Contacts of the helix formed by residues 452 - 470 (chain H) in PDB entry 4DVQ
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 452 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H VAL* 4.6 5.8 - - - -
450H CYS* 3.2 9.0 - - - -
451H LEU* 1.3 79.3 - - - +
453H ARG* 1.3 64.5 + - - +
454H ARG 3.1 3.3 + - - -
455H LEU* 3.1 7.6 + - - +
456H ALA* 2.9 21.8 + - - +
601H HEM 3.7 36.3 - - - -
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Residues in contact with ARG 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H LEU* 3.8 8.7 - - + +
366H ARG* 3.6 21.4 - - - +
443H PHE* 3.7 39.0 - - + -
449H GLN* 4.4 19.0 + - - -
450H CYS* 3.3 24.9 - - + +
451H LEU 3.4 2.2 - - - -
452H GLY* 1.3 76.1 - - - +
454H ARG* 1.3 99.7 + - - +
456H ALA* 3.1 2.5 + - - +
457H GLU* 2.6 63.0 + - - +
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Residues in contact with ARG 454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H VAL 5.1 0.4 + - - +
149H LEU* 2.6 59.1 + - + +
150H SER* 4.2 0.4 - - - +
151H PRO* 3.7 25.5 - - - +
154H VAL* 3.7 29.4 - - + +
157H PHE* 4.2 6.5 - - + -
366H ARG* 5.6 1.0 - - - +
452H GLY 3.2 0.6 - - - -
453H ARG* 1.3 121.6 - - - +
455H LEU* 1.3 65.3 + - - +
457H GLU* 4.3 5.9 - - - +
458H ALA* 3.3 22.9 + - - +
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Residues in contact with LEU 455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H VAL* 4.9 6.4 + - + +
157H PHE* 3.7 29.8 - - + -
161H VAL* 4.0 8.1 - - + -
200H SER* 4.6 6.7 - - - +
203H ALA* 3.5 30.3 - - + -
204H LEU* 4.7 10.8 - - + -
289H ILE* 4.3 18.2 - - + -
315H SER* 4.9 1.3 - - - -
452H GLY* 3.1 11.0 + - - +
454H ARG* 1.3 75.8 - - - +
456H ALA* 1.3 63.2 + - - +
458H ALA* 3.3 3.6 + - - +
459H GLU* 3.0 49.8 + - - +
601H HEM 3.9 24.5 - - + -
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Residues in contact with ALA 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H THR* 3.8 22.4 - - + +
443H PHE* 4.5 2.0 - - + -
452H GLY 2.9 12.3 + - - +
453H ARG* 3.3 9.6 - - - +
455H LEU* 1.3 76.7 - - - +
457H GLU* 1.3 62.4 + - - +
459H GLU* 3.3 5.0 + - - +
460H MET* 3.1 30.1 + - - +
601H HEM 3.8 36.5 - - + +
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Residues in contact with GLU 457 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H ARG* 3.5 32.5 + - - +
369H LEU* 4.3 12.2 - - + +
370H LYS* 5.0 4.7 + - - -
440H HIS* 5.6 3.2 + - - -
443H PHE* 4.3 20.7 - - + -
453H ARG* 2.6 61.7 + - - +
454H ARG* 4.4 6.3 - - + +
456H ALA* 1.3 73.4 - - - +
458H ALA* 1.3 56.8 + - - +
460H MET* 3.8 7.4 - - - +
461H LEU* 2.8 35.3 + - + +
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Residues in contact with ALA 458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H VAL* 5.2 2.2 - - + -
157H PHE* 4.7 6.1 - - + -
158H LEU* 4.5 17.7 - - + -
161H VAL* 4.0 16.8 - - + -
359H THR* 5.8 3.8 - - + -
454H ARG 3.3 18.4 + - - +
455H LEU* 3.6 5.2 - - - +
456H ALA 3.3 0.6 - - - -
457H GLU* 1.3 73.8 - - - +
459H GLU* 1.3 67.8 + - - +
461H LEU* 4.5 6.1 - - - -
462H LEU* 2.9 38.4 + - + +
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Residues in contact with GLU 459 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H VAL* 3.7 12.3 - - + +
195H TYR* 2.7 37.6 + - + +
196H THR* 3.8 21.1 - - - -
199H ALA* 3.7 21.5 - - + +
200H SER* 2.8 37.1 + - - -
315H SER* 4.3 0.4 - - - +
319H THR* 3.9 19.1 + - + +
455H LEU* 3.0 32.7 + - - +
456H ALA* 3.3 5.6 + - - +
458H ALA* 1.3 79.5 - - - +
460H MET* 1.3 63.0 + - - +
463H LEU* 3.4 6.1 + - - +
601H HEM 6.1 0.4 - - - -
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Residues in contact with MET 460 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H THR* 3.3 24.5 - - + +
322H PRO* 3.5 16.2 - - + +
323H LEU* 3.4 43.9 - - + +
326H THR* 4.3 0.2 - - - +
369H LEU* 3.6 39.0 - - + -
372H THR* 5.4 0.9 - - + -
373H LEU* 5.4 6.7 - - + -
443H PHE* 6.1 0.4 - - - -
456H ALA 3.1 18.7 + - - +
457H GLU* 3.9 2.7 - - - +
459H GLU* 1.3 78.9 - - - +
461H LEU* 1.3 61.9 + - - +
463H LEU* 4.0 0.9 - - - +
464H LEU* 3.3 31.3 + - - +
601H HEM 4.3 19.7 - - - -
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Residues in contact with LEU 461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H LEU* 6.3 0.4 - - + -
358H ALA* 3.4 37.7 - - + +
359H THR* 3.9 17.0 - - + +
362H LEU* 4.3 13.9 - - + +
365H LEU* 3.8 31.2 - - + +
366H ARG* 4.0 30.3 - - + +
369H LEU* 4.3 10.3 - - + +
457H GLU* 2.8 21.1 + - + +
458H ALA* 3.2 4.9 + - - +
460H MET* 1.3 75.6 - - - +
462H LEU* 1.3 60.1 + - + +
464H LEU* 3.8 4.2 - - - +
465H HIS* 2.9 30.4 + - - +
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Residues in contact with LEU 462 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H LEU* 3.8 33.0 - - + +
161H VAL* 3.6 27.1 - - + -
162H ASP* 3.5 25.4 - - + +
165H ALA* 3.7 14.4 - - + -
351H ILE* 4.9 6.1 - - + -
355H PRO 4.4 6.7 - - - +
358H ALA* 3.7 29.6 - - + -
458H ALA* 2.9 17.7 + - + +
461H LEU* 1.3 77.4 - - + +
463H LEU* 1.3 59.3 + - - +
465H HIS* 3.4 5.1 + - + +
466H HIS* 3.0 38.3 + - + -
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Residues in contact with LEU 463 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H ALA* 3.8 12.2 - - - +
168H PHE* 4.5 13.2 - - + -
192H ILE* 3.6 21.8 - - + -
195H TYR* 3.2 40.6 - - + -
323H LEU* 3.3 26.5 - - + -
327H LEU* 4.8 5.2 - - + -
459H GLU 3.4 17.4 + - - +
460H MET 4.0 2.2 - - - +
462H LEU* 1.3 74.1 - - - +
464H LEU* 1.3 77.2 + - + +
466H HIS* 3.1 3.6 + - - +
467H VAL* 2.9 40.5 + - + +
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Residues in contact with LEU 464 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H LEU* 3.8 17.5 - - + -
326H THR* 3.7 21.1 - - + -
327H LEU* 3.5 33.4 - - + -
330H LEU* 5.3 7.0 - - + -
365H LEU* 4.1 22.2 - - + -
369H LEU* 3.6 30.3 - - + -
460H MET 3.3 19.4 + - - +
461H LEU* 3.8 3.1 - - - +
463H LEU* 1.3 79.9 - - + +
465H HIS* 1.3 65.0 + - - +
467H VAL* 3.1 4.2 + - + +
468H LEU* 2.9 33.5 + - + +
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Residues in contact with HIS 465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344H SER* 2.7 49.7 + - - -
348H ALA* 4.5 3.4 - - - -
351H ILE* 3.4 42.9 - - + +
362H LEU* 3.7 17.2 - - + +
365H LEU* 3.9 3.8 - - + +
461H LEU 2.9 19.8 + - - +
462H LEU* 3.5 9.4 - - + +
464H LEU* 1.3 77.8 - - - +
466H HIS* 1.3 90.9 + + - +
468H LEU* 3.4 9.7 + - - +
469H LYS* 3.5 32.9 + - + +
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Residues in contact with HIS 466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H ASP* 3.0 29.8 - - - -
165H ALA* 3.9 17.0 - - - +
166H ARG* 3.6 41.6 + - + -
169H SER* 3.1 18.0 + - - +
351H ILE* 5.2 0.8 - - + +
462H LEU* 3.0 26.6 + - + +
463H LEU 3.1 3.1 + - - +
465H HIS* 1.3 97.5 + + - +
467H VAL* 1.3 59.2 + - - +
469H LYS* 3.4 30.2 + - - +
470H HIS* 2.9 34.0 + + + +
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Residues in contact with VAL 467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H PHE* 4.3 19.1 - - + -
169H SER* 4.0 8.5 - - - +
172H LEU* 5.3 1.3 - - + -
327H LEU* 4.8 7.4 - - + -
463H LEU* 2.9 37.2 + - + +
464H LEU* 3.7 7.0 - - - +
466H HIS* 1.3 72.7 - - - +
468H LEU* 1.3 65.3 + - + +
469H LYS 3.1 2.5 - - - -
470H HIS 3.1 1.6 + - - -
471H PHE* 2.8 48.6 + - + +
473H VAL* 4.2 12.1 - - + -
499H PHE* 3.9 27.8 - - + -
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Residues in contact with LEU 468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H LEU* 6.5 0.9 - - + -
330H LEU* 3.9 23.6 - - + -
337H GLN* 4.1 24.2 - - + +
340H LEU* 3.8 33.9 - - + +
341H ARG* 3.1 47.6 + - - +
344H SER* 4.2 13.2 - - - +
365H LEU* 4.3 18.6 - - + -
464H LEU* 2.9 23.5 + - + +
465H HIS 3.8 3.6 - - - +
467H VAL* 1.3 78.8 - - + +
469H LYS* 1.3 59.7 + - - +
470H HIS 3.6 0.2 + - - -
471H PHE 3.8 5.5 - - - +
473H VAL* 5.5 5.6 - - + -
502H ILE* 4.0 0.2 - - - +
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Residues in contact with LYS 469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H ARG* 4.4 10.5 - - - +
344H SER* 4.5 8.3 - - - -
345H LEU* 4.3 28.8 - - + +
348H ALA* 3.8 33.2 + - + +
352H SER* 5.3 3.6 + - - -
465H HIS* 3.5 26.0 + - + +
466H HIS* 3.4 42.5 + - - +
467H VAL 3.1 0.4 - - - -
468H LEU* 1.3 77.3 - - - +
470H HIS* 1.3 84.2 + - + +
502H ILE* 3.7 12.9 - - - +
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Residues in contact with HIS 470 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H SER* 3.9 11.0 - - - -
170H GLN* 4.3 16.4 + - - -
173H LYS* 4.0 31.1 - - + +
466H HIS* 2.9 27.6 + + - +
467H VAL 3.1 1.8 + - - -
469H LYS* 1.3 112.5 + - + +
471H PHE* 1.3 81.7 + - + +
501H ALA* 3.3 6.1 - - - +
502H ILE* 3.1 27.0 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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