Contacts of the helix formed by residues 450 - 464 (chain A) in PDB entry 3W6R
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 ASP 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A ILE* 3.5 4.8 - - + +
449A THR* 1.3 76.3 + - - +
451A GLU* 1.3 61.8 + - - +
452A ASP* 3.6 11.0 + - - +
453A ASN* 2.9 50.6 + - + +
454A SER* 2.8 31.1 + - - -
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Residues in contact with GLU 451 (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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449A THR 3.2 7.7 + - - +
450A ASP* 1.3 72.8 + - - +
452A ASP* 1.3 62.7 + - - +
454A SER* 3.3 3.7 + - - -
455A ILE* 2.9 50.8 + - + +
530A ARG* 2.8 32.8 + - - +
533A SER* 5.8 2.9 - - - -
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Residues in contact with ASP 452 (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 ASP* 3.4 9.9 + - - +
451A GLU* 1.3 81.9 - - - +
453A ASN* 1.3 61.4 + - - +
455A ILE* 3.5 5.6 + - - +
456A ALA* 2.9 29.9 + - - +
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Residues in contact with ASN 453 (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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448A ILE* 3.9 22.1 - - + +
450A ASP* 2.9 29.5 + - - +
452A ASP* 1.3 76.4 - - - +
454A SER* 1.3 60.6 + - - +
456A ALA* 3.5 8.0 + - - +
457A ALA* 2.9 29.6 + - - +
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Residues in contact with SER 454 (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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445A ALA 2.8 24.0 + - - +
448A ILE* 3.4 19.8 + - - +
450A ASP 2.8 17.4 + - - -
451A GLU 3.7 3.4 - - - -
453A ASN* 1.3 73.7 - - - +
455A ILE* 1.3 60.2 + - - +
457A ALA* 3.3 3.3 + - - +
458A MET* 2.8 34.0 + - - +
530A ARG* 2.9 36.3 + - - -
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Residues in contact with ILE 455 (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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451A GLU* 2.9 43.7 + - + +
452A ASP* 3.8 5.6 - - - +
454A SER* 1.3 75.5 - - - +
456A ALA* 1.3 57.2 + - - +
458A MET* 3.2 6.8 + - + +
459A TYR* 2.8 61.2 + - + +
530A ARG* 4.6 18.6 - - - +
533A SER* 5.6 6.3 - - - +
534A LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 456 (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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452A ASP 2.9 19.0 + - - +
453A ASN* 3.7 9.9 - - - +
455A ILE* 1.3 78.2 - - - +
457A ALA* 1.3 56.6 + - - +
459A TYR* 3.4 12.3 + - - +
460A GLN* 3.0 26.9 + - - +
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Residues in contact with ALA 457 (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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445A ALA* 3.6 27.1 - - + +
448A ILE* 4.0 11.4 - - + -
453A ASN 2.9 18.3 + - - +
454A SER 3.7 2.0 - - - +
456A ALA* 1.3 73.6 - - - +
458A MET* 1.3 65.8 + - - +
460A GLN* 3.4 7.5 + - - +
461A ALA* 3.1 23.9 + - - +
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Residues in contact with MET 458 (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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442A PHE* 3.6 32.7 - - + +
445A ALA* 3.6 20.2 - - - -
446A ALA* 3.9 11.9 - - - -
454A SER* 2.8 25.2 + - - +
455A ILE* 3.4 11.7 - - + +
457A ALA* 1.3 74.1 - - - +
459A TYR* 1.3 65.4 + - - +
461A ALA* 3.2 3.7 + - - +
462A VAL* 3.0 29.9 + - - +
527A VAL* 4.1 9.0 - - + +
530A ARG* 4.0 26.2 - - + -
531A LEU* 3.6 32.1 - - + +
534A LEU* 4.6 13.7 - - + -
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Residues in contact with TYR 459 (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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455A ILE* 2.8 45.3 + - + +
456A ALA* 3.6 9.6 - - - +
458A MET* 1.3 72.8 - - - +
460A GLN* 1.3 62.0 + - - +
462A VAL* 3.6 2.1 + - - +
463A GLY* 3.1 19.8 + - - -
534A LEU* 3.6 22.8 - - + +
535A PRO* 4.2 15.4 - - - +
538A TYR* 3.5 54.9 + + + +
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Residues in contact with GLN 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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456A ALA 3.0 16.4 + - - +
457A ALA* 3.5 9.6 - - - +
458A MET 3.2 0.2 - - - -
459A TYR* 1.3 77.6 - - - +
461A ALA* 1.3 60.1 + - - +
463A GLY* 3.3 3.9 + - - -
464A GLU* 3.3 44.7 + - - +
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Residues in contact with ALA 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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438A LEU* 3.6 14.0 - - + +
441A ALA* 4.8 9.9 - - + +
442A PHE* 3.6 43.5 - - + +
445A ALA* 5.2 0.4 - - + -
457A ALA 3.1 16.4 + - - +
458A MET* 3.2 2.0 + - - +
460A GLN* 1.3 73.3 - - - +
462A VAL* 1.3 65.2 + - - +
464A GLU* 3.2 20.7 + - - +
465A LEU* 3.5 7.6 + - - +
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Residues in contact with VAL 462 (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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442A PHE* 3.9 7.9 - - + -
458A MET 3.0 17.9 + - - +
459A TYR 3.9 0.4 - - - +
461A ALA* 1.3 75.6 - - - +
463A GLY* 1.3 58.9 + - - +
465A LEU* 3.1 23.3 + - + +
470A ARG* 3.0 42.8 + - + -
473A LEU* 4.5 1.6 - - + -
531A LEU* 3.9 28.3 - - + -
534A LEU* 4.8 2.7 - - + -
538A TYR* 3.3 25.4 - - + +
539A TRP* 3.9 19.3 - - + -
542A PHE* 4.7 0.4 - - + -
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Residues in contact with GLY 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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459A TYR 3.1 14.7 + - - -
460A GLN* 3.3 5.1 + - - -
461A ALA 3.3 0.4 - - - -
462A VAL* 1.3 75.7 - - - +
464A GLU* 1.3 59.6 + - - +
465A LEU 3.3 0.9 - - - +
470A ARG* 3.4 18.7 + - - -
538A TYR* 4.9 1.5 + - - -
542A PHE* 6.4 0.4 - - - -
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Residues in contact with GLU 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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437A ARG* 3.0 33.5 + - - +
438A LEU* 3.8 23.8 - - + +
441A ALA* 5.4 2.3 - - - +
460A GLN* 3.3 34.6 + - + +
461A ALA* 3.2 17.7 + - - +
462A VAL 3.1 1.0 - - - -
463A GLY* 1.3 75.8 - - - +
465A LEU* 1.3 64.4 + - - +
466A PRO* 3.8 0.9 - - - +
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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