Contacts of the helix formed by residues 445 - 457 (chain A) in PDB entry 5L04
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 CYS 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A PRO* 4.5 11.4 - - + -
444A ILE* 1.3 77.5 - - - +
446A THR* 1.3 65.7 + - - +
447A GLU* 3.8 19.3 - - - +
448A TYR* 3.1 26.4 + - + +
449A ALA 3.5 6.1 + - - -
469A CYS* 4.6 7.6 - - - -
553A ASN* 3.0 37.3 + - - +
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Residues in contact with THR 446 (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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444A ILE 3.6 1.6 + - - -
445A CYS* 1.3 71.3 - - - +
447A GLU* 1.3 65.1 + - - +
449A ALA* 3.0 6.1 + - - +
450A ILE* 2.9 40.2 + - + +
466A ARG* 3.4 25.8 + - - +
478A THR* 5.1 0.2 - - - +
497A ASN* 4.2 13.7 - - - +
285B GLU* 2.9 31.5 + - - +
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Residues in contact with GLU 447 (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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131A PRO* 3.9 38.1 - - + +
445A CYS* 3.2 8.0 + - - +
446A THR* 1.3 91.6 + - - +
448A TYR* 1.3 58.0 + - - +
450A ILE* 3.7 8.7 - - - +
451A ASN* 2.9 37.9 + - - +
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Residues in contact with TYR 448 (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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129A HIS* 3.8 9.2 - - - +
130A SER 3.2 31.0 + - - -
131A PRO* 3.5 35.7 - - + -
444A ILE* 4.3 13.5 - - + -
445A CYS* 3.1 14.4 + - + +
447A GLU* 1.3 77.1 - - - +
449A ALA* 1.3 59.8 + - - +
451A ASN* 3.2 12.8 + - + +
452A LYS* 2.9 29.5 + - - +
551A ILE* 3.8 26.3 - - + +
552A SER* 3.6 11.6 - - - -
553A ASN* 3.4 37.0 - - + -
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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
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444A ILE* 4.0 9.3 - - + +
445A CYS 3.5 2.2 + - - -
446A THR 3.0 10.4 + - - +
448A TYR* 1.3 78.5 - - - +
450A ILE* 1.3 62.8 + - - +
452A LYS* 3.2 5.9 + - - +
453A LEU* 3.1 27.9 + - - +
464A VAL* 3.8 22.2 - - + +
466A ARG* 3.8 32.3 - - - +
478A THR* 4.3 8.3 - - + +
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Residues in contact with ILE 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 THR* 2.9 30.7 + - + +
447A GLU* 3.7 9.9 - - - +
449A ALA* 1.3 72.3 - - - +
451A ASN* 1.3 64.2 + - - +
453A LEU* 3.1 7.0 + - - +
454A ARG* 2.8 44.3 + - - +
478A THR* 3.5 29.2 - - + -
495A PHE* 3.6 46.9 - - + -
497A ASN* 5.4 0.9 - - - +
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Residues in contact with ASN 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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131A PRO* 4.7 12.9 - - - +
447A GLU* 2.9 26.3 + - - +
448A TYR* 3.2 15.0 + - + +
450A ILE* 1.3 80.4 - - - +
452A LYS* 1.3 63.3 + - - +
454A ARG* 3.5 15.2 + - - +
455A GLN* 3.0 38.1 + - - +
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Residues in contact with LYS 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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441A HIS* 3.0 28.1 + - + +
444A ILE* 6.1 1.1 - - - -
448A TYR 2.9 12.9 + - - +
449A ALA* 3.6 9.0 - - - +
450A ILE 3.2 0.2 - - - -
451A ASN* 1.3 79.0 - - - +
453A LEU* 1.3 56.9 + - - +
455A GLN* 3.9 7.8 - - - +
456A GLU* 2.8 54.5 + - + +
457A GLY 3.6 0.2 + - - -
464A VAL* 4.3 4.9 - - + -
544A CYS* 4.0 17.9 - - + +
545A GLN 2.6 24.9 + - - -
546A PRO* 3.4 0.6 - - - +
547A LYS* 3.6 3.3 - - - +
550A GLU* 2.9 32.1 + - - -
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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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449A ALA 3.1 16.9 + - - +
450A ILE 3.1 6.0 + - - +
452A LYS* 1.3 74.3 - - - +
454A ARG* 1.3 63.5 + - - +
457A GLY* 2.8 35.3 + - - +
458A SER* 3.2 2.1 + - - -
462A MET 3.7 27.6 - - - +
463A TYR 4.0 0.7 - - - -
464A VAL* 3.9 13.2 - - + -
478A THR* 3.6 43.3 - - + +
479A VAL 4.2 0.7 - - - +
480A THR* 3.6 19.7 - - - +
493A LYS* 4.7 2.0 - - - -
495A PHE* 3.7 15.3 - - + -
544A CYS* 3.9 19.1 - - - -
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Residues in contact with ARG 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 ILE* 2.8 34.7 + - - +
451A ASN* 3.5 16.2 + - - +
453A LEU* 1.3 70.1 - - - +
455A GLN* 1.3 62.5 + - + +
458A SER* 4.9 5.2 + - - -
493A LYS* 4.1 27.2 + - - +
495A PHE* 3.9 32.5 - - + -
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Residues in contact with GLN 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 ASN* 3.0 30.7 + - - +
452A LYS* 3.9 5.4 - - - +
453A LEU 3.9 0.2 - - - -
454A ARG* 1.3 82.9 - - + +
456A GLU* 1.3 62.9 + - + +
457A GLY 3.7 0.4 - - - -
458A SER* 4.9 6.3 - - - -
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Residues in contact with GLU 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 LYS* 2.8 45.7 + - + +
455A GLN* 1.3 76.3 - - + +
457A GLY* 1.3 53.4 + - - +
458A SER* 3.7 3.1 + - - -
462A MET* 3.5 17.3 - - - +
544A CYS* 3.6 19.6 - - - +
545A GLN 3.7 8.8 + - - +
547A LYS* 3.2 37.0 + - - +
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Residues in contact with GLY 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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452A LYS 3.6 1.4 + - - -
453A LEU* 2.8 22.9 + - - +
456A GLU* 1.3 72.6 - - - +
458A SER* 1.3 64.4 + - - +
459A GLU 3.3 7.2 - - - +
462A MET* 3.4 24.2 - - - +
480A THR* 2.8 27.4 + - - +
544A CYS* 3.8 6.7 - - - -
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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