Contacts of the helix formed by residues 454 - 470 (chain B) in PDB entry 5FS9
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 HIS 454 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B ASP* 3.8 0.7 + - - +
450B ARG* 5.8 2.2 - - - -
452B VAL* 3.3 24.9 + - + +
453B GLU* 1.3 88.9 + - + +
455B HIS* 1.3 65.5 + - - +
457B HIS* 3.1 10.5 + - + +
458B ALA* 2.9 18.5 + - - +
480B SER* 4.3 4.9 + - - -
481B MET 3.9 17.3 + - - +
482B PHE* 3.5 41.6 - + + +
494B ALA* 5.6 2.0 - - + -
495B ILE* 6.4 0.9 - - - -
496B GLY 5.7 4.9 - - - -
1000B FAD 3.1 20.7 + - - +
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Residues in contact with HIS 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR* 3.9 26.1 + - + +
171B MET* 4.0 24.5 - - + -
173B PRO* 3.9 16.0 - - + +
205B PHE* 4.2 9.7 - + - -
454B HIS* 1.3 69.9 - - - +
456B ASP* 1.3 63.5 + - - +
458B ALA* 3.0 5.8 + - - +
459B VAL* 3.0 30.9 + - + +
483B TRP* 3.9 18.2 - + + -
528B ILE* 3.7 16.2 - - + +
530B SER 3.3 24.6 + - - -
1000B FAD 3.1 44.5 + - + +
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Residues in contact with ASP 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B HIS* 3.3 2.0 - - - +
455B HIS* 1.3 81.4 - - - +
457B HIS* 1.3 57.4 + - - +
459B VAL* 3.3 8.2 + - - +
460B VAL* 2.8 39.6 + - - +
478B HIS* 4.9 0.9 + - - -
480B SER* 3.4 8.9 - - - -
481B MET* 3.1 44.8 + - + +
483B TRP* 5.2 0.4 - - + -
530B SER* 3.1 40.3 + - - +
589B ARG* 4.6 1.7 + - - -
1000B FAD 4.4 1.4 + - - -
1001B GOL 4.3 6.2 + - - -
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Residues in contact with HIS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 6.0 0.4 - - + +
437B GLY 4.0 15.5 + - - -
438B ASP* 5.8 0.2 - - - -
440B ALA* 5.0 1.6 + - - +
442B PHE* 3.4 38.3 - + - -
452B VAL* 3.5 40.5 + - + +
454B HIS* 3.1 12.0 + - + +
456B ASP* 1.3 77.9 - - - +
458B ALA* 1.3 55.4 + - - +
460B VAL* 4.4 0.7 - - - -
461B SER* 2.6 59.0 + - - -
476B TYR* 3.2 35.9 + + - -
480B SER* 3.3 19.6 + - - +
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Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR* 3.6 15.0 - - + -
142B ALA* 3.4 21.0 - - + +
437B GLY* 4.1 7.0 - - - -
438B ASP* 5.2 0.2 - - - +
454B HIS 2.9 9.2 + - - +
455B HIS 3.0 8.0 + - - +
457B HIS* 1.3 77.1 - - - +
459B VAL* 1.3 57.3 + - - +
461B SER* 3.8 4.7 - - - -
462B GLY* 2.9 24.3 + - - -
1000B FAD 3.5 35.7 - - - +
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Residues in contact with VAL 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR* 3.7 17.3 - - + -
145B ALA* 3.5 15.5 - - + +
205B PHE* 5.7 3.4 - - + -
455B HIS* 3.0 31.5 + - + +
456B ASP* 3.6 13.5 - - - +
458B ALA* 1.3 75.3 - - - +
460B VAL* 1.3 58.6 + - + +
463B ARG* 2.9 66.2 + - - +
530B SER 4.8 2.5 - - - +
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ASP* 2.8 40.6 + - - +
457B HIS* 4.1 3.8 - - - +
459B VAL* 1.3 75.5 - - + +
461B SER* 1.3 60.2 + - - +
463B ARG* 3.6 12.5 - - - +
464B LEU* 3.0 28.5 + - + +
476B TYR* 3.9 18.2 - - + +
478B HIS* 3.7 47.6 - - + +
480B SER* 4.5 2.7 - - - -
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Residues in contact with SER 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 3.3 28.4 - - - +
436B ALA* 3.8 4.5 - - - -
437B GLY* 3.0 26.5 + - - -
457B HIS* 2.6 47.5 + - - -
458B ALA 3.6 1.2 + - - -
460B VAL* 1.3 74.5 - - - +
462B GLY* 1.3 59.7 + - - +
464B LEU* 4.3 2.2 - - - -
465B ALA* 2.8 27.0 + - - +
476B TYR* 4.6 4.5 - - - -
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Residues in contact with GLY 462 (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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142B ALA 3.4 22.9 - - - -
145B ALA* 4.3 0.2 - - - -
146B ALA* 3.2 19.9 - - - +
436B ALA* 3.8 11.6 - - - +
458B ALA 2.9 15.9 + - - -
459B VAL 3.9 0.7 - - - -
461B SER* 1.3 77.0 + - - +
463B ARG* 1.3 56.3 + - - +
465B ALA* 3.3 1.1 + - - +
466B GLY 2.9 24.6 + - - -
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Residues in contact with ARG 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA* 4.0 11.2 + - + +
149B SER* 2.8 38.3 + - - +
459B VAL* 2.9 46.4 + - - +
460B VAL* 3.6 11.7 - - - +
462B GLY* 1.3 75.8 - - - +
464B LEU* 1.3 57.0 + - - +
466B GLY 3.2 1.4 + - - -
467B GLU* 3.0 29.7 + - - +
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Residues in contact with LEU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ALA 4.5 0.4 - - - +
427B LEU* 3.9 20.2 - - + -
460B VAL* 3.0 19.0 + - + +
461B SER 3.7 4.0 - - - +
463B ARG* 1.3 73.2 - - - +
465B ALA* 1.3 61.5 + - - +
467B GLU* 3.1 18.6 + - - +
468B ASN* 2.8 36.0 + - - +
474B LYS* 3.6 35.0 - - + +
475B PRO 4.0 4.5 - - - +
476B TYR* 3.6 42.6 - - + +
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Residues in contact with ALA 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 3.7 31.6 - - + -
427B LEU* 4.1 12.7 - - + +
434B TRP* 4.3 12.8 - - + -
436B ALA* 4.3 3.1 - - + -
461B SER 2.8 21.1 + - - +
462B GLY 3.7 4.3 - - - +
464B LEU* 1.3 71.9 - - - +
466B GLY* 1.3 51.4 + - - +
468B ASN* 3.0 8.8 + - - +
469B MET* 2.7 42.4 + - - +
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Residues in contact with GLY 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 4.1 6.6 - - - +
149B SER* 3.9 7.9 - - - -
150B ILE* 3.7 26.5 - - - +
462B GLY 2.9 14.9 + - - -
463B ARG 3.5 4.7 - - - -
464B LEU 3.2 0.2 - - - -
465B ALA* 1.3 76.1 - - - +
467B GLU* 1.3 60.6 + - - +
469B MET* 3.3 5.8 + - - +
470B THR* 3.0 25.5 + - - +
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Residues in contact with GLU 467 (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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149B SER* 3.5 9.0 + - - +
153B ARG* 3.8 21.4 - - - +
463B ARG* 3.0 30.5 + - - +
464B LEU* 3.1 17.6 + - - +
466B GLY* 1.3 74.8 - - - +
468B ASN* 1.3 60.3 + - - +
470B THR* 2.9 19.8 + - - -
472B ALA* 3.0 33.2 + - + +
474B LYS* 3.0 33.5 + - - -
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Residues in contact with ASN 468 (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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426B GLU* 2.9 27.7 + - + +
434B TRP* 3.6 32.2 - - + +
464B LEU* 2.8 23.6 + - - +
465B ALA 3.7 2.0 - - - +
467B GLU* 1.3 77.6 - - - +
469B MET* 1.3 57.3 + - - +
471B GLY* 3.1 17.0 + - - -
472B ALA* 3.4 9.7 + - - +
473B ALA* 3.1 11.3 + - - +
474B LYS* 2.8 48.9 + - - +
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Residues in contact with MET 469 (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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134B PHE* 3.7 26.4 - - + -
136B LEU* 3.8 17.7 - - + -
146B ALA* 5.3 0.2 - - - -
150B ILE* 4.2 10.5 - - + -
255B LYS* 3.0 36.6 + - + +
256B CYS 3.7 14.6 - - - +
257B LEU* 3.7 43.5 - - - +
434B TRP* 3.5 32.5 - - + -
465B ALA* 2.7 30.2 + - - +
466B GLY* 3.7 7.2 - - - +
467B GLU 3.2 0.4 - - - -
468B ASN* 1.3 71.8 - - - +
470B THR* 1.3 57.4 - - - +
471B GLY 3.4 1.1 - - - -
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Residues in contact with THR 470 (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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134B PHE* 4.0 23.3 - - + -
150B ILE* 4.1 13.5 - - + +
153B ARG* 3.0 44.4 + - + +
154B ASP* 4.3 15.5 - - + +
255B LYS* 5.1 1.1 - - - +
466B GLY 3.0 12.6 + - - +
467B GLU 2.9 15.1 + - - -
469B MET* 1.3 79.9 - - - +
471B GLY* 1.3 55.3 + - - +
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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