Contacts of the helix formed by residues 487 - 504 (chain D) in PDB entry 3D8F
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 PRO 487 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399C ARG 4.8 3.6 - - - +
400C GLN 4.4 0.7 - - - +
402C SER 3.8 7.6 - - - +
403C TYR* 3.8 39.7 - - + +
462D GLU 5.6 1.6 - - - +
463D ARG* 4.6 2.2 - - + -
486D ALA* 1.3 82.4 - - + +
488D ALA* 1.3 64.5 + - - +
489D LYS* 2.6 20.5 + - + +
490D ASN* 2.7 52.7 + - - +
491D ILE* 3.8 2.2 + - - +
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Residues in contact with ALA 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D VAL* 3.7 17.5 - - + +
462D GLU 4.7 2.2 + - - +
463D ARG* 3.9 5.7 - - - +
464D ASP 3.1 45.3 - - - +
465D PHE* 3.9 8.9 - - + +
484D CYS* 4.5 9.2 - - - -
486D ALA 2.6 10.7 + - - -
487D PRO* 1.3 69.9 - - - +
489D LYS* 1.3 54.9 + - - +
491D ILE* 3.0 23.5 + - - +
492D ALA 3.4 9.0 + - - -
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Residues in contact with LYS 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D VAL* 3.8 20.6 - - + +
462D GLU 5.8 0.2 + - - -
487D PRO* 2.6 18.9 + - + +
488D ALA* 1.3 72.4 - - - +
490D ASN* 1.3 73.5 + - - +
492D ALA* 3.8 3.1 + - + +
493D THR* 2.7 45.5 + - - +
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Residues in contact with ASN 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C ARG 4.0 2.3 + - - +
400C GLN* 2.8 53.4 + - - +
370D PHE* 4.6 6.1 - - + -
486D ALA* 5.4 0.2 - - + -
487D PRO* 2.7 44.4 + - - +
489D LYS* 1.3 92.3 + - - +
491D ILE* 1.3 59.9 + - - +
493D THR* 3.5 8.7 + - - +
494D SER* 2.8 31.9 + - - -
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Residues in contact with ILE 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D PHE* 3.8 45.3 - - + -
372D VAL* 4.5 0.2 - - + -
424D LEU* 4.3 26.2 - - + -
426D LEU* 4.7 6.3 - - + -
431D LEU* 5.6 0.2 - - + -
465D PHE* 3.8 30.1 - - + -
484D CYS* 3.8 28.3 - - + -
486D ALA* 5.8 0.9 - - + -
487D PRO 4.7 2.2 - - - +
488D ALA* 3.0 13.9 + - - +
490D ASN* 1.3 73.4 - - - +
492D ALA* 1.3 67.0 + - - +
494D SER* 3.0 8.1 + - - -
495D LEU* 2.9 25.9 + - + +
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Residues in contact with ALA 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D TRP* 3.2 35.8 + - + +
454D GLY* 5.4 0.4 - - - -
455D VAL* 4.4 14.6 - - + -
465D PHE* 4.0 4.7 - - + -
488D ALA 3.4 8.1 + - - +
489D LYS 4.0 7.0 - - - +
491D ILE* 1.3 76.7 - - - +
493D THR* 1.3 64.7 + - - +
495D LEU* 3.0 6.8 + - - +
496D HIS* 2.9 29.0 + - + +
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Residues in contact with THR 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C GLN* 6.1 0.9 - - - +
368D LYS* 6.1 0.9 - - - +
489D LYS* 2.7 36.0 + - - +
490D ASN* 3.5 10.7 - - - +
492D ALA* 1.3 74.3 - - - +
494D SER* 1.3 66.1 + - - +
496D HIS* 3.1 23.2 - - - +
497D GLU* 3.1 24.9 - - - +
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Residues in contact with SER 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C GLN* 4.3 1.2 + - - -
368D LYS* 3.0 29.6 + - - +
370D PHE* 3.9 10.0 - - - -
426D LEU* 3.5 22.7 - - - -
490D ASN 2.8 16.6 + - - -
491D ILE* 3.0 8.0 + - - -
493D THR* 1.3 76.0 - - - +
495D LEU* 1.3 62.9 + - - +
496D HIS 2.9 1.6 + - - -
497D GLU* 2.9 21.8 + - - +
498D ILE* 3.0 17.5 + - - +
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Residues in contact with LEU 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426D LEU* 4.2 18.6 - - + -
431D LEU* 4.7 2.9 - - + -
447D ILE* 3.7 39.3 - - + -
450D ILE* 4.5 11.7 - - + -
453D TRP* 3.6 41.5 - - + -
465D PHE* 3.7 27.4 - - + -
491D ILE* 2.9 18.8 + - + +
492D ALA* 3.5 6.3 - - - +
494D SER* 1.3 74.7 - - - +
496D HIS* 1.3 56.0 + - - +
498D ILE* 3.6 6.8 + - - +
499D CYS* 2.8 35.7 + - - -
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Residues in contact with HIS 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D TRP* 3.5 31.3 + + - -
492D ALA* 2.9 14.5 + - + +
493D THR* 3.1 14.8 - - - +
495D LEU* 1.3 75.7 - - - +
497D GLU* 1.3 68.9 + - + +
499D CYS* 4.1 2.6 - - - +
500D SER* 2.9 27.5 + - - -
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Residues in contact with GLU 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D LYS* 4.6 11.5 + - - +
493D THR* 3.1 27.6 - - - +
494D SER* 3.4 11.2 - - - +
496D HIS* 1.3 74.6 - - + +
498D ILE* 1.3 55.1 + - + +
500D SER* 3.0 8.1 + - - -
501D LYS* 2.7 48.4 + - - +
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Residues in contact with ILE 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D GLY 6.0 2.0 - - - +
368D LYS* 6.4 1.3 - - + -
426D LEU* 4.0 33.7 - - + +
427D GLU* 6.1 0.4 - - - -
429D GLU* 4.5 11.7 - - + +
447D ILE* 3.7 36.1 - - + -
494D SER* 3.0 14.9 + - - +
495D LEU* 3.7 7.9 - - - +
497D GLU* 1.3 80.2 - - + +
499D CYS* 1.3 51.4 + - - +
501D LYS* 2.9 19.6 + - - +
502D ILE* 2.8 49.8 + - + +
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Residues in contact with CYS 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D ILE* 3.6 26.9 - - - -
448D ILE* 5.7 5.6 - - + -
453D TRP* 3.7 21.1 - - + -
495D LEU 2.8 30.5 + - - +
496D HIS* 4.1 3.1 - - - +
498D ILE* 1.3 68.9 - - - +
500D SER* 1.3 54.8 + - - +
502D ILE* 3.3 10.1 + - - +
503D MET* 2.7 42.0 + - + +
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Residues in contact with SER 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D HIS* 2.9 21.1 + - - -
497D GLU* 3.0 11.4 + - - -
499D CYS* 1.3 74.1 - - - +
501D LYS* 1.3 62.5 + - - +
503D MET* 2.9 32.1 - - - +
504D ALA* 3.3 7.6 + - - +
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Residues in contact with LYS 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D GLU* 2.7 32.6 + - - +
498D ILE* 3.3 20.2 - - - +
500D SER* 1.3 76.6 + - - +
502D ILE* 1.3 64.9 + - - +
504D ALA* 3.1 20.9 + - + +
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Residues in contact with ILE 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D GLU* 3.6 37.0 - - + -
447D ILE* 5.2 3.6 - - + -
448D ILE* 3.5 36.3 - - + -
498D ILE* 2.8 29.4 + - + +
499D CYS* 3.6 8.7 - - - +
501D LYS* 1.3 66.3 - - + +
503D MET* 1.3 64.9 + - - +
504D ALA 2.7 6.8 + - - -
505D GLU* 2.8 44.6 + - + +
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Residues in contact with MET 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D CYS* 2.7 26.1 + - + +
500D SER* 2.9 23.6 - - - +
502D ILE* 1.3 74.6 - - - +
504D ALA* 1.3 53.8 + - - +
505D GLU* 3.1 11.1 + - - +
506D LEU* 3.6 27.5 + - + +
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Residues in contact with ALA 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D SER 3.3 7.7 + - - +
501D LYS* 3.1 17.3 + - + +
502D ILE 2.7 6.4 + - - -
503D MET* 1.3 70.3 - - - +
505D GLU* 1.3 53.9 + - - -
506D LEU* 3.2 12.1 - - - +
507D GLU* 3.4 20.8 - - - +
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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