Contacts of the helix formed by residues 371 - 385 (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 THR 371 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358B LEU* 4.3 4.7 - - - -
369B GLU* 4.3 6.1 - - + +
370B ALA* 1.3 78.0 - - - +
372B LEU* 1.3 65.2 + - - +
373B GLU* 3.6 6.1 + - - +
374B ASP* 3.0 44.8 + - - +
375B ILE* 3.2 15.2 + - - +
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Residues in contact with LEU 372 (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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351B PRO 4.7 3.6 - - - +
354B ALA* 3.8 12.3 - - + +
355B GLN* 3.7 48.5 - - + +
358B LEU* 4.2 19.4 - - + +
371B THR* 1.3 74.5 - - - +
373B GLU* 1.3 59.2 + - - +
375B ILE* 3.2 7.3 + - - +
376B VAL* 3.0 36.1 + - + +
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Residues in contact with GLU 373 (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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371B THR* 3.3 5.8 + - - +
372B LEU* 1.3 75.9 - - - +
374B ASP* 1.3 60.4 + - - +
376B VAL* 4.0 23.3 - - - +
377B GLU* 2.8 38.6 + - + +
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Residues in contact with ASP 374 (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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291B TYR* 2.7 43.4 + - + +
368B ARG* 4.3 11.3 + - - -
369B GLU 4.0 1.9 - - - +
370B ALA* 3.8 2.7 - - + -
371B THR* 3.0 44.1 + - - +
373B GLU* 1.3 77.7 - - - +
375B ILE* 1.3 58.0 + - - +
377B GLU* 3.3 7.5 + - - +
378B LEU* 3.0 32.7 + - - +
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Residues in contact with ILE 375 (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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261B LEU* 3.9 27.1 - - + -
265B MSE 3.9 8.5 - - + -
354B ALA* 3.7 26.2 - - + +
357B ALA* 3.9 7.4 - - + -
358B LEU* 3.8 47.3 - - + +
363B THR* 4.9 0.7 - - + -
370B ALA* 4.0 10.8 - - + -
371B THR 3.5 8.3 - - - +
372B LEU* 3.2 7.3 + - - +
374B ASP* 1.3 75.8 - - - +
376B VAL* 1.3 65.5 + - - +
378B LEU* 3.1 9.1 + - - +
379B TYR* 3.0 36.3 + - + -
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Residues in contact with VAL 376 (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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350B ILE* 4.0 15.7 - - + +
351B PRO* 4.7 10.8 - - + -
354B ALA* 3.4 20.0 - - + -
372B LEU* 3.0 26.9 + - + +
373B GLU* 3.6 28.0 - - - +
375B ILE* 1.3 75.6 - - - +
377B GLU* 1.3 64.1 + - - +
379B TYR* 3.3 2.9 + - - +
380B HIS* 3.1 47.4 + - + +
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Residues in contact with GLU 377 (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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373B GLU* 2.8 26.9 + - + +
374B ASP* 3.5 7.6 - - - +
376B VAL* 1.3 79.1 - - - +
378B LEU* 1.3 59.4 + - + +
380B HIS* 3.3 9.6 + - - +
381B THR* 2.8 49.1 + - - +
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Residues in contact with LEU 378 (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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261B LEU* 3.5 32.1 - - + -
265B MSE 3.5 23.3 - - + -
284B LEU* 5.1 0.8 - - + +
287B HIS* 3.5 42.3 - - + +
288B VAL* 4.1 5.4 - - + +
291B TYR* 4.0 26.5 - - + -
374B ASP 3.0 20.9 + - - +
375B ILE* 3.1 3.1 + - - +
377B GLU* 1.3 79.0 - - + +
379B TYR* 1.3 56.8 + - - +
381B THR* 3.2 8.4 + - + +
382B ALA* 2.9 30.3 + - - +
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Residues in contact with TYR 379 (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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265B MSE 2.6 52.8 + - + +
268B PRO* 3.9 8.7 - - - +
269B LEU* 4.0 21.7 - - + +
284B LEU* 4.3 2.0 - - + -
340B LEU* 3.7 24.6 - - + +
345B VAL* 5.8 0.4 - - + -
350B ILE* 3.7 33.7 - - + +
353B LEU* 3.7 21.9 + - + -
354B ALA* 3.6 23.8 - - - -
357B ALA* 3.9 0.2 - - - +
375B ILE* 3.0 37.3 + - + -
376B VAL 3.3 5.8 + - - +
378B LEU* 1.3 76.9 - - - +
380B HIS* 1.3 57.3 + - - +
382B ALA* 3.3 2.0 + - - -
383B TRP* 2.9 27.2 + - - +
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Residues in contact with HIS 380 (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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347B LYS* 4.4 29.5 + - + +
350B ILE* 3.6 31.9 - - + +
351B PRO* 5.7 1.4 - - - +
376B VAL* 3.1 44.5 + - + +
377B GLU* 3.7 12.8 - - - +
379B TYR* 1.3 74.6 - - - +
381B THR* 1.3 65.0 + - - +
383B TRP* 3.1 19.6 - - - +
384B GLU* 4.2 3.6 + - - +
385B GLY 5.6 0.2 - - - -
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Residues in contact with THR 381 (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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287B HIS* 3.6 27.0 - - + +
290B ARG* 6.1 1.1 - - - +
377B GLU* 2.8 41.0 + - - +
378B LEU* 3.6 10.4 - - + +
379B TYR 3.2 0.2 - - - -
380B HIS* 1.3 76.6 - - - +
382B ALA* 1.3 59.6 + - - +
383B TRP 3.1 0.2 - - - -
385B GLY* 3.1 45.3 + - - +
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Residues in contact with ALA 382 (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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283B ILE* 4.1 8.6 - - + +
284B LEU* 4.3 11.4 - - + -
287B HIS* 3.7 27.8 - - + -
338B PRO 4.2 1.0 - - - +
339B HIS* 3.5 7.1 - - - -
340B LEU* 2.8 44.8 + - + -
378B LEU 2.9 17.3 + - - +
379B TYR 3.7 0.2 - - - -
381B THR* 1.3 75.9 - - - +
383B TRP* 1.3 62.0 + - - +
384B GLU 3.4 0.6 + - - -
385B GLY 4.2 1.9 + - - +
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Residues in contact with TRP 383 (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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339B HIS* 3.1 7.1 - - - +
340B LEU* 4.0 6.5 - - + -
341B ARG* 3.1 71.6 + - + +
345B VAL* 3.0 44.9 - - + -
346B ARG* 4.0 1.1 - - - -
347B LYS* 3.3 58.6 - - + +
350B ILE* 5.0 5.6 - - + -
379B TYR 2.9 12.7 + - - +
380B HIS* 3.1 20.2 - - - +
381B THR 3.1 0.4 - - - -
382B ALA* 1.3 76.2 - - - +
384B GLU* 1.3 88.8 + - + +
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Residues in contact with GLU 384 (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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339B HIS* 3.3 23.5 + - + -
341B ARG* 3.0 39.2 + - - +
347B LYS* 4.3 8.8 + - - -
380B HIS 4.2 2.6 + - - +
381B THR 3.9 1.0 + - - -
383B TRP* 1.3 101.2 + - + +
385B GLY* 1.3 62.8 + - - +
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Residues in contact with GLY 385 (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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287B HIS* 4.4 12.9 - - - -
339B HIS* 3.3 17.3 + - - -
381B THR* 3.1 36.6 + - - +
382B ALA 4.2 1.0 - - - -
383B TRP 3.8 0.2 - - - -
384B GLU* 1.3 83.9 - - - +
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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