LEU* 1.3 92.9 - - + +
278C GLY* 1.3 62.4 + - - +
279C ILE* 3.2 17.5 + - + +
316C VAL* 4.9 2.7 - - + -
317C ARG* 3.6 8.1 - - - +
332C TYR* 2.5 56.2 + - + +
335C CYS* 3.7 37.9 - - + +
336C VAL* 4.0 19.5 - - + +
339C LEU* 4.5 7.4 - - + -
----------------------------------------------------------
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