Contacts of the helix formed by residues 450 - 461 (chain A) in PDB entry 3U44
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 GLU 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A TYR 5.0 1.2 - - - +
410A GLN 3.8 4.8 - - - +
412A THR 2.8 20.6 + - - +
413A ASN* 4.4 6.9 - - - +
414A LEU* 5.0 18.8 - - + -
445A ARG* 4.9 3.1 + - - -
448A LEU 4.0 1.5 + - - +
449A ALA* 1.3 72.9 - - - +
451A PRO* 1.3 67.9 - - - +
452A LEU* 2.9 37.4 + - + +
453A LEU* 3.2 33.5 - - + +
454A PHE 4.1 0.9 + - - -
826A LYS* 2.8 40.8 + - - +
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Residues in contact with PRO 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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410A GLN* 3.4 16.5 - - + +
439A VAL* 4.2 15.4 - - + +
442A SER* 3.7 28.0 - - - +
445A ARG* 4.1 32.5 - - + +
449A ALA 3.2 13.7 - - - +
450A GLU* 1.3 84.9 - - - +
452A LEU* 1.3 61.3 + - - +
453A LEU 3.0 3.1 - - - -
454A PHE* 3.0 7.7 + - + +
455A LEU* 2.8 29.4 + - - +
502A GLU* 5.1 1.1 - - - +
865A ARG* 4.8 7.4 - - - +
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Residues in contact with LEU 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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445A ARG* 6.1 1.1 - - - +
450A GLU* 2.9 24.6 + - + +
451A PRO* 1.3 80.0 - - + +
453A LEU* 1.3 53.4 + - - +
455A LEU* 3.6 20.9 - - + -
456A SER* 2.7 46.6 + - - +
502A GLU* 6.0 2.0 - - - +
826A LYS* 6.6 0.4 - - + -
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Residues in contact with LEU 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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409A TYR* 4.0 12.6 - - + +
412A THR* 4.3 12.6 - - + -
413A ASN 3.9 12.6 - - - +
414A LEU* 4.9 15.3 - - + -
417A GLU* 3.4 48.5 - - + +
450A GLU* 3.2 23.4 + - + +
451A PRO 3.0 0.2 - - - -
452A LEU* 1.3 79.9 - - - +
454A PHE* 1.3 58.2 + - - +
456A SER* 2.9 20.9 + - - +
457A LYS* 3.4 19.8 - - - +
460A ARG* 6.1 1.1 - - - +
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Residues in contact with PHE 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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27A LEU* 3.3 39.1 - - + +
29A ALA* 4.2 14.4 - - + -
409A TYR* 3.4 36.2 - + + +
410A GLN* 4.0 24.7 - - + -
437A GLY 3.7 39.5 - - - -
438A ASP* 4.4 1.1 - - - -
439A VAL* 3.1 28.3 - - + -
450A GLU 4.1 0.6 + - - -
451A PRO 3.0 9.5 + - - +
453A LEU* 1.3 80.9 - - - +
455A LEU* 1.3 58.5 + - + +
457A LYS* 3.2 3.7 + - - +
458A TYR* 3.1 34.4 + + + -
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Residues in contact with LEU 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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439A VAL* 4.2 15.0 - - + -
451A PRO 2.8 16.2 + - - +
452A LEU* 3.9 19.5 - - + +
454A PHE* 1.3 78.6 - - + +
456A SER* 1.3 64.2 + - - +
458A TYR* 3.3 18.6 + - + -
459A LYS* 3.2 24.4 + - + +
502A GLU* 3.3 33.9 - - + +
503A VAL* 3.6 25.1 - - + -
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Residues in contact with SER 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 LEU* 2.7 30.0 + - - +
453A LEU* 2.9 26.9 + - - +
455A LEU* 1.3 73.4 - - - +
457A LYS* 1.3 56.9 + - - +
459A LYS* 3.6 4.9 + - - +
460A ARG* 3.1 42.3 + - - +
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Residues in contact with LYS 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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25A ASP* 5.5 0.6 + - - -
27A LEU* 4.0 9.4 - - + -
409A TYR* 2.8 29.9 + - + +
417A GLU* 2.9 18.8 + - - -
421A GLN* 5.0 3.2 + - - -
428A GLU* 4.3 11.6 + - - -
433A LEU* 3.6 11.9 - - - +
435A MET* 3.5 31.9 - - + +
453A LEU* 3.4 17.3 - - - +
454A PHE 3.2 8.6 + - - +
455A LEU 3.2 0.4 - - - -
456A SER* 1.3 81.3 + - - +
458A TYR* 1.3 60.3 + - - +
460A ARG* 3.5 26.5 - - - +
461A PHE* 2.8 47.6 + - + -
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Residues in contact with TYR 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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27A LEU* 3.5 23.0 - - + +
29A ALA* 4.1 18.4 - - + -
454A PHE* 3.1 16.9 + + + +
455A LEU* 3.3 23.5 + - + +
457A LYS* 1.3 76.9 - - - +
459A LYS* 1.3 63.5 + - + +
461A PHE* 3.4 3.4 - - - +
471A LYS* 2.9 67.3 + - + +
472A ILE 5.3 0.9 - - - -
473A ASP* 2.7 31.5 + - - -
508A GLN* 3.2 24.9 + - - +
509A ALA* 6.1 0.3 - - - +
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Residues in contact with LYS 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 LEU* 3.2 16.9 + - + +
456A SER* 4.1 5.2 - - - +
458A TYR* 1.3 79.9 - - + +
460A ARG* 1.3 61.2 + - - +
461A PHE 3.3 4.0 - - - +
471A LYS* 4.8 2.6 + - - +
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Residues in contact with ARG 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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428A GLU* 2.7 45.6 + - - -
453A LEU* 6.1 1.2 - - - +
456A SER* 3.1 30.1 + - - +
457A LYS* 3.1 32.4 + - - +
459A LYS* 1.3 78.0 - - - +
461A PHE* 1.3 62.0 + - + +
462A THR* 4.9 2.3 - - - +
468A THR* 3.5 15.5 + - - +
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Residues in contact with PHE 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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25A ASP* 4.3 8.5 - - + -
27A LEU* 3.9 22.9 - - + -
428A GLU* 3.0 42.8 - - + -
435A MET* 4.0 25.8 - - + -
457A LYS* 2.8 30.2 + - + +
458A TYR 3.4 2.3 + - - +
459A LYS 3.3 3.5 - - - +
460A ARG* 1.3 92.7 - - + +
462A THR* 1.3 60.4 + - - +
468A THR* 4.2 0.9 - - - -
469A GLY* 2.9 41.7 - - - +
470A ARG 4.0 3.8 - - - -
471A LYS* 3.2 36.8 + - + -
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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