Contacts of the helix formed by residues 302 - 317 (chain C) in PDB entry 1RR8
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 PHE 302 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 3.6 22.2 - + - -
257C ALA* 3.9 30.7 - - + -
260C PHE* 3.7 32.3 - + + -
261C ALA* 4.3 11.9 - - + -
264C LEU* 4.4 15.9 - - + +
278C PHE* 4.5 2.5 - + - -
282C TRP* 3.7 27.6 - + - -
297C LEU* 3.7 21.1 - - + -
300C CYS* 3.7 25.4 - - + -
301C ASP* 1.3 73.3 + - - +
303C THR* 1.3 54.4 + - - +
304C GLN 3.2 3.1 - - - -
305C MET* 2.8 36.6 + - - +
306C SER* 3.0 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LEU* 4.4 13.3 - - + +
301C ASP* 2.7 31.6 + - - +
302C PHE* 1.3 75.7 - - - +
304C GLN* 1.3 58.1 + - - +
306C SER* 3.5 9.3 + - - -
307C GLN* 3.1 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ASN 2.9 26.3 - - - +
238C VAL* 3.8 7.2 - - - +
239C LYS* 3.0 32.5 + - - +
241C TYR* 3.2 40.1 + - + -
301C ASP* 5.1 1.2 + - - +
302C PHE 3.0 1.4 + - - -
303C THR* 1.3 79.9 + - - +
305C MET* 1.3 63.7 + - - +
307C GLN* 3.6 18.1 + - - +
308C TYR* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU* 3.7 33.7 - - + -
238C VAL* 3.9 12.8 - - + -
239C LYS 4.4 9.9 - - - +
240C PHE* 3.9 31.9 - - + -
249C LEU* 5.4 1.1 - - + -
254C GLU* 4.4 2.0 - - + +
257C ALA* 3.8 14.6 - - + +
258C THR* 3.8 38.1 - - + +
261C ALA* 3.8 7.6 - - + -
302C PHE* 2.8 19.1 + - - +
304C GLN* 1.3 73.1 - - - +
306C SER* 1.3 65.3 + - - +
308C TYR* 3.2 5.2 + - - +
309C PHE* 3.1 32.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C ALA* 3.3 28.9 + - - +
262C LYS* 5.8 0.4 - - - +
264C LEU* 4.0 21.8 - - - +
265C ASP* 4.9 3.3 + - - -
302C PHE 3.0 11.0 + - - -
303C THR* 3.6 9.9 - - - -
305C MET* 1.3 76.0 - - - +
307C GLN* 1.3 61.4 + - - +
309C PHE* 3.3 7.0 + - - +
310C LYS* 3.2 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C THR* 3.1 27.5 + - - +
304C GLN* 3.8 20.3 - - - +
305C MET 3.3 0.2 - - - -
306C SER* 1.3 77.2 - - - +
308C TYR* 1.3 55.7 + - - +
310C LYS* 3.4 15.5 + - + +
311C ALA* 2.9 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C PRO 5.4 1.1 - - - -
234C LEU* 4.2 6.1 - - + -
235C PRO* 3.8 34.8 - - + +
237C ASN* 5.6 1.1 - - - -
238C VAL* 3.6 33.9 - - + -
304C GLN 3.4 8.0 + - - +
305C MET 3.2 7.7 + - - +
307C GLN* 1.3 77.2 - - - +
309C PHE* 1.3 82.8 + + - +
311C ALA* 3.2 10.9 + - + +
312C GLN* 2.9 66.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 5.8 2.2 - + - -
232C GLU 5.9 3.4 - - - -
234C LEU* 3.7 25.6 - - + -
258C THR* 3.8 36.3 - - + -
261C ALA* 4.5 4.9 - - + -
262C LYS* 3.9 43.1 - - + -
305C MET* 3.1 30.4 + - + -
306C SER* 3.3 6.9 + - - +
308C TYR* 1.3 92.7 - + - +
310C LYS* 1.3 61.0 + - + +
312C GLN* 3.6 9.6 + - + +
313C THR* 2.9 27.0 + - - -
316C ARG* 4.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ASP* 3.3 36.8 + - - +
306C SER* 3.2 26.0 + - - +
307C GLN* 3.7 16.3 - - + +
308C TYR 3.2 0.2 - - - -
309C PHE* 1.3 74.8 - - - +
311C ALA* 1.3 58.7 + - - +
313C THR* 3.2 9.1 + - - -
314C GLU* 3.0 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLN 2.9 18.3 + - - +
308C TYR* 3.2 15.5 + - + +
310C LYS* 1.3 78.6 - - - +
312C GLN* 1.3 58.9 + - - +
314C GLU* 3.5 7.9 + - - +
315C ALA* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C TYR* 2.9 60.3 + - + +
309C PHE* 3.9 13.0 - - + +
310C LYS 3.3 0.2 - - - -
311C ALA* 1.3 77.5 + - - +
313C THR* 1.3 58.9 + - - +
315C ALA* 3.6 9.7 - - - +
316C ARG* 2.9 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A A 3.3 38.2 + - - +
309C PHE 2.9 14.7 + - - -
310C LYS* 3.2 11.5 + - - -
312C GLN* 1.3 75.7 - - - +
314C GLU* 1.3 63.9 + - + +
316C ARG* 3.4 30.5 + - - +
317C LYS* 3.7 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LYS* 3.0 20.5 + - + +
311C ALA* 3.7 9.0 - - - +
312C GLN 3.3 0.2 - - - -
313C THR* 1.3 77.5 - - + +
315C ALA* 1.3 59.0 + - - +
317C LYS* 3.5 33.6 + - - +
318C GLN* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ALA 3.0 17.7 + - - +
312C GLN* 3.6 15.7 - - - +
313C THR 3.2 0.2 - - - -
314C GLU* 1.3 76.9 - - - +
316C ARG* 1.3 61.7 + - - +
317C LYS 3.4 0.9 - - - -
318C GLN* 3.6 17.8 + - - +
319C MET* 4.0 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A A 3.5 27.3 + - - -
17A A 4.9 5.0 + - - -
309C PHE 4.9 1.0 + - - -
312C GLN* 2.9 27.2 + - + +
313C THR* 3.4 31.9 + - - +
315C ALA* 1.3 78.7 - - - +
317C LYS* 1.3 55.9 + - - +
318C GLN 3.3 2.9 - - - -
319C MET* 3.4 42.4 - - + +
324C LYS* 5.0 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A A 5.8 2.7 - - + -
17A A 4.4 16.6 - - - +
18A T 6.5 2.5 - - + -
313C THR 3.7 8.4 + - - +
314C GLU* 3.5 35.6 + - - +
316C ARG* 1.3 75.0 - - - +
318C GLN* 1.3 78.5 + - - +
319C MET 3.4 4.3 + - - +
324C LYS* 4.6 14.3 - - - +
----------------------------------------------------------
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