Contacts of the helix formed by residues 447 - 463 (chain A) in PDB entry 3P4P
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 ASN 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A GLY 3.6 4.0 + - - -
446A GLU* 1.3 72.2 + - - +
448A TRP* 1.3 78.8 + - - +
449A ALA* 3.4 21.6 + - - +
450A LYS* 3.0 38.4 + - + +
451A ILE* 3.4 10.7 + - - +
489A VAL* 4.6 1.1 - - - -
45B ASP 3.0 26.7 + - - +
46B ASN* 4.8 2.6 - - - +
49B PRO* 5.8 3.0 - - - +
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Residues in contact with TRP 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLU 3.5 5.7 + - - -
447A ASN* 1.3 79.0 + - - +
449A ALA* 1.3 80.5 + - - +
451A ILE* 2.8 7.1 + - - +
452A ARG* 2.8 66.5 + - + +
489A VAL* 4.2 14.5 - - + +
501A ASP* 4.2 16.4 + - - +
504A TYR* 3.4 57.9 - + + -
505A THR* 3.8 26.2 - - + +
508A LEU* 3.7 32.4 - - + +
44B LYS* 5.4 12.4 + - + +
45B ASP* 4.4 7.4 + - - +
49B PRO* 6.0 2.7 - - + +
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ASN* 3.2 20.3 - - - +
448A TRP* 1.3 95.2 - - + +
450A LYS* 1.3 60.9 + - - +
452A ARG* 3.2 12.3 + - - +
453A ASP* 2.9 31.2 + - - -
45B ASP* 3.5 36.1 - - + +
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Residues in contact with LYS 450 (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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446A GLU* 5.7 0.7 - - - +
447A ASN* 3.0 34.1 + - + +
449A ALA* 1.3 76.4 - - - +
451A ILE* 1.3 60.9 + - - +
453A ASP* 3.1 21.8 + - + +
454A GLU* 2.8 45.3 + - + +
485A ARG* 4.9 5.6 - - - +
45B ASP* 4.6 8.7 + - - +
46B ASN* 3.4 29.6 + - - +
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Residues in contact with ILE 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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446A GLU* 4.3 4.0 - - + +
447A ASN 3.4 8.0 + - - +
448A TRP* 2.8 8.3 + - - +
450A LYS* 1.3 74.0 - - - +
452A ARG* 1.3 56.3 + - - +
454A GLU* 3.0 6.5 + - - +
455A MET* 2.7 34.4 + - - +
482A LEU* 3.8 28.6 - - + +
485A ARG* 3.9 27.8 - - + +
486A PHE* 3.9 24.2 - - + +
489A VAL* 3.6 31.0 - - + -
508A LEU* 4.1 12.1 - - + -
512A LEU* 4.2 15.7 - - + -
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Residues in contact with ARG 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG 5.7 3.4 - - - +
448A TRP* 2.8 45.4 + - + +
449A ALA* 3.2 17.7 + - - +
451A ILE* 1.3 72.4 - - - +
453A ASP* 1.3 89.4 + - - +
454A GLU 3.0 0.7 + - - -
455A MET* 3.0 11.0 + - + +
456A GLY* 2.9 21.1 + - - -
508A LEU* 3.7 20.9 - - + +
45B ASP* 2.7 41.8 + - - -
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Residues in contact with ASP 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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200A ARG* 5.2 3.6 - - - +
449A ALA 2.9 19.3 + - - +
450A LYS* 3.1 33.0 + - + +
452A ARG* 1.3 101.3 + - - +
454A GLU* 1.3 61.3 + - + +
456A GLY* 3.4 2.2 + - - -
457A LEU* 3.1 36.7 + - + +
45B ASP* 5.0 0.2 - - - +
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Residues in contact with GLU 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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450A LYS* 2.8 25.6 + - + +
451A ILE 3.6 3.8 - - - +
452A ARG 3.0 0.2 - - - -
453A ASP* 1.3 76.8 - - + +
455A MET* 1.3 66.0 + - - +
457A LEU* 3.3 14.1 + - + +
458A ALA* 3.0 22.7 + - - +
478A LYS* 3.0 29.4 + - - +
482A LEU* 3.8 13.3 - - + +
485A ARG* 2.6 42.0 + - - -
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Residues in contact with MET 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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197A ARG 4.2 6.3 - - - +
198A VAL* 3.9 36.3 - - + +
451A ILE 2.7 13.4 + - - +
452A ARG* 3.3 17.3 - - + +
454A GLU* 1.3 73.8 - - - +
456A GLY* 1.3 65.8 + - - +
458A ALA* 2.9 5.5 + - - +
459A MET* 2.9 29.4 + - + +
479A LEU* 3.8 19.2 - - + +
482A LEU* 3.4 15.1 - - + +
508A LEU* 4.0 20.4 - - + -
511A GLY* 3.9 23.8 - - - +
512A LEU* 3.8 21.5 - - + -
515A ALA* 4.5 1.8 - - + -
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Residues in contact with GLY 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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197A ARG 5.8 0.2 - - - -
198A VAL 3.3 15.9 - - - -
199A TYR 3.8 0.9 - - - -
200A ARG* 3.1 34.5 + - - +
452A ARG 2.9 12.1 + - - -
453A ASP* 3.8 3.8 - - - -
455A MET* 1.3 77.8 - - - +
457A LEU* 1.3 60.9 + - - +
459A MET* 3.5 1.2 + - - +
460A GLU* 3.1 18.0 + - - +
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Residues in contact with LEU 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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200A ARG* 3.5 49.1 - - - +
201A TYR* 5.7 0.2 - - + -
453A ASP* 3.1 25.4 + - + +
454A GLU* 3.6 13.9 - - + +
455A MET 3.1 0.2 - - - -
456A GLY* 1.3 74.3 - - - +
458A ALA* 1.3 66.5 + - - +
460A GLU* 3.2 6.0 + - + +
461A GLU* 3.0 26.2 + - - +
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Residues in contact with ALA 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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454A GLU 3.0 12.3 + - - +
455A MET* 2.9 9.8 + - - +
457A LEU* 1.3 76.1 - - - +
459A MET* 1.3 58.2 + - - +
461A GLU* 4.6 6.5 - - - -
462A GLY 2.8 27.4 + - - -
475A THR* 2.9 29.8 + - + +
478A LYS* 3.9 28.3 - - + -
479A LEU* 4.9 4.7 - - + -
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Residues in contact with MET 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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198A VAL* 3.1 35.4 - - + +
199A TYR* 3.3 25.8 - - + +
455A MET* 2.9 15.5 + - + +
456A GLY 3.8 0.7 - - - +
458A ALA* 1.3 72.4 - - - +
460A GLU* 1.3 66.7 + - - +
463A CYS* 3.1 49.9 + - + +
475A THR* 3.9 15.9 - - - -
479A LEU* 4.0 8.3 - - - -
515A ALA* 3.7 25.1 - - + +
518A MET* 4.0 33.7 - - + -
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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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199A TYR* 3.5 10.9 - - - -
200A ARG* 3.3 13.0 + - + -
201A TYR* 3.0 61.1 + - + +
231A TYR* 3.4 29.3 + - + +
352A PRO 5.1 1.7 - - - +
353A THR* 4.9 1.9 - - - -
354A ALA 4.3 0.7 + - - -
456A GLY 3.1 14.5 + - - +
457A LEU* 3.2 6.9 + - + +
459A MET* 1.3 78.3 - - - +
461A GLU* 1.3 63.1 + - - +
464A GLY* 3.8 15.9 + - - -
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Residues in contact with GLU 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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457A LEU 3.0 16.2 + - - +
458A ALA* 3.9 5.9 - - - +
460A GLU* 1.3 78.9 - - - +
462A GLY* 1.3 60.2 + - - +
463A CYS 4.0 0.2 + - - -
464A GLY 4.8 1.6 + - - -
466A TYR 5.3 3.5 - - - +
471A LEU* 3.9 35.7 - - + +
474A LYS* 3.3 39.1 + - - +
475A THR* 5.1 2.4 + - - -
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Residues in contact with GLY 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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458A ALA 2.8 8.5 + - - -
461A GLU* 1.3 79.3 - - - +
463A CYS* 1.3 62.4 + - - +
464A GLY 3.8 1.6 - - - -
466A TYR 5.7 0.7 - - - -
467A ARG* 4.2 5.9 - - - +
468A THR 4.9 0.2 - - - +
471A LEU* 3.6 17.3 - - - +
472A MET* 3.3 30.7 + - - +
475A THR* 3.0 22.0 + - - -
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Residues in contact with CYS 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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199A TYR* 2.8 28.9 + - - +
231A TYR* 4.0 1.4 + - - -
459A MET* 3.1 40.4 + - + +
462A GLY* 1.3 82.7 - - - +
464A GLY* 1.3 55.4 + - - +
467A ARG* 3.1 31.0 + - - +
472A MET* 5.2 3.1 - - - -
475A THR* 4.4 6.1 - - - -
518A MET* 4.9 3.4 - - - -
519A ALA* 4.0 26.7 - - - -
522A ALA* 5.0 5.8 - - - -
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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