Contacts of the helix formed by residues 327 - 345 (chain C) in PDB entry 1ZRT
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 327 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C VAL* 4.4 0.2 - - - -
319C ASP* 3.9 25.6 - - - +
324C GLY 3.1 20.3 - - - +
325C ILE* 3.1 8.7 - - - +
326C VAL* 1.3 75.0 - - - +
328C ALA* 1.3 55.1 + - - +
329C LYS* 2.9 27.8 + - - +
330C PHE* 3.0 7.6 + - - +
331C PHE* 2.8 28.2 + - - -
170R PRO 5.8 0.2 - - - +
172R PRO* 3.7 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LEU 4.9 1.9 - - - +
308C PHE 3.3 26.2 - - - +
309C ALA* 3.5 4.5 - - - -
310C ALA* 3.4 32.4 - - + +
315C VAL* 3.7 17.1 - - + +
327C ASP* 1.3 70.2 - - - +
329C LYS* 1.3 66.2 + - - +
331C PHE* 3.8 4.0 - - - -
332C GLY* 3.5 7.7 + - - -
94R ARG* 5.7 0.4 - - - +
135R HIS* 5.0 0.9 + - - -
170R PRO* 4.0 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C GLY 5.2 1.3 - - - -
167C GLY 4.3 12.9 + - - -
168C ALA* 3.7 31.3 + - + +
305C LEU* 5.3 0.9 - - - +
327C ASP* 2.9 14.2 + - - +
328C ALA* 1.3 75.1 - - - +
330C PHE* 1.3 55.8 + - + +
332C GLY* 2.8 24.4 + - - -
333C VAL* 3.3 14.2 + - + +
134R THR 3.6 12.4 + - - -
135R HIS* 3.2 49.1 + - + +
136R LEU* 4.9 4.3 - - + -
170R PRO 3.7 7.9 + - - +
172R PRO* 4.0 23.6 - - + +
173R ARG* 5.2 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ALA* 3.1 33.4 - - + +
169C ILE* 3.9 21.8 - - + -
170C PRO* 3.5 34.3 - - + -
325C ILE* 4.0 22.2 - - + +
326C VAL* 4.4 10.3 - - + -
327C ASP* 3.0 9.0 + - - +
329C LYS* 1.3 77.2 - - + +
331C PHE* 1.3 64.4 + - - +
333C VAL* 3.3 11.8 - - + +
334C ILE* 3.1 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 3.4 46.9 - + + -
314C VAL* 3.6 39.3 - - + -
315C VAL* 3.6 16.2 - - + -
318C VAL* 3.9 18.2 - - + -
326C VAL* 3.7 33.0 - - + +
327C ASP 2.8 21.3 + - - +
328C ALA* 3.8 8.5 - - - -
330C PHE* 1.3 74.0 - - - +
332C GLY* 1.3 50.6 + - - +
334C ILE* 3.4 6.3 + - + +
335C ALA* 2.7 37.8 + - + +
401C PHE* 6.4 2.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LEU* 3.6 32.3 - - - +
308C PHE* 4.6 3.4 - - - -
328C ALA 3.5 7.0 + - - -
329C LYS 2.8 12.5 + - - -
331C PHE* 1.3 75.6 - - - +
333C VAL* 1.3 58.6 + - - +
335C ALA* 3.4 10.8 - - - +
336C MET* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 3.7 40.4 - - + +
168C ALA* 3.7 20.2 - - + -
169C ILE* 5.2 3.1 - - + -
305C LEU* 3.9 9.0 - - + -
329C LYS* 3.5 17.0 - - + +
330C PHE* 3.3 19.5 - - + +
332C GLY* 1.3 75.1 - - - +
334C ILE* 1.3 55.0 - - + +
336C MET* 2.9 10.3 + - + +
337C PHE* 2.8 53.6 + - + +
135R HIS* 6.1 0.9 - - - +
136R LEU* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C VAL* 4.8 11.4 - - + -
330C PHE* 3.2 52.3 - - + +
331C PHE* 3.5 8.7 - - + +
333C VAL* 1.3 78.2 - - + +
335C ALA* 1.3 55.7 + - - +
337C PHE* 4.6 5.6 - - - -
338C GLY* 2.8 31.5 + - - -
401C PHE* 5.3 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C ILE* 3.7 6.3 - - + +
308C PHE* 3.6 37.9 - - + -
331C PHE* 2.7 26.6 + - + +
332C GLY* 3.4 8.7 - - - +
334C ILE* 1.3 72.8 - - - +
336C MET* 1.3 56.7 + - - +
338C GLY 3.6 1.2 - - - -
339C ALA* 2.9 27.5 + - - +
401C PHE* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 4.1 14.8 - - + -
301C PHE* 3.3 40.0 - - + +
304C ILE* 3.8 12.1 - - + -
305C LEU* 3.8 22.9 - - + -
332C GLY 3.0 11.9 + - - +
333C VAL* 2.9 13.0 + - - +
335C ALA* 1.3 71.0 - - - +
337C PHE* 1.3 93.4 + - + +
339C ALA* 3.0 20.3 + - - +
340C ILE* 3.3 11.4 - - - +
503C SMA 3.8 40.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 5.6 8.5 - - + -
166C PHE* 4.4 31.2 - + - -
169C ILE* 5.5 7.2 - - + -
333C VAL* 2.8 31.2 + - + +
334C ILE* 4.2 4.3 - - - +
336C MET* 1.3 89.2 - - + +
338C GLY* 1.3 63.9 + - - +
339C ALA 3.2 1.4 + - - -
340C ILE* 3.2 22.7 + - + +
341C ALA* 3.3 9.0 + - - +
503C SMA 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ILE 2.8 20.1 + - - -
335C ALA 3.6 2.2 - - - -
337C PHE* 1.3 78.1 - - - +
339C ALA* 1.3 59.7 + - - -
340C ILE 3.1 0.2 - - - -
341C ALA* 3.6 13.1 - - - +
342C VAL* 3.2 29.6 + - - +
401C PHE* 4.3 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C PHE* 5.2 6.5 - - + -
304C ILE* 3.8 22.7 - - + -
335C ALA 2.9 15.7 + - - +
336C MET 3.0 12.3 + - - +
338C GLY* 1.3 77.6 - - - +
340C ILE* 1.3 56.9 - - + +
342C VAL* 3.4 14.4 - - - +
343C MET* 4.2 3.4 + - - +
400C TRP* 2.9 43.3 + - + +
401C PHE* 4.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C MET* 3.9 17.2 - - + +
136C TYR* 4.3 13.2 - - + -
137C LEU* 4.6 15.9 - - + -
140C MET* 4.2 10.1 - - + -
301C PHE* 3.5 21.3 - - + -
336C MET 3.3 11.9 - - - +
337C PHE* 3.3 17.7 - - + +
339C ALA* 1.3 74.8 - - - +
341C ALA* 1.3 56.3 + - - +
342C VAL 3.2 1.8 - - - -
343C MET* 2.8 45.0 + - + +
344C ALA* 3.1 8.5 + - - +
503C SMA 4.1 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C PHE 3.3 4.3 + - - +
338C GLY* 3.3 19.6 + - - +
340C ILE* 1.3 77.0 - - - +
342C VAL* 1.3 59.6 + - + +
344C ALA* 3.2 8.8 + - - +
345C LEU* 3.0 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C GLY 3.2 15.4 + - - +
339C ALA* 3.4 18.2 - - - +
341C ALA* 1.3 76.6 - - + +
343C MET* 1.3 57.4 + - - +
345C LEU* 3.9 12.7 - - + +
346C ALA 4.1 6.8 + - - -
349C LEU* 5.4 0.7 - - + +
400C TRP* 4.4 1.6 - - + +
401C PHE* 3.7 32.1 - - + +
404C PHE* 3.1 48.3 - - + +
405C LEU* 4.3 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 4.6 21.1 - - + -
116C LEU* 5.2 6.3 - - + -
129C TRP* 3.0 34.2 + - + -
133C MET* 4.3 11.9 - - + -
136C TYR* 5.1 4.5 - - + -
301C PHE* 4.4 15.9 - - + -
339C ALA 4.2 3.6 - - - +
340C ILE* 2.8 39.5 + - + +
342C VAL* 1.3 77.6 - - - +
344C ALA* 1.3 60.7 + - - +
345C LEU 3.2 1.1 - - - -
346C ALA* 3.4 9.2 - - - +
400C TRP* 4.1 27.6 - - + -
404C PHE* 4.2 17.9 - - + -
502C HEM 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C TRP* 3.5 8.2 + - - +
130C ILE* 3.7 17.0 - - + +
133C MET* 3.7 29.1 - - + +
340C ILE 3.1 7.8 + - - +
341C ALA* 3.4 13.7 - - - +
343C MET* 1.3 80.1 - - - +
345C LEU* 1.3 63.7 + - + +
346C ALA 3.2 3.0 + - - -
347C PRO* 3.4 13.9 - - - +
348C TRP* 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ALA* 3.0 28.4 + - + +
342C VAL* 4.0 11.0 - - + -
343C MET 3.2 0.4 - - - -
344C ALA* 1.3 82.1 - - + +
346C ALA* 1.3 54.7 + - - +
347C PRO* 3.4 1.6 - - - -
348C TRP* 2.9 51.5 + - + +
349C LEU* 3.4 31.5 + - + +
----------------------------------------------------------
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