Contacts of the helix formed by residues 298 - 307 (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 GLU 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B THR 3.3 0.2 + - - -
297B GLY* 1.3 71.5 - - - -
299B LYS* 1.3 59.0 + - - +
300B TYR 3.3 3.1 - - - -
301B ARG* 2.9 61.9 + - + +
302B ASP* 3.4 11.2 + - - +
316B LEU* 3.3 32.9 - - - +
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Residues in contact with LYS 299 (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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205B TYR* 2.7 57.3 + - + +
206B ILE* 4.2 15.3 - - + +
210B ALA* 3.8 9.5 - - - +
215B ASP* 3.1 32.6 + - - -
296B THR* 3.1 18.4 + - - +
298B GLU* 1.3 78.6 - - - +
300B TYR* 1.3 58.4 + - - +
302B ASP* 3.1 14.8 + - - +
303B ILE* 3.0 28.8 + - - +
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Residues in contact with TYR 300 (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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202B ILE* 5.5 0.2 - - + -
206B ILE* 4.1 17.7 - - + +
289B MSE 2.7 58.1 + - + +
292B ASN* 3.7 9.2 - - - +
293B ALA* 3.6 16.6 + - + -
296B THR* 3.5 32.3 + - + +
297B GLY 4.9 0.2 + - - -
298B GLU 3.3 1.4 - - - -
299B LYS* 1.3 74.6 - - - +
301B ARG* 1.3 62.7 + - - +
303B ILE* 4.0 19.1 - - + -
304B ALA* 2.9 29.8 + - - +
319B ALA 4.0 2.0 - - - +
320B ARG* 3.8 49.6 - - + -
323B ALA* 3.6 13.1 - - + +
324B VAL* 4.5 3.4 - - + -
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Residues in contact with ARG 301 (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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298B GLU* 2.9 39.2 + - - +
300B TYR* 1.3 78.1 - - - +
302B ASP* 1.3 60.3 + - - +
304B ALA* 3.8 2.7 - - - +
305B ARG* 2.9 52.9 + - - +
311B VAL* 3.0 34.2 + - + +
312B GLU* 5.1 0.8 - - - +
313B GLY 5.2 0.6 - - - +
314B MSE 2.8 32.5 + - - +
315B SER* 3.4 0.8 - - - +
316B LEU* 3.4 28.3 - - + +
319B ALA* 4.0 19.6 - - + +
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Residues in contact with ASP 302 (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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205B TYR* 2.8 27.9 + - - +
219B ILE* 3.9 13.2 - - + -
298B GLU* 3.8 9.9 - - - +
299B LYS* 3.1 22.0 + - - +
301B ARG* 1.3 80.0 - - - +
303B ILE* 1.3 62.4 + - - +
305B ARG* 3.1 28.2 + - - +
306B VAL* 3.2 27.2 + - - +
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Residues in contact with ILE 303 (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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202B ILE* 4.0 39.3 - - + -
205B TYR* 4.1 17.3 - - + -
206B ILE* 4.8 2.9 - - + -
219B ILE* 4.4 0.9 - - - -
222B ILE* 3.9 18.8 - - + -
289B MSE 4.6 4.5 - - + -
299B LYS 3.0 19.8 + - - +
300B TYR* 3.8 26.0 - - + +
301B ARG 3.3 0.2 - - - -
302B ASP* 1.3 73.9 - - - +
304B ALA* 1.3 66.0 + - - +
306B VAL* 3.3 9.1 - - - +
307B MSE 3.1 50.8 + - + +
323B ALA* 4.5 9.2 - - + -
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Residues in contact with ALA 304 (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 2.9 18.5 + - - +
301B ARG 4.4 0.2 - - - -
303B ILE* 1.3 76.2 - - - +
305B ARG* 1.3 63.4 + - - +
307B MSE 3.0 13.6 + - - -
308B GLY 3.5 0.2 + - - -
309B VAL* 3.0 34.5 + - + +
311B VAL* 3.6 19.3 - - + -
319B ALA 4.0 5.6 - - - +
322B ALA* 4.4 1.8 - - + -
323B ALA* 4.0 25.5 - - - +
326B ALA* 5.5 0.2 - - - -
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Residues in contact with ARG 305 (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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301B ARG* 2.9 45.7 + - - +
302B ASP* 3.1 42.9 + - - +
303B ILE 3.2 0.2 - - - -
304B ALA* 1.3 79.4 - - - +
306B VAL* 1.3 66.8 + - + +
307B MSE 3.3 0.3 + - - -
308B GLY* 3.3 9.7 + - - -
309B VAL 3.6 15.4 - - - +
311B VAL* 3.8 19.0 - - + +
312B GLU* 6.2 1.4 - - - +
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Residues in contact with VAL 306 (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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219B ILE* 4.0 21.1 - - + +
222B ILE* 3.5 27.1 - - + -
223B GLU* 3.7 44.9 - - + +
226B ALA* 4.0 10.4 - - - +
227B GLY* 5.2 0.9 + - - -
302B ASP 3.2 13.4 + - - +
303B ILE 3.3 13.7 - - - +
305B ARG* 1.3 83.8 - - + +
307B MSE 1.3 56.8 + - - +
308B GLY 3.3 2.8 + - - -
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Residues in contact with MSE 307 (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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198B LEU* 4.1 13.2 - - + -
202B ILE* 4.8 1.6 - - - -
222B ILE* 4.2 12.1 - - + -
226B ALA* 3.7 25.3 - - + +
230B ARG* 5.9 2.3 + - - +
303B ILE* 3.1 34.3 + - - +
304B ALA 3.0 7.3 + - - +
306B VAL* 1.3 78.0 - - - +
308B GLY* 1.3 59.0 + - - +
309B VAL* 3.4 6.2 + - - +
323B ALA 4.7 0.9 - - - +
326B ALA* 3.8 43.9 - - + +
327B VAL* 4.1 15.7 - - + -
330B LEU* 4.1 24.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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