Contacts of the helix formed by residues 360 - 376 (chain C) in PDB entry 3RMD
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 SER 360 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357C SER* 3.1 12.7 + - - +
358C VAL 4.5 1.3 - - - -
359C PHE* 1.3 80.3 - - - +
361C PRO* 1.3 65.4 - - - +
362C ILE* 3.7 2.4 - - - +
363C LYS* 3.0 22.8 + - - +
364C THR* 3.0 25.7 + - - -
1I C 4.1 3.2 + - - -
2I G 2.6 22.6 + - - -
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Residues in contact with PRO 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LYS* 4.9 4.0 - - - +
358C VAL 5.7 0.7 - - - +
359C PHE 3.6 9.4 - - - +
360C SER* 1.3 76.6 - - - +
362C ILE* 1.3 65.4 + - - +
364C THR* 3.0 7.0 + - - -
365C TRP* 2.8 33.2 + - + +
565C SER* 4.2 28.5 - - - +
569C ALA* 4.9 5.6 - - + -
2I G 2.8 67.8 - - + +
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Residues in contact with ILE 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C SER* 3.7 1.8 - - - +
361C PRO* 1.3 78.3 - - - +
363C LYS* 1.3 61.4 + - + +
366C ASP* 2.9 33.7 + - + +
569C ALA* 3.4 23.1 - - + -
572C ASN* 3.8 13.7 - - + +
574C TRP 4.3 13.7 - - - +
575C PHE* 3.4 41.3 - - + -
576C ARG 5.7 0.4 - - - +
1I C 3.7 14.1 - - - +
2I G 2.8 31.2 + - - +
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Residues in contact with LYS 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ASP* 2.9 33.9 + - - +
90C LEU* 4.0 22.5 - - + +
353C ILE* 4.8 6.1 - - + -
357C SER* 3.7 29.6 - - - +
360C SER* 3.0 23.9 + - - +
362C ILE* 1.3 77.7 - - + +
364C THR* 1.3 67.0 + - - +
366C ASP* 3.2 9.8 + - + +
367C ALA* 3.1 22.5 + - - +
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Residues in contact with THR 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C MET* 4.5 15.0 - - + -
351C ALA* 4.0 11.0 - - + +
353C ILE* 3.6 14.4 - - + +
357C SER 3.3 13.0 + - - -
358C VAL* 3.9 8.8 + - - -
360C SER 3.0 18.0 + - - -
361C PRO* 3.6 7.2 - - - -
363C LYS* 1.3 78.7 - - - +
365C TRP* 1.3 62.9 + - - +
367C ALA* 3.3 2.8 + - - +
368C ILE* 3.0 32.6 + - + +
562C LEU* 3.8 27.4 - - + -
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Residues in contact with TRP 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C PRO* 2.8 23.7 + - + +
364C THR* 1.3 71.6 - - - +
366C ASP* 1.3 66.4 + - - +
368C ILE* 3.2 27.9 + - + -
369C ILE* 2.9 36.6 + - + +
474C GLU* 4.2 23.8 - - + -
475C ILE* 4.8 4.5 - - + -
478C VAL* 3.8 23.6 - - + -
562C LEU* 3.2 51.9 + - + +
563C ILE* 4.4 3.4 - - - -
565C SER* 3.3 15.8 + - - -
566C LEU* 3.3 46.3 - - + +
569C ALA* 5.0 3.1 - - + -
575C PHE* 4.1 19.1 - - + -
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Residues in contact with ASP 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C MET* 3.6 12.1 - - - +
87C ASP* 5.9 0.2 - - - +
90C LEU* 4.6 3.5 - - - +
362C ILE* 2.9 23.0 + - + +
363C LYS* 3.2 14.3 + - + +
365C TRP* 1.3 77.0 - - - +
367C ALA* 1.3 57.9 + - - +
369C ILE* 3.9 1.9 - - - +
370C PHE* 2.9 28.6 + - - +
575C PHE* 4.1 8.4 - - + -
576C ARG* 2.7 59.8 + - - +
577C TYR* 3.9 6.1 + - - -
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Residues in contact with ALA 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 4.0 18.3 - - + +
351C ALA 3.5 9.4 - - - +
352C LYS 4.6 0.2 - - - +
353C ILE* 3.3 35.2 - - + -
363C LYS 3.1 5.0 + - - +
364C THR 3.6 4.5 - - - +
366C ASP* 1.3 76.6 + - - +
368C ILE* 1.3 66.8 + - - +
370C PHE* 3.0 7.2 + - - -
371C ASN* 2.9 33.9 + - - +
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Residues in contact with ILE 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C TYR* 3.5 37.7 - - + +
351C ALA* 3.7 19.3 - - + +
364C THR* 3.0 22.0 + - + +
365C TRP* 3.7 28.5 - - + +
367C ALA* 1.3 75.9 - - - +
369C ILE* 1.3 63.3 + - - +
371C ASN* 4.2 4.0 - - - +
372C SER* 3.3 20.4 + - - -
474C GLU* 4.5 8.7 - - + +
477C LYS* 5.2 6.0 + - - -
478C VAL* 5.4 2.9 - - + -
562C LEU* 3.7 27.8 - - + -
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Residues in contact with ILE 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C TRP* 2.9 35.8 + - + +
366C ASP 3.9 3.1 - - - +
368C ILE* 1.3 73.9 - - - +
370C PHE* 1.3 70.5 + - - +
372C SER* 3.1 5.9 + - - -
373C LEU* 2.9 34.4 + - + +
470C VAL* 4.0 12.6 - - + -
471C VAL* 5.2 11.4 - - + -
474C GLU* 4.3 16.8 - - + +
566C LEU* 5.4 4.3 - - + -
575C PHE* 3.9 12.8 - - + -
577C TYR* 3.1 53.8 - - + +
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Residues in contact with PHE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C MET* 3.6 42.6 - - + -
90C LEU* 3.9 14.4 - - + -
91C ALA* 3.9 13.5 - - + -
94C SER* 3.8 28.3 - - - -
95C ASP* 6.1 0.2 - - - -
366C ASP 2.9 15.6 + - - +
367C ALA* 3.3 8.7 - - - +
369C ILE* 1.3 78.8 - - - +
371C ASN* 1.3 66.1 + - - +
373C LEU* 3.0 2.1 + - - +
374C LYS* 2.8 51.3 + - + -
378C LYS 6.2 0.2 - - - -
380C ILE* 3.6 31.9 - - + -
577C TYR* 4.5 0.2 + - - -
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Residues in contact with ASN 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 5.4 1.0 + - - +
94C SER* 3.0 32.8 + - - -
351C ALA 3.4 21.2 + - - -
352C LYS* 3.6 29.6 + - + +
367C ALA* 2.9 27.0 + - - +
368C ILE* 4.2 4.7 - - - +
370C PHE* 1.3 85.5 - - - +
372C SER* 1.3 63.2 + - - +
374C LYS* 3.4 8.6 + - - +
375C GLU* 3.2 21.8 + - - +
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Residues in contact with SER 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C ILE 3.3 13.8 + - - -
369C ILE 3.1 8.8 + - - -
371C ASN* 1.3 80.0 - - - +
373C LEU* 1.3 63.5 + - - +
375C GLU* 3.4 11.1 + - - +
376C GLN* 3.2 29.5 + - - +
474C GLU* 2.7 37.1 + - - -
477C LYS* 3.1 14.8 + - - +
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Residues in contact with LEU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ILE* 3.7 24.2 - - + -
369C ILE* 2.9 29.9 + - + +
370C PHE 3.5 6.1 - - - +
372C SER* 1.3 75.7 - - - +
374C LYS* 1.3 61.5 + - - +
376C GLN* 2.9 28.5 + - - +
378C LYS* 2.9 54.5 + - + +
380C ILE* 3.7 29.2 - - + +
470C VAL* 4.0 22.7 - - + -
474C GLU* 5.2 1.6 - - - +
577C TYR* 3.9 2.5 - - + +
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Residues in contact with LYS 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C SER* 2.7 41.7 + - - +
95C ASP* 2.6 30.8 + - - +
98C ASN* 5.4 4.3 - - - +
370C PHE* 2.8 37.3 + - + +
371C ASN* 3.7 8.1 - - - +
372C SER 3.3 0.2 - - - -
373C LEU* 1.3 78.2 - - - +
375C GLU* 1.3 58.2 + - - +
377C ASN* 2.8 24.3 + - - +
378C LYS 4.2 9.6 + - - -
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Residues in contact with GLU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C ASN 3.2 9.6 + - - +
372C SER* 3.5 13.7 - - - +
373C LEU 3.2 0.4 - - - -
374C LYS* 1.3 80.3 - - - +
376C GLN* 1.3 65.1 + - + +
377C ASN* 3.3 7.8 + - - -
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Residues in contact with GLN 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C SER* 3.2 34.9 + - - +
373C LEU* 2.9 19.5 + - - +
375C GLU* 1.3 86.4 - - + +
377C ASN* 1.3 74.9 + - - +
378C LYS* 3.1 30.3 + - + +
473C THR* 6.3 0.8 - - - +
474C GLU* 5.1 2.6 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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