Contacts of the helix formed by residues 365 - 380 (chain B) in PDB entry 1RHU
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 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B LYS 4.1 0.2 + - - -
364B LEU* 1.3 73.9 - - - +
366B PHE* 1.3 83.6 + - - +
367B MET* 2.9 40.6 + - - +
368B HIS* 3.0 35.8 + - + +
369B ILE* 3.1 9.1 + - - +
394B LEU* 5.7 1.2 - - - +
396B LYS 5.0 0.5 - - - +
397B GLU* 3.6 23.5 - - + +
398B LEU* 2.9 36.1 + - - +
399B TYR* 3.5 26.5 - - + +
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Residues in contact with PHE 366 (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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193A PHE* 6.6 0.2 - + - -
279A LEU* 3.9 21.3 - - + -
281A ILE* 5.5 9.6 - - + -
328B LEU* 3.7 28.9 - - + -
330B ALA* 5.7 2.5 - - + -
353B LEU* 5.0 6.5 - - + -
357B LEU* 4.5 12.1 - - + -
364B LEU 3.7 1.0 + - - -
365B GLU* 1.3 73.4 - - - +
367B MET* 1.3 63.7 + - + +
369B ILE* 3.1 14.8 + - + +
370B LEU* 3.0 57.9 + - + +
398B LEU* 2.7 42.4 + - + +
400B PHE* 3.4 31.4 - + + -
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Residues in contact with MET 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.1 37.9 - - + -
365B GLU* 2.9 28.1 + - - +
366B PHE* 1.3 73.7 - - + +
368B HIS* 1.3 63.1 + - + +
370B LEU* 3.1 9.7 + - + +
371B THR* 2.9 31.8 + - - +
389B ILE* 4.1 21.1 - - + +
392B SER* 4.0 27.4 - - - +
394B LEU* 4.0 8.3 - - + -
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Residues in contact with HIS 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 4.4 17.3 - - + +
365B GLU* 3.0 34.2 + - + +
367B MET* 1.3 79.8 - - + +
369B ILE* 1.3 66.1 + - - +
371B THR* 3.3 12.0 + - - -
372B ARG* 3.1 27.8 + - - +
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Residues in contact with ILE 369 (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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353B LEU* 5.3 0.4 - - + -
356B MET* 3.9 27.5 - - + +
357B LEU* 4.2 22.7 - - + +
360B TYR* 3.8 21.5 - - + +
361B ALA* 3.9 15.0 - - - +
364B LEU* 3.6 36.6 - - + +
365B GLU 3.1 6.4 + - - +
366B PHE* 3.1 20.8 + - + +
368B HIS* 1.3 76.0 - - - +
370B LEU* 1.3 65.7 + - + +
372B ARG* 3.1 20.2 + - - +
373B VAL* 3.1 15.0 + - + +
400B PHE* 4.8 4.0 - - + -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 4.3 8.3 - - + -
330B ALA* 4.5 16.4 - - + -
349B PHE* 5.3 5.2 - - + -
353B LEU* 3.8 28.9 - - + -
366B PHE* 3.0 50.5 + - + +
367B MET* 3.5 12.8 - - + +
369B ILE* 1.3 75.6 - - + +
371B THR* 1.3 63.5 + - - +
373B VAL* 3.2 10.8 + - + +
374B ASN* 3.0 26.2 + - - +
389B ILE* 3.4 39.4 - - + +
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Residues in contact with THR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B MET* 2.9 18.9 + - - +
368B HIS* 3.5 16.6 - - - -
369B ILE 3.2 0.4 - - - -
370B LEU* 1.3 74.2 - - - +
372B ARG* 1.3 66.4 + - - +
374B ASN* 3.1 22.8 + - + +
375B ARG* 3.1 22.3 + - - +
389B ILE* 4.1 5.8 - - - +
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Residues in contact with ARG 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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356B MET* 3.5 21.6 - - - +
360B TYR* 3.0 45.5 + - + -
364B LEU* 3.7 28.0 - - + +
368B HIS* 3.1 16.0 + - - +
369B ILE* 3.1 10.7 + - - +
371B THR* 1.3 78.6 - - - +
373B VAL* 1.3 62.4 + - - +
375B ARG* 3.4 36.7 + - - +
376B LYS* 3.0 24.6 + - - +
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Residues in contact with VAL 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B PHE* 3.9 34.3 - - + -
352B SER* 4.0 15.3 - - - -
353B LEU* 3.8 27.1 - - + +
356B MET* 3.7 22.4 - - + -
369B ILE* 3.1 15.6 + - + +
370B LEU* 3.2 15.7 + - + +
372B ARG* 1.3 77.4 - - - +
374B ASN* 1.3 58.0 + - - +
376B LYS* 3.2 3.7 + - - +
377B VAL* 2.9 32.5 + - + +
387B PRO* 4.6 1.6 - - + -
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Residues in contact with ASN 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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370B LEU 3.0 16.7 + - - +
371B THR* 3.1 14.0 + - + +
373B VAL* 1.3 77.3 - - - +
375B ARG* 1.3 57.3 + - - +
377B VAL* 4.0 0.9 - - - +
378B ALA* 2.9 33.6 + - - +
386B ILE* 4.0 12.9 - - + +
387B PRO* 3.1 44.4 + - - +
389B ILE* 3.7 28.9 - - - +
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Residues in contact with ARG 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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371B THR* 3.1 17.3 + - - +
372B ARG* 3.7 40.9 - - - +
373B VAL 3.3 0.2 - - - -
374B ASN* 1.3 78.4 - - - +
376B LYS* 1.3 59.2 + - - +
378B ALA* 3.3 3.3 + - - -
379B THR* 2.7 49.8 + - + +
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Residues in contact with LYS 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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351B GLN* 5.2 1.3 - - - -
352B SER* 3.3 38.8 - - - +
355B ALA* 4.4 13.2 - - - +
356B MET* 4.4 20.9 - - + +
372B ARG 3.0 16.6 + - - +
373B VAL* 3.6 3.1 - - - +
375B ARG* 1.3 78.0 - - - +
377B VAL* 1.3 58.1 + - - +
379B GLU* 2.9 74.1 + - + +
380B PHE* 3.6 11.0 - - + -
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Residues in contact with VAL 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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348B TRP* 4.1 12.0 - - + +
349B PHE* 4.1 15.3 - - - -
352B SER* 3.6 22.7 - - - +
373B VAL* 2.9 21.7 + - + +
376B LYS* 1.3 76.7 - - - +
378B ALA* 1.3 60.5 + - - +
380B PHE* 3.7 27.9 + - - +
385B GLN* 3.5 39.8 + - + +
387B PRO* 3.7 28.0 - - + -
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Residues in contact with ALA 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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374B ASN 2.9 19.8 + - - +
375B ARG* 3.9 3.6 - - - +
377B VAL* 1.3 78.4 - - - +
379B THR* 1.3 60.5 + - - +
384B LYS* 3.0 27.0 + - - +
385B GLN 3.5 11.4 - - - +
386B ILE* 3.9 21.1 - - + -
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Residues in contact with THR 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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375B ARG* 2.7 36.1 + - + +
376B LYS* 4.3 0.9 - - - -
378B ALA* 1.3 79.3 - - - +
379B GLU* 1.3 73.2 + - + +
380B PHE 3.5 1.9 + - - -
384B LYS* 3.8 9.7 + - - +
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Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LYS* 2.9 59.6 + - + +
379B THR* 1.3 82.3 - - + +
380B PHE* 1.3 70.7 + + + +
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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