Contacts of the helix formed by residues 298 - 307 (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 GLU 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A THR 3.2 0.2 + - - -
297A GLY* 1.3 73.1 - - - -
299A LYS* 1.3 60.0 + - - +
300A TYR 3.3 2.7 - - - -
301A ARG* 2.9 57.3 + - + +
302A ASP* 3.5 10.7 + - - +
316A LEU* 3.5 31.6 - - - +
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Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 2.7 56.0 + - + +
206A ILE* 4.1 19.1 - - + +
210A ALA* 3.8 11.1 - - - +
215A ASP* 3.2 31.9 + - - -
296A THR* 2.9 19.5 + - - +
298A GLU* 1.3 79.4 - - - +
300A TYR* 1.3 62.4 + - - +
302A ASP* 3.0 13.7 + - - +
303A ILE* 3.0 24.7 + - - +
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Residues in contact with TYR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 5.6 0.2 - - + -
206A ILE* 4.1 15.4 - - + +
289A MSE 2.6 60.6 + - + +
292A ASN* 3.8 7.8 - - - +
293A ALA* 3.7 14.6 + - + -
296A THR* 3.4 35.2 + - + +
297A GLY 4.9 0.6 + - - -
298A GLU 3.3 1.2 - - - -
299A LYS* 1.3 77.2 - - - +
301A ARG* 1.3 58.0 + - - +
303A ILE* 3.7 17.9 - - + -
304A ALA* 2.9 30.3 + - - +
316A LEU* 5.9 0.2 - - + -
319A ALA 4.0 1.7 - - - +
320A ARG* 3.7 49.4 - - + +
323A ALA* 3.5 11.9 - - + +
324A VAL* 4.3 4.3 - - + -
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLU* 2.9 37.7 + - - +
300A TYR* 1.3 81.4 - - - +
302A ASP* 1.3 62.7 + - - +
304A ALA* 3.6 2.9 + - - +
305A ARG* 3.1 41.7 + - - +
311A VAL* 3.6 30.7 + - + +
314A MSE 3.3 22.2 + - - -
315A SER* 3.4 1.4 - - - +
316A LEU* 3.3 38.8 - - + +
319A ALA* 4.0 21.7 - - + +
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Residues in contact with ASP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 2.7 28.3 + - - +
219A ILE* 3.8 13.5 - - + -
298A GLU* 3.8 9.7 - - - +
299A LYS* 3.0 20.8 + - - +
301A ARG* 1.3 78.3 - - - +
303A ILE* 1.3 64.8 + - - +
305A ARG* 2.7 34.6 + - - +
306A VAL* 3.1 28.3 + - + +
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 4.0 39.3 - - + -
205A TYR* 4.1 17.7 - - + -
206A ILE* 4.9 2.9 - - + -
219A ILE* 4.5 0.2 - - - -
222A ILE* 3.9 18.4 - - + -
289A MSE 4.7 4.9 - - + -
299A LYS 3.0 13.2 + - - +
300A TYR* 3.8 26.2 - - + +
302A ASP* 1.3 76.6 - - - +
304A ALA* 1.3 64.1 + - - +
306A VAL* 3.1 12.0 - - - +
307A MSE 3.1 42.8 + - - +
323A ALA* 4.4 10.3 - - + -
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A TYR 2.9 18.4 + - - +
301A ARG 4.5 0.2 - - - -
303A ILE* 1.3 76.4 - - - +
305A ARG* 1.3 61.1 + - - +
307A MSE 3.1 9.5 + - - -
308A GLY 3.5 0.2 + - - -
309A VAL* 2.9 40.1 + - + +
311A VAL* 3.8 19.1 - - + -
319A ALA 3.9 5.8 - - - +
322A ALA* 4.3 1.6 - - + -
323A ALA* 3.9 25.3 - - - +
326A ALA* 5.4 0.2 - - - -
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ARG* 3.1 30.2 + - - +
302A ASP* 2.7 36.4 + - - +
303A ILE 3.2 0.2 - - - -
304A ALA* 1.3 77.1 - - - +
306A VAL* 1.3 69.0 + - + +
307A MSE 3.1 1.0 + - - -
308A GLY* 3.2 13.7 + - - -
309A VAL 3.5 14.2 + - - +
311A VAL* 3.6 24.8 - - + +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 3.9 22.4 - - + +
222A ILE* 3.5 28.3 - - + -
223A GLU* 3.8 45.4 - - + +
226A ALA* 4.1 6.1 - - - +
227A GLY* 5.2 0.9 + - - -
302A ASP* 3.1 13.8 + - - +
303A ILE* 3.1 17.5 - - - +
305A ARG* 1.3 82.4 - - + +
307A MSE 1.3 55.3 + - - +
308A GLY 3.3 3.8 + - - -
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Residues in contact with MSE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU* 4.3 5.6 - - + -
202A ILE* 4.7 4.9 - - - -
222A ILE* 4.1 11.0 - - + -
226A ALA* 3.6 26.2 - - + +
230A ARG* 6.1 1.3 - - - +
303A ILE* 3.1 37.0 + - - +
304A ALA* 3.1 4.7 + - - +
305A ARG 3.0 1.6 - - - -
306A VAL* 1.3 78.1 - - - +
308A GLY* 1.3 60.2 + - - +
309A VAL* 3.4 6.7 + - - +
323A ALA 4.7 0.7 - - - +
326A ALA* 3.7 45.4 - - + +
327A VAL* 4.0 20.6 - - + +
330A LEU* 4.2 20.9 - - + -
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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