Contacts of the helix formed by residues 459 - 477 (chain A) in PDB entry 6DWN
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.2 9.0 - - - -
457A CYS* 3.2 12.6 - - - -
458A ILE* 1.3 82.0 - - - +
460A GLU* 1.3 62.6 + - - -
461A THR 3.4 2.0 - - - -
462A ILE* 3.3 12.5 + - - +
463A ALA* 3.0 23.4 + - - +
601A HEM 3.8 22.2 - - - +
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Residues in contact with GLU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A PHE* 3.5 36.7 - - + +
456A LYS* 4.9 12.1 + - - +
457A CYS* 3.3 21.6 - - - +
458A ILE 3.4 3.4 + - - -
459A GLY* 1.3 76.5 - - - +
461A THR* 1.3 60.7 + - - +
463A ALA* 3.1 4.0 + - - +
464A ARG* 2.5 65.4 + - + +
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Residues in contact with THR 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 4.1 20.4 - - + +
458A ILE 5.4 0.2 + - - -
459A GLY 3.4 0.6 - - - -
460A GLU* 1.3 79.2 - - - +
462A ILE* 1.3 65.7 + - - +
464A ARG* 3.3 5.7 + - - +
465A TRP* 3.0 66.6 + - + +
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Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.6 37.9 - - + -
146A SER* 3.5 35.4 - - - +
147A ILE* 5.4 4.3 - - + -
159A LEU* 3.8 25.2 - - + +
198A ILE* 5.9 1.3 - - + -
201A ILE* 4.9 7.2 - - + -
458A ILE 5.5 0.2 - - - +
459A GLY* 3.3 12.2 + - - +
460A GLU 3.3 0.2 - - - -
461A THR* 1.3 80.9 - - + +
463A ALA* 1.3 57.2 + - - +
466A GLU* 2.7 51.8 + - - +
601A HEM 4.5 15.7 - - + -
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Residues in contact with ALA 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A VAL* 4.1 14.8 - - + -
376A PHE* 5.7 0.7 - - - -
450A PHE* 4.0 7.0 - - + -
459A GLY 3.0 17.7 + - - +
460A GLU 3.5 3.8 - - - +
462A ILE* 1.3 78.0 - - - +
464A ARG* 1.3 57.7 + - - +
466A GLU* 4.5 0.2 - - - -
467A VAL* 2.9 37.4 + - - +
601A HEM 3.5 42.1 - - + +
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Residues in contact with ARG 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A ARG* 3.7 29.5 + - - +
369A GLU* 4.4 7.1 + - - -
372A ILE* 5.0 7.3 - - + +
373A LEU* 4.0 22.4 - - - +
376A PHE* 4.4 19.2 - - + -
444A SER 5.4 2.0 + - - -
447A VAL* 4.9 10.3 + - - +
449A ILE* 5.2 1.2 - - - +
450A PHE* 3.2 33.3 - - + -
460A GLU* 2.5 52.9 + - - +
461A THR* 3.9 5.4 - - - +
463A ALA* 1.3 75.0 - - - +
465A TRP* 1.3 67.2 + - + +
467A VAL* 4.3 3.2 - - - +
468A PHE* 3.3 22.5 + - - +
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Residues in contact with TRP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 4.0 36.3 - - + -
157A CYS* 4.7 6.1 - - - -
159A LEU* 3.8 22.2 - - + -
359A LEU* 3.2 40.4 - - + -
362A ARG* 3.9 30.9 - - - +
461A THR* 3.0 40.6 + - + +
464A ARG* 1.3 81.5 - - + +
466A GLU* 1.3 63.9 + - - +
468A PHE* 3.2 6.9 + - - +
469A LEU* 3.0 28.0 + - - +
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Residues in contact with GLU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU* 4.3 5.3 - - + +
163A VAL* 3.8 17.0 - - + -
194A VAL* 3.7 20.8 - - - +
197A VAL* 3.6 31.2 - - - +
198A ILE* 5.0 4.4 + - - +
318A GLY 5.6 0.4 - - - +
322A VAL* 3.9 21.5 - - + +
462A ILE* 2.7 39.9 + - - +
463A ALA* 4.0 3.1 - - - +
465A TRP* 1.3 74.4 - - - +
467A VAL* 1.3 61.7 + - - +
469A LEU* 4.1 1.1 - - - +
470A PHE* 3.2 50.1 + - + -
601A HEM 5.3 0.9 - - - +
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Residues in contact with VAL 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A VAL* 4.1 20.9 - - + -
325A ALA* 4.1 21.1 - - + -
326A ILE* 4.5 15.7 - - + -
329A SER* 4.9 6.3 - - - +
372A ILE* 4.1 20.2 - - + -
376A PHE* 4.7 11.7 - - + -
463A ALA* 2.9 25.3 + - + +
464A ARG* 4.3 3.6 - - - +
466A GLU* 1.3 76.6 - - - +
468A PHE* 1.3 64.5 + - - +
470A PHE* 3.6 1.2 + - - +
471A LEU* 3.2 39.8 + - + +
601A HEM 5.2 0.7 - - + -
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Residues in contact with PHE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A PRO* 5.1 1.3 - - + -
358A ARG 3.5 26.0 - - - -
359A LEU* 4.3 4.7 - - + -
361A ASP* 4.9 0.4 - - + -
362A ARG* 3.4 55.6 - - + +
365A LEU* 3.7 27.6 - - + -
368A MET* 3.7 23.6 - - + +
369A GLU* 5.7 1.3 - - - -
372A ILE* 3.9 14.3 - - + +
464A ARG 3.3 17.6 + - - +
465A TRP* 3.2 7.2 + - - +
467A VAL* 1.3 81.1 - - - +
469A LEU* 1.3 67.2 + - + +
471A LEU* 3.3 2.0 + - - +
472A ALA* 2.8 44.3 + - + +
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Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU* 5.1 1.6 - - + -
160A GLU* 3.8 22.4 - - + +
163A VAL* 3.5 35.4 - - + -
164A SER* 4.6 3.4 - - - +
357A PRO* 3.8 27.6 - - + +
358A ARG* 4.4 5.4 - - - -
359A LEU* 3.2 35.2 - - + -
465A TRP 3.0 15.4 + - - +
466A GLU 4.1 0.4 - - - +
468A PHE* 1.3 83.9 - - + +
470A PHE* 1.3 63.4 + - - +
472A ALA* 3.1 1.3 + - - -
473A ILE* 2.8 45.1 + - + +
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Residues in contact with PHE 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A VAL* 3.7 17.0 - - + +
166A GLU* 4.3 3.1 - - + -
167A ALA* 4.0 32.3 - - + -
170A LEU* 4.6 13.5 - - + -
190A VAL* 6.1 1.3 - - + -
193A SER* 4.1 37.7 - - - -
194A VAL* 4.3 8.3 - - + -
197A VAL* 4.1 6.7 - - + -
326A ILE* 3.7 29.8 - - + -
466A GLU* 3.2 50.5 + - + +
467A VAL 4.1 1.6 - - - +
469A LEU* 1.3 77.2 - - - +
471A LEU* 1.3 64.8 + - + +
474A LEU* 3.1 36.8 + - + +
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ILE* 4.6 12.8 - - + -
329A SER* 4.0 26.5 - - - +
330A LEU* 4.6 18.4 - - + -
333A LEU* 4.7 9.4 - - + -
368A MET* 3.7 29.8 - - + -
371A PHE* 3.8 15.7 - - + -
372A ILE* 4.1 7.0 - - + -
467A VAL* 3.2 30.0 + - + +
468A PHE 3.8 2.2 - - - +
469A LEU 3.2 0.4 - - - -
470A PHE* 1.3 76.2 - - + +
472A ALA* 1.3 60.5 + - - +
474A LEU* 4.6 4.3 - - + -
475A LEU* 2.8 42.7 + - + +
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Residues in contact with ALA 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A LEU* 4.0 16.5 - - + +
357A PRO* 3.6 29.1 - - + +
368A MET* 4.5 5.8 - - - -
468A PHE* 2.8 39.4 + - + +
469A LEU* 3.7 4.7 - - - +
471A LEU* 1.3 73.6 - - - +
473A ILE* 1.3 63.9 + - - +
476A GLN* 3.2 26.3 + - - +
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Residues in contact with ILE 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A VAL 4.5 0.4 - - - +
164A SER* 3.9 25.6 - - - +
167A ALA* 3.7 33.9 - - + -
168A GLU* 4.3 17.5 - - - +
171A ILE* 4.3 8.0 - - + +
356A ARG* 4.0 13.9 - - + +
357A PRO* 4.1 21.8 - - + +
469A LEU* 2.8 44.9 + - + +
470A PHE 4.3 0.2 - - - +
472A ALA* 1.3 72.3 - - - +
474A LEU* 1.3 66.0 + - + +
476A GLN* 4.0 2.0 - - - +
477A ARG* 3.4 24.9 + - - +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA* 4.0 23.1 - - + +
170A LEU* 3.8 26.2 - - + -
171A ILE* 4.0 27.4 - - + -
174A LEU* 5.7 1.8 - - + -
190A VAL* 6.1 0.4 - - + -
326A ILE* 6.0 4.5 - - + -
330A LEU* 5.3 9.2 - - + -
470A PHE* 3.1 28.3 + - + +
471A LEU* 3.9 5.2 - - + +
473A ILE* 1.3 76.6 - - - +
475A LEU* 1.3 62.8 + - + +
476A GLN 3.1 1.8 - - - -
477A ARG* 2.8 6.8 + - - +
478A VAL* 2.8 42.3 + - + +
480A PHE* 4.1 22.9 - - + -
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LEU* 5.6 0.2 - - + -
333A LEU* 3.8 33.9 - - + -
340A GLN* 4.3 15.9 - - + +
343A ILE* 3.5 34.1 - - + -
344A GLN* 3.3 31.9 + - + +
347A LEU* 4.1 11.2 - - + -
368A MET* 4.5 1.3 - - + -
471A LEU* 2.8 38.1 + - + +
474A LEU* 1.3 75.1 - - + +
476A GLN* 1.3 59.9 + - - +
478A VAL 3.4 8.6 - - - +
480A PHE* 4.2 23.6 - - + -
511A ARG* 3.6 2.9 + - - -
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Residues in contact with GLN 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A LEU* 3.7 18.0 - - + +
348A ASP* 5.2 0.4 - - - +
351A ILE* 4.3 3.0 - - - +
352A GLY 2.8 26.8 + - - +
353A ARG* 3.7 19.8 + - + +
355A ARG 2.6 29.3 + - - +
356A ARG* 3.9 5.2 - - - +
357A PRO* 3.4 22.8 - - + +
472A ALA 3.2 17.7 + - - +
473A ILE* 4.0 3.1 - - - +
474A LEU 3.0 1.0 + - - -
475A LEU* 1.3 78.2 - - - +
477A ARG* 1.3 74.7 + - + +
511A ARG* 2.9 30.5 + - - +
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Residues in contact with ARG 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLU* 2.4 44.1 + - - -
171A ILE* 3.9 27.2 - - + +
175A GLN* 4.9 7.3 - - - +
356A ARG* 5.5 4.7 - - - +
473A ILE* 3.4 18.4 - - - +
474A LEU 2.8 8.1 + - - +
476A GLN* 1.3 97.1 - - - +
478A VAL* 1.3 68.0 + - + +
510A LEU* 3.7 16.3 - - + +
511A ARG* 3.5 23.1 + - - +
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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