Contacts of the helix formed by residues 459 - 477 (chain C) in PDB entry 6DWM
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 GLY 459 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C LEU* 4.3 5.6 - - - -
457C CYS* 3.2 11.8 - - - -
458C ILE* 1.3 81.3 - - - +
460C GLU* 1.3 57.3 + - - +
461C THR* 3.4 2.9 - - - -
462C ILE* 3.3 11.3 + - - +
463C ALA* 2.8 32.6 + - - +
601C HEM 4.0 23.4 - - - +
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Residues in contact with GLU 460 (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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450C PHE* 3.7 36.2 - - + +
451C GLY 5.8 0.2 - - - +
456C LYS* 4.6 15.1 + - - +
457C CYS* 3.2 22.0 - - + +
458C ILE 3.4 2.4 - - - -
459C GLY* 1.3 76.8 - - - +
461C THR* 1.3 68.4 + - + +
463C ALA* 3.3 1.6 + - - +
464C ARG* 2.7 63.3 + - - +
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Residues in contact with THR 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ILE* 4.1 23.6 - - + +
458C ILE 5.3 2.8 + - - -
459C GLY 5.0 0.3 - - - -
460C GLU* 1.3 79.8 + - + +
462C ILE* 1.3 69.4 + - - +
464C ARG* 3.3 6.3 + - - +
465C TRP* 3.1 43.3 + - - +
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Residues in contact with ILE 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 3.7 40.2 - - + -
146C SER* 3.6 34.1 - - - +
147C ILE* 5.4 3.8 - - + -
159C LEU* 3.9 27.9 - - + +
198C ILE* 6.1 1.3 - - + -
201C ILE* 5.2 6.5 - - + -
458C ILE 5.3 0.7 - - - +
459C GLY* 3.3 12.2 + - - +
461C THR* 1.3 87.8 + - - +
463C ALA* 1.3 63.5 + - - +
465C TRP* 3.3 3.5 + - + +
466C GLU* 2.9 33.8 + - - +
601C HEM 4.5 13.5 - - + -
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Residues in contact with ALA 463 (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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322C VAL* 4.4 12.6 - - + -
376C PHE* 5.9 0.4 - - - -
450C PHE* 4.1 8.3 - - + -
459C GLY 2.8 20.3 + - - +
460C GLU 3.8 4.0 - - - +
462C ILE* 1.3 75.4 - - - +
464C ARG* 1.3 58.7 + - - +
466C GLU* 3.9 1.7 - - - +
467C VAL* 3.0 36.2 + - - +
601C HEM 3.7 41.5 - - + +
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Residues in contact with ARG 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C ARG* 3.7 32.7 + - - +
369C GLU* 4.7 5.7 + - - -
372C ILE* 5.2 4.0 - - + +
373C LEU* 4.0 24.0 - - - +
376C PHE* 4.4 18.1 - - + -
444C SER 5.7 1.4 + - - -
447C VAL* 5.1 8.9 + - - +
449C ILE* 5.5 1.0 - - - +
450C PHE* 3.2 34.5 - - + -
460C GLU* 2.7 49.3 + - - +
461C THR* 3.9 5.6 - - - +
463C ALA* 1.3 77.4 - - - +
465C TRP* 1.3 62.5 + - - +
467C VAL* 4.4 3.3 - - - +
468C PHE* 3.3 23.6 + - - +
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Residues in contact with TRP 465 (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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147C ILE* 3.7 45.1 - - + -
157C CYS* 4.4 9.6 - - - -
159C LEU* 3.4 30.3 - - + -
359C LEU* 3.8 39.2 - - + +
362C ARG* 3.0 39.1 - - - +
461C THR* 3.1 25.5 + - - +
462C ILE* 5.6 0.7 - - + -
464C ARG* 1.3 76.4 - - + +
466C GLU* 1.3 59.1 + - - +
468C PHE* 3.4 4.0 + - - +
469C LEU* 3.0 34.4 + - - +
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Residues in contact with GLU 466 (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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159C LEU* 4.2 4.2 - - + +
163C VAL* 3.8 24.0 - - + -
194C VAL* 3.7 16.9 - - - +
197C VAL* 3.3 35.3 - - - +
198C ILE* 4.8 3.5 + - - +
318C GLY 5.1 0.9 - - - +
322C VAL* 3.8 29.0 - - + +
326C ILE* 5.2 0.2 - - - -
462C ILE* 2.9 29.3 + - - +
463C ALA* 3.9 2.9 - - - +
465C TRP* 1.3 78.6 - - - +
467C VAL* 1.3 62.3 + - - +
469C LEU* 4.1 0.5 - - - +
470C PHE* 3.2 40.7 + - + -
601C HEM 5.2 0.9 - - - +
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Residues in contact with VAL 467 (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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322C VAL* 4.3 11.0 - - + -
325C ALA* 4.3 19.5 - - + -
326C ILE* 4.3 24.5 - - + -
329C SER* 4.7 6.7 - - - +
372C ILE* 4.2 22.9 - - + -
376C PHE* 4.8 9.0 - - + -
463C ALA* 3.0 24.5 + - + +
464C ARG* 4.4 3.6 - - - +
466C GLU* 1.3 75.8 - - - +
468C PHE* 1.3 64.3 + - - +
470C PHE* 4.1 0.9 - - - +
471C LEU* 3.2 43.8 + - + +
601C HEM 5.4 0.9 - - + -
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Residues in contact with PHE 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C PRO* 5.2 1.6 - - + -
358C ARG 3.8 22.2 - - - -
359C LEU* 4.3 13.2 - - + -
361C ASP* 4.8 0.7 - - + -
362C ARG* 3.6 44.2 - - + +
365C LEU* 3.4 35.4 - - + -
368C MET* 3.6 24.1 - - + +
369C GLU* 5.9 1.6 - - - +
372C ILE* 3.9 15.7 - - + +
464C ARG 3.3 18.8 + - - +
465C TRP* 3.7 5.2 - - - +
466C GLU 3.3 0.4 - - - -
467C VAL* 1.3 79.8 - - - +
469C LEU* 1.3 74.9 + - + +
471C LEU* 3.4 1.9 + - - +
472C ALA* 2.9 33.8 + - + +
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Residues in contact with LEU 469 (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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159C LEU* 5.1 1.6 - - + -
160C GLU* 3.7 37.5 - - + +
163C VAL* 3.5 26.0 - - + -
164C SER* 4.6 3.4 - - - +
357C PRO* 3.9 23.8 - - + +
358C ARG* 4.5 7.9 - - - -
359C LEU* 3.8 24.9 - - + -
465C TRP 3.0 13.8 + - - +
468C PHE* 1.3 86.6 - - + +
470C PHE* 1.3 64.8 + - - +
472C ALA* 3.2 1.3 + - - +
473C ILE* 2.8 51.2 + - + +
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Residues in contact with PHE 470 (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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163C VAL* 3.7 18.6 - - + +
166C GLU* 4.1 8.5 - - + -
167C ALA* 4.0 32.1 - - + -
170C LEU* 4.5 13.5 - - + -
193C SER* 4.1 22.4 - - - -
194C VAL* 4.3 10.3 - - + -
197C VAL* 4.0 17.7 - - + -
326C ILE* 3.7 27.1 - - + -
466C GLU* 3.2 43.9 + - + +
467C VAL 4.1 2.7 - - - +
469C LEU* 1.3 77.0 - - - +
471C LEU* 1.3 64.9 + - + +
473C ILE* 3.9 2.0 - - - -
474C LEU* 3.0 37.2 + - + +
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Residues in contact with LEU 471 (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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326C ILE* 4.7 12.3 - - + -
329C SER* 4.0 22.4 - - - +
330C LEU* 4.6 11.7 - - + -
333C LEU* 4.3 17.0 - - + -
368C MET* 4.1 15.9 - - + -
371C PHE* 3.9 23.1 - - + -
372C ILE* 4.0 12.8 - - + -
467C VAL* 3.2 36.5 + - + +
468C PHE 3.9 2.0 - - - +
470C PHE* 1.3 77.5 - - + +
472C ALA* 1.3 58.0 + - - +
474C LEU* 4.6 5.4 - - + -
475C LEU* 2.9 40.0 + - + +
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Residues in contact with ALA 472 (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 LEU* 3.6 20.0 - - + +
357C PRO* 3.8 24.4 - - + +
368C MET* 4.3 5.3 - - - -
468C PHE* 2.9 38.1 + - + +
469C LEU* 3.8 3.4 - - - +
471C LEU* 1.3 78.0 - - - +
473C ILE* 1.3 62.6 + - - +
476C GLN* 3.1 27.2 + - - +
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Residues in contact with ILE 473 (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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163C VAL 4.5 1.1 - - - +
164C SER* 4.1 23.1 - - - +
167C ALA* 3.6 33.4 - - + -
168C GLU* 4.8 4.9 - - - +
171C ILE* 4.4 11.2 - - + +
356C ARG* 4.5 11.4 - - + +
357C PRO* 4.3 22.2 - - + +
469C LEU* 2.8 47.3 + - + +
470C PHE 4.0 2.0 - - - +
472C ALA* 1.3 73.4 - - - +
474C LEU* 1.3 67.4 + - + +
476C GLN* 3.7 5.8 + - - +
477C ARG* 3.7 28.8 + - - +
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Residues in contact with LEU 474 (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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167C ALA* 4.2 21.5 - - + +
170C LEU* 4.0 26.9 - - + -
171C ILE* 4.2 25.8 - - + -
174C LEU* 5.5 1.8 - - + -
190C VAL* 6.2 0.7 - - + -
326C ILE* 6.1 4.3 - - + -
330C LEU* 5.2 8.5 - - + -
470C PHE* 3.0 29.5 + - + +
471C LEU* 4.0 5.8 - - + +
473C ILE* 1.3 77.5 - - - +
475C LEU* 1.3 61.3 + - + +
477C ARG* 2.8 21.1 + - - +
478C VAL* 2.8 21.1 + - + +
480C PHE* 3.9 32.8 - - + -
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Residues in contact with LEU 475 (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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333C LEU* 4.0 28.7 - - + -
340C GLN* 3.5 34.1 - - + +
343C ILE* 3.4 35.9 - - + -
344C GLN* 3.2 27.6 - - + +
347C LEU* 4.0 11.9 - - + -
368C MET* 4.6 5.2 - - + -
471C LEU* 2.9 29.6 + - + +
474C LEU* 1.3 74.3 - - + +
476C GLN* 1.3 61.5 + - - +
477C ARG 3.4 0.3 + - - -
478C VAL 3.5 10.0 - - - +
480C PHE* 4.2 14.6 - - + -
511C ARG* 3.7 2.8 + - - -
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Residues in contact with GLN 476 (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 LEU* 3.6 20.7 + - + +
348C ASP* 4.9 6.7 - - - +
351C ILE* 4.7 2.6 - - - +
352C GLY 3.2 19.4 + - - +
353C ARG* 4.0 19.4 - - + +
355C ARG 2.8 27.2 + - - +
356C ARG* 4.1 8.0 - - - +
357C PRO* 3.4 24.8 - - + +
472C ALA 3.1 20.0 + - - +
473C ILE* 3.8 7.1 - - - +
474C LEU 3.0 0.8 + - - -
475C LEU* 1.3 78.3 - - - +
477C ARG* 1.3 64.9 + - - +
511C ARG* 3.2 26.8 + - - +
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Residues in contact with ARG 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C GLU* 2.8 41.8 + - - -
171C ILE* 3.7 33.2 - - + +
356C ARG* 3.8 20.2 - - - +
473C ILE* 3.7 14.0 + - - +
474C LEU 2.8 7.0 + - - +
476C GLN* 1.3 89.1 + - + +
478C VAL* 1.3 62.2 + - + +
510C LEU* 3.7 17.1 - - + +
511C ARG* 3.1 27.7 + - - +
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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
------------------------------------------------------------
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