Contacts of the helix formed by residues 315 - 334 (chain A) in PDB entry 1RRM
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 315 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 3.4 3.8 - - - +
313A GLY 4.0 0.2 + - - -
314A MSE 1.3 75.7 - - - +
316A LEU* 1.3 54.5 + - - +
317A GLU* 3.7 9.4 + - - +
318A GLU* 2.9 35.9 + - - +
319A ALA* 2.7 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLY 3.4 18.6 - - - +
298A GLU* 3.5 38.4 - - - +
301A ARG* 3.3 20.3 - - + +
315A SER* 1.3 75.0 - - - +
317A GLU* 1.3 57.3 + - - +
319A ALA* 3.5 2.8 - - + +
320A ARG* 2.8 74.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A SER* 3.2 8.9 + - - +
316A LEU* 1.3 80.8 - - - +
318A GLU* 1.3 60.6 + - + +
320A ARG* 3.5 10.5 + - - +
321A ASN* 2.8 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLY 4.7 0.3 - - - +
314A MSE 3.2 23.2 - - + +
315A SER* 2.9 39.8 + - - +
317A GLU* 1.3 78.1 - - + +
319A ALA* 1.3 61.1 + - - +
321A ASN* 3.2 12.0 + - - +
322A ALA* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 4.0 2.7 - - - +
301A ARG* 4.0 43.3 - - + +
304A ALA* 3.9 4.5 - - - +
311A VAL* 4.8 4.0 - - + -
314A MSE 3.8 15.4 - - - -
315A SER 2.7 20.2 + - - +
316A LEU* 3.5 6.7 - - + +
318A GLU* 1.3 73.6 - - - +
320A ARG* 1.3 58.2 + - - +
322A ALA* 3.2 3.4 + - - +
323A ALA* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA* 3.2 34.1 + - + -
294A ASP* 3.2 35.7 + - - +
296A THR* 4.1 1.8 + - - -
297A GLY* 2.8 38.8 + - - +
300A TYR* 3.7 30.0 - - + -
316A LEU* 2.8 47.9 + - + +
317A GLU* 3.7 9.0 - - - +
319A ALA* 1.3 77.6 - - - +
321A ASN* 1.3 63.2 + - - +
323A ALA* 3.4 2.9 + - - +
324A VAL* 3.3 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ARG* 5.8 1.7 + - - -
317A GLU* 2.8 34.8 + - - +
318A GLU* 3.2 12.1 + - - +
320A ARG* 1.3 77.1 - - - +
322A ALA* 1.3 57.8 + - - +
324A VAL* 3.3 8.1 + - - +
325A GLU* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA* 4.3 4.0 - - + -
309A VAL* 3.8 30.2 - - + +
314A MSE 3.9 12.3 - - + -
318A GLU 2.8 17.3 + - - +
319A ALA 3.2 5.8 + - - +
321A ASN* 1.3 75.5 - - - +
323A ALA* 1.3 65.3 + - - +
325A GLU* 3.4 5.9 + - - +
326A ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MSE 3.9 15.6 - - + +
300A TYR* 3.5 35.7 - - + +
303A ILE* 4.4 4.7 - - + -
304A ALA* 3.9 15.0 - - + +
307A MSE 4.7 1.4 - - - +
319A ALA 3.0 8.2 + - - +
320A ARG 3.7 8.1 - - - +
321A ASN 3.3 0.2 - - - -
322A ALA* 1.3 76.9 - - - +
324A VAL* 1.3 62.2 + - - +
326A ALA* 3.3 13.7 + - - +
327A VAL* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A PRO* 3.7 16.2 - - + +
289A MSE 4.1 16.8 - - + -
290A ARG* 3.7 44.4 - - + +
293A ALA* 6.1 0.7 - - + -
300A TYR* 4.3 7.4 - - + -
320A ARG 3.3 14.3 + - - +
321A ASN* 3.6 9.0 - - - +
322A ALA 3.3 0.4 - - - -
323A ALA* 1.3 77.2 - - - +
325A GLU* 1.3 63.0 + - - +
327A VAL* 3.1 6.8 + - - +
328A PHE* 3.1 43.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ARG* 5.8 0.6 + - - +
321A ASN 3.0 17.6 + - - +
322A ALA* 3.8 7.0 - - - +
324A VAL* 1.3 74.0 - - - +
326A ALA* 1.3 61.0 + - - +
328A PHE* 3.1 16.8 + - - +
329A ALA* 2.8 31.2 + - + +
332A ARG* 2.9 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ARG* 4.8 2.3 + - - -
307A MSE 3.7 30.8 - - + +
309A VAL* 4.2 17.7 - - + -
322A ALA 2.9 18.1 + - - +
323A ALA* 3.4 8.5 - - - +
324A VAL 3.2 0.2 - - - -
325A GLU* 1.3 76.8 - - - +
327A VAL* 1.3 57.2 + - - +
329A ALA* 3.5 7.0 + - - +
330A LEU* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 4.7 4.5 - - + -
202A ILE* 4.2 9.0 - - + -
285A LEU* 3.6 29.8 - - + -
286A PRO* 3.9 17.9 - - + -
289A MSE 3.6 23.8 - - + -
307A MSE 4.0 21.3 - - + -
323A ALA 3.6 13.0 - - - +
324A VAL 3.1 8.6 + - - +
325A GLU 3.1 0.4 - - - -
326A ALA* 1.3 75.7 - - - +
328A PHE* 1.3 65.8 + - - +
330A LEU* 3.3 3.9 + - + +
331A ASN* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A PRO* 3.5 29.2 - - + -
287A HIS* 3.7 30.5 - + - -
290A ARG* 3.7 19.3 - - - -
324A VAL* 3.1 41.2 + - + -
325A GLU* 3.5 21.3 - - - +
327A VAL* 1.3 76.7 - - - +
329A ALA* 1.3 62.9 + - - +
331A ASN* 3.4 7.5 + - + +
332A ARG* 3.1 43.1 + - - +
338A PRO* 5.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ARG* 4.7 6.7 - - - +
325A GLU* 2.8 18.9 + - + +
326A ALA* 3.6 8.1 - - - +
328A PHE* 1.3 75.7 - - - +
330A LEU* 1.3 60.2 + - - +
332A ARG* 3.1 23.4 + - - +
333A ASP* 2.8 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 4.8 4.3 - - + -
198A LEU* 3.5 31.9 - - + -
225A ILE* 5.8 0.7 - - + -
226A ALA* 5.1 8.3 - - - +
229A LEU* 4.2 27.1 - - + -
230A ARG* 3.5 39.2 - - + +
307A MSE 4.2 11.0 - - + -
326A ALA 3.0 17.8 + - - +
327A VAL* 3.3 4.9 + - + +
329A ALA* 1.3 76.0 - - - +
331A ASN* 1.3 67.5 + - - +
333A ASP* 3.0 3.2 + - - +
334A VAL* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 3.6 30.5 - - - +
198A LEU* 6.1 0.2 - - - +
282A ALA* 2.8 35.5 + - - +
283A ILE* 5.0 0.6 - - - +
286A PRO* 4.1 6.7 - - - +
327A VAL* 3.0 33.5 + - - +
328A PHE* 3.7 7.8 - - + +
330A LEU* 1.3 77.4 - - - +
332A ARG* 1.3 62.3 + - + +
334A VAL* 3.6 5.9 + - - +
335A GLY 3.3 3.5 + - - -
336A ILE* 3.0 39.9 + - + +
337A PRO 5.8 0.7 - - - +
338A PRO* 6.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLU* 2.9 26.5 + - - -
328A PHE* 3.1 32.7 + - - +
329A ALA* 3.1 26.2 + - - +
331A ASN* 1.3 75.5 - - - +
333A ASP* 1.3 68.0 + - - +
335A GLY* 3.2 13.2 + - - -
336A ILE 5.0 3.6 - - - +
338A PRO* 5.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ARG* 2.9 47.6 + - + +
233A VAL* 5.8 0.3 - - - +
329A ALA* 2.8 22.0 + - - +
330A LEU 3.5 4.3 - - - +
332A ARG* 1.3 81.7 + - - +
334A VAL* 1.3 60.3 + - - +
335A GLY 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ALA* 5.4 1.9 - - - -
191A ALA* 3.4 28.3 - - + +
195A VAL* 4.5 8.7 - - + -
229A LEU* 4.2 9.9 - - + -
230A ARG* 4.4 12.8 - - + -
233A VAL* 3.8 31.1 - - + +
330A LEU* 2.9 38.0 + - + +
331A ASN* 3.8 9.0 - - - +
333A ASP* 1.3 78.4 - - - +
335A GLY* 1.3 60.0 + - - +
336A ILE* 4.0 21.5 - - + -
----------------------------------------------------------
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