Contacts of the helix formed by residues 349 - 360 (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 ASP 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ARG* 4.8 7.8 + - - -
272B PHE* 4.1 21.7 - - + -
273B TYR* 2.6 36.8 + - - +
346B ARG* 3.0 34.8 + - - +
347B LYS 3.0 1.4 - - - -
348B GLU* 1.3 78.4 - - - +
350B ILE* 1.3 64.1 + - - +
351B PRO* 3.3 3.1 - - - -
352B ALA* 3.1 10.1 + - - +
353B LEU* 2.9 26.7 + - + +
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Residues in contact with ILE 350 (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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345B VAL* 5.1 4.3 - - + -
346B ARG 4.0 7.2 - - - +
347B LYS* 3.0 25.6 + - + +
349B ASP* 1.3 77.2 - - - +
351B PRO* 1.3 66.9 - - + +
353B LEU* 3.7 12.3 - - + +
354B ALA* 2.8 22.9 + - - +
376B VAL* 4.0 16.6 - - + +
379B TYR* 3.7 36.6 - - + +
380B HIS* 3.6 50.7 - - + +
383B TRP* 5.0 7.4 - - + -
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Residues in contact with PRO 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LYS 3.8 3.6 - - - +
348B GLU* 3.5 13.7 - - - +
349B ASP 3.5 4.3 - - - -
350B ILE* 1.3 95.3 - - + +
352B ALA* 1.3 59.4 + - - +
354B ALA* 3.6 4.9 + - + +
355B GLN* 3.2 22.3 + - - +
372B LEU* 4.7 4.0 - - - +
376B VAL* 4.7 9.6 - - + -
380B HIS* 5.7 1.3 - - - +
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Residues in contact with ALA 352 (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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272B PHE* 3.9 23.1 - - + -
349B ASP* 3.1 10.7 + - - +
351B PRO* 1.3 76.4 - - - +
353B LEU* 1.3 65.0 + - - +
355B GLN* 3.4 6.2 + - - +
356B ALA* 3.0 23.9 + - - +
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Residues in contact with LEU 353 (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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268B PRO* 3.6 29.9 - - + +
269B LEU* 4.0 21.1 - - + +
272B PHE* 3.6 33.2 - - + -
273B TYR* 3.9 15.7 - - - +
345B VAL* 4.2 9.4 - - + -
349B ASP* 2.9 30.2 + - + +
350B ILE* 3.7 11.7 - - + +
352B ALA* 1.3 76.3 - - - +
354B ALA* 1.3 57.5 + - - +
356B ALA* 3.3 3.7 + - - +
357B ALA* 2.8 29.5 + - - +
379B TYR* 3.7 21.2 + - + -
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Residues in contact with ALA 354 (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 2.8 17.3 + - - +
351B PRO 3.8 1.3 - - - +
353B LEU* 1.3 74.2 - - - +
355B GLN* 1.3 59.8 + - - +
357B ALA* 3.2 2.3 + - - +
358B LEU* 2.8 29.1 + - - +
372B LEU* 3.8 10.0 - - + +
375B ILE* 3.7 27.8 - - + +
376B VAL* 3.4 31.2 - - + +
379B TYR* 3.6 2.9 - - + -
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Residues in contact with GLN 355 (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 3.2 13.9 + - - +
352B ALA* 3.8 7.4 - - - +
353B LEU 3.3 0.2 - - - -
354B ALA* 1.3 78.2 - - - +
356B ALA* 1.3 61.9 + - - +
358B LEU* 3.2 15.4 + - - +
359B ASP* 3.0 61.5 + - - +
372B LEU* 3.7 26.2 - - + +
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Residues in contact with ALA 356 (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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161B ARG* 5.8 10.5 + - + +
268B PRO* 3.7 21.3 - - + +
272B PHE* 5.3 7.2 - - + -
352B ALA 3.0 18.2 + - - +
353B LEU* 3.4 5.4 - - - +
355B GLN* 1.3 77.4 - - - +
357B ALA* 1.3 56.8 + - - +
359B ASP* 3.2 7.0 + - - +
360B ASP* 3.0 27.2 + - - +
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Residues in contact with ALA 357 (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* 5.0 0.2 - - + -
264B GLY 3.3 24.9 - - - +
265B MSE 3.9 12.6 - - + -
268B PRO* 3.7 0.9 - - - +
353B LEU 2.8 17.0 + - - +
354B ALA 3.5 5.2 - - - +
356B ALA* 1.3 74.9 - - - +
358B LEU* 1.3 62.8 + - - +
360B ASP* 3.1 6.6 + - - +
363B THR* 2.6 27.3 + - - +
375B ILE* 3.9 22.0 - - + -
379B TYR* 3.9 4.5 - - - +
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Residues in contact with LEU 358 (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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354B ALA 2.8 14.0 + - - +
355B GLN* 3.2 28.5 + - - +
357B ALA* 1.3 76.0 - - - +
359B ASP* 1.3 64.8 + - - +
360B ASP 3.7 0.7 + - - +
363B THR* 4.3 15.3 - - + +
370B ALA* 3.5 25.6 - - + +
371B THR* 4.3 5.4 - - - -
372B LEU* 4.2 23.6 - - + +
375B ILE* 3.8 17.9 - - + +
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Residues in contact with ASP 359 (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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123B GLU* 4.9 4.5 - - - +
161B ARG* 4.9 14.0 + - - +
355B GLN* 3.0 41.4 + - - +
356B ALA* 3.6 5.9 - - - +
357B ALA 3.1 0.2 - - - -
358B LEU* 1.3 83.5 - - - +
360B ASP* 1.3 63.5 + - - +
361B VAL* 3.6 2.3 + - - +
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Residues in contact with ASP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ARG* 5.7 3.4 - - - +
162B LYS 4.1 10.2 - - - +
164B VAL* 4.2 4.5 + - - +
264B GLY* 3.6 16.6 - - - +
267B HIS* 2.9 36.2 + - - +
268B PRO* 5.0 0.8 - - + +
356B ALA 3.0 12.0 + - - +
357B ALA 3.1 13.9 + - - +
358B LEU 4.4 0.7 - - - +
359B ASP* 1.3 79.5 - - - +
361B VAL* 1.3 68.1 + - - +
362B CYS* 2.8 37.8 + - - +
363B THR* 3.2 18.1 + - - +
364B GLY 4.2 1.2 + - - -
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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