Contacts of the helix formed by residues 315 - 334 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ARG* 3.4 1.1 - - - +
313B GLY 4.2 0.6 + - - -
314B MSE 1.3 76.3 - - - +
316B LEU* 1.3 58.6 + - - +
317B GLU* 3.6 8.9 + - - +
318B GLU* 2.9 42.8 + - - +
319B ALA* 2.8 26.5 + - - +
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLY 3.5 17.9 - - - +
298B GLU* 3.3 41.7 - - - +
301B ARG* 3.4 17.9 - - + +
315B SER* 1.3 73.7 - - - +
317B GLU* 1.3 58.6 + - - +
319B ALA* 3.3 2.3 + - + -
320B ARG* 2.9 72.9 + - + +
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B SER* 3.2 8.3 + - - +
316B LEU* 1.3 79.5 - - - +
318B GLU* 1.3 64.3 + - + +
320B ARG* 3.3 10.6 + - - +
321B ASN* 3.0 39.6 + - - +
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLY 4.5 1.9 - - - +
314B MSE 3.4 25.9 - - + +
315B SER* 2.9 40.8 + - - +
317B GLU* 1.3 78.9 - - + +
319B ALA* 1.3 59.2 + - - +
321B ASN* 3.3 11.8 + - - +
322B ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B TYR* 4.0 5.3 - - - +
301B ARG* 4.0 42.8 - - + +
304B ALA* 4.0 1.4 - - - +
311B VAL* 4.8 4.5 - - + -
314B MSE 3.8 14.3 - - - +
315B SER 2.8 17.0 + - - +
316B LEU* 3.6 6.7 - - + +
318B GLU* 1.3 73.8 - - - +
320B ARG* 1.3 61.3 + - - +
322B ALA* 3.2 2.7 + - - +
323B ALA* 2.9 28.9 + - - +
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ALA* 3.2 34.3 + - + -
294B ASP* 3.5 33.7 + - - +
296B THR* 4.0 2.0 + - - -
297B GLY* 2.8 40.6 + - - +
300B TYR* 3.8 31.1 - - + -
316B LEU* 2.9 45.7 + - + +
317B GLU* 3.6 9.5 - - - +
319B ALA* 1.3 77.4 - - - +
321B ASN* 1.3 62.9 + - - +
323B ALA* 3.4 3.1 + - - +
324B VAL* 3.3 26.8 + - - +
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Residues in contact with ASN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ARG* 5.5 6.7 + - - +
317B GLU* 3.0 33.1 + - - +
318B GLU* 3.6 11.4 - - - +
320B ARG* 1.3 77.4 - - - +
322B ALA* 1.3 59.0 + - - +
324B VAL* 3.4 7.4 + - - +
325B GLU* 2.9 29.7 + - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ALA* 4.4 4.5 - - + -
309B VAL* 3.8 30.5 - - + +
314B MSE 3.9 13.7 - - + -
318B GLU 2.9 17.7 + - - +
319B ALA* 3.2 6.0 + - - +
321B ASN* 1.3 76.0 - - - +
323B ALA* 1.3 59.7 + - - +
325B GLU* 3.8 5.5 - - - +
326B ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B MSE 3.9 16.1 - - + +
300B TYR* 3.6 35.7 - - + +
303B ILE* 4.5 4.3 - - + -
304B ALA* 4.0 14.8 - - + +
307B MSE 4.7 1.6 - - - +
319B ALA 2.9 8.0 + - - +
320B ARG 3.7 8.3 - - - +
321B ASN 3.3 0.2 - - - -
322B ALA* 1.3 75.0 - - - +
324B VAL* 1.3 63.8 + - - +
326B ALA* 3.3 12.3 + - - +
327B VAL* 3.3 19.1 + - - +
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO* 3.6 19.2 - - + +
289B MSE 4.0 17.5 - - + -
290B ARG* 3.6 56.1 - - + +
293B ALA* 5.9 0.9 - - + -
300B TYR* 4.5 6.7 - - + -
320B ARG 3.3 15.1 + - - +
321B ASN* 3.7 9.2 - - - +
323B ALA* 1.3 76.7 - - - +
325B GLU* 1.3 62.4 + - - +
327B VAL* 3.1 7.5 + - - +
328B PHE* 3.1 29.3 + - + -
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B ARG* 5.8 0.7 + - - +
321B ASN 2.9 17.6 + - - +
322B ALA* 3.9 7.4 - - - +
324B VAL* 1.3 75.0 - - - +
326B ALA* 1.3 61.1 + - - +
328B PHE* 3.2 17.5 + - - +
329B ALA* 2.9 29.3 + - + +
332B ARG* 2.8 31.4 + - - -
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ARG* 4.8 2.1 + - - -
304B ALA* 5.5 0.2 - - - -
307B MSE 3.8 34.5 - - + +
309B VAL* 4.2 13.9 - - + -
322B ALA 2.9 18.5 + - - +
323B ALA* 3.6 7.9 - - - +
324B VAL 3.3 0.2 - - - -
325B GLU* 1.3 76.2 - - - +
327B VAL* 1.3 58.1 + - - +
329B ALA* 3.5 6.6 + - - +
330B LEU* 2.9 28.4 + - - +
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 4.7 5.2 - - + -
202B ILE* 4.2 9.0 - - + -
285B LEU* 3.6 28.9 - - + -
286B PRO* 3.9 17.3 - - + -
289B MSE 3.6 22.9 - - + -
307B MSE 4.1 22.2 - - + -
323B ALA 3.5 12.8 - - - +
324B VAL 3.1 8.3 + - - +
326B ALA* 1.3 75.6 - - - +
328B PHE* 1.3 65.9 + - - +
330B LEU* 3.2 4.6 + - + +
331B ASN* 3.0 31.5 + - - +
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO* 3.4 28.9 - - + -
287B HIS* 3.7 32.1 - + - -
290B ARG* 3.6 28.9 - - - -
324B VAL* 3.1 33.1 + - + -
325B GLU* 3.6 21.1 - - - +
327B VAL* 1.3 77.0 - - - +
329B ALA* 1.3 63.3 + - - +
331B ASN* 3.4 8.6 + - + +
332B ARG* 3.1 42.1 + - - +
338B PRO* 5.9 5.6 - - + -
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ARG* 4.7 4.0 - - - +
325B GLU* 2.9 20.4 + - + +
326B ALA* 3.6 8.1 - - - +
328B PHE* 1.3 75.5 - - - +
330B LEU* 1.3 65.9 + - - +
332B ARG* 3.1 24.1 + - - +
333B ASP* 2.9 35.3 + - - +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B VAL* 4.8 6.3 - - + -
198B LEU* 3.6 31.2 - - + -
225B ILE* 5.8 0.2 - - + -
226B ALA* 5.1 8.5 - - - +
229B LEU* 4.2 26.9 - - + -
230B ARG* 3.4 39.0 - - + +
307B MSE 4.1 11.2 - - + -
326B ALA 2.9 18.6 + - - +
327B VAL* 3.2 5.8 + - + +
329B ALA* 1.3 75.4 - - - +
331B ASN* 1.3 65.3 + - - +
333B ASP* 3.1 1.7 + - - +
334B VAL* 3.0 44.8 + - + +
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Residues in contact with ASN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 3.6 29.8 - - - +
282B ALA* 3.0 35.4 + - - +
283B ILE* 5.1 0.8 - - - +
286B PRO* 4.1 6.7 - - - +
327B VAL* 3.0 29.6 + - - +
328B PHE* 3.6 10.9 - - + +
329B ALA 3.3 0.2 - - - -
330B LEU* 1.3 78.3 - - - +
332B ARG* 1.3 63.5 + - + +
334B VAL* 3.6 5.6 + - - +
335B GLY 3.3 3.8 + - - -
336B ILE* 3.1 39.6 + - + +
337B PRO 5.9 0.7 - - - +
338B PRO* 6.3 2.0 - - + -
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLU* 2.8 28.5 + - - -
328B PHE* 3.1 30.8 + - - +
329B ALA* 3.5 25.0 - - - +
331B ASN* 1.3 77.3 - - + +
333B ASP* 1.3 68.9 + - - +
335B GLY* 3.1 13.3 + - - -
336B ILE 5.1 3.8 - - - -
338B PRO* 5.9 6.7 - - + -
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Residues in contact with ASP 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ARG* 2.8 48.9 + - + +
233B VAL* 5.8 0.2 - - - +
329B ALA* 2.9 22.3 + - - +
330B LEU 3.1 4.0 + - - +
332B ARG* 1.3 82.4 + - - +
334B VAL* 1.3 59.4 + - - +
335B GLY 3.3 0.9 + - - -
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PRO 5.3 0.2 - - - +
188B ALA* 5.5 2.3 - - - -
191B ALA* 3.4 34.4 - - + +
195B VAL* 4.5 8.5 - - + -
229B LEU* 4.2 8.5 - - + -
230B ARG* 4.4 13.0 - - + -
233B VAL* 3.9 30.7 - - + +
330B LEU* 3.0 34.9 + - + +
331B ASN* 3.7 10.3 - - - +
332B ARG 3.3 0.2 - - - -
333B ASP* 1.3 78.2 - - - +
335B GLY* 1.3 58.6 + - - +
336B ILE* 4.0 14.4 - - + -
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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) + - + + + + + -
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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