Contacts of the helix formed by residues 447 - 461 (chain A) in PDB entry 1H7B
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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446A GLU* 1.3 81.2 - - + +
448A LEU* 1.3 65.6 + - - +
449A CYS 3.0 2.7 - - - -
450A TYR* 2.9 28.1 + - - +
451A ARG* 3.1 20.1 + - - +
1588A PO4 2.8 16.5 + - - +
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Residues in contact with LEU 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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64A HIS* 3.4 37.9 - - + +
66A HIS* 3.7 26.0 - - + -
316A THR* 3.8 16.4 - - + +
402A ILE* 4.7 1.8 - - + -
443A THR* 4.3 5.4 - - + -
445A ALA* 3.6 13.0 + - + -
447A ASN* 1.3 77.3 + - - +
449A CYS* 1.3 63.2 + - - +
451A ARG* 3.9 11.4 - - - +
452A PHE* 3.0 62.4 + - + +
1588A PO4 3.0 19.5 + - - +
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Residues in contact with CYS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ILE* 3.9 16.2 - - + -
445A ALA* 3.4 21.3 + - - +
446A GLU 3.7 16.2 - - - -
447A ASN 3.0 0.8 - - - -
448A LEU* 1.3 79.3 - - - +
450A TYR* 1.3 79.9 + - - +
452A PHE* 5.4 0.2 - - - -
453A CYS* 3.7 7.6 + - - +
471A TRP* 3.3 13.0 - - - -
472A TYR* 3.1 42.1 + - - +
474A ASN* 5.9 1.3 - - - +
579A CYS* 4.6 11.7 - - - -
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Residues in contact with TYR 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 3.9 12.6 - - - -
447A ASN* 2.9 21.2 + - - +
449A CYS* 1.3 91.5 - - - +
451A ARG* 1.3 62.5 + - - +
452A PHE 3.4 0.2 - - - -
453A CYS* 3.3 3.5 + - - +
454A LYS* 2.8 31.4 + - - +
470A GLY 3.8 12.7 - - - +
471A TRP* 3.8 34.5 - + + -
579A CYS* 5.1 9.3 - - - -
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Residues in contact with ARG 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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58A HIS* 3.1 44.1 + - - -
59A GLU* 4.2 9.5 + - - +
61A GLY* 4.3 0.2 - - - -
63A ILE 3.9 8.9 + - - -
64A HIS* 3.0 41.8 + - - -
447A ASN* 3.1 20.7 + - - +
448A LEU* 3.3 12.1 + - - +
450A TYR* 1.3 79.3 - - - +
452A PHE* 1.3 68.3 + - - +
454A LYS* 3.3 6.3 + - - +
455A LEU* 3.0 47.5 + - + +
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Residues in contact with PHE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY* 3.4 31.2 - - - -
63A ILE 3.6 16.2 - - - -
64A HIS* 3.4 31.9 - - + -
316A THR* 3.8 10.3 - - + -
318A ASN* 3.5 25.4 - - + +
402A ILE* 3.5 33.7 - - + -
448A LEU* 3.0 38.5 + - + +
451A ARG* 1.3 82.5 - - - +
453A CYS* 1.3 64.5 + - - +
455A LEU* 3.4 3.2 + - - +
456A ASP* 3.0 29.6 + - - +
472A TYR* 3.8 13.5 - - + -
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Residues in contact with CYS 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 CYS 3.7 11.1 + - - +
450A TYR 3.3 4.6 + - - +
452A PHE* 1.3 79.1 - - - +
454A LYS* 1.3 56.5 + - - +
456A ASP* 3.3 2.6 + - - +
457A THR* 2.8 35.1 + - - -
467A THR* 3.7 32.5 - - - +
470A GLY* 3.2 42.2 - - - +
471A TRP* 3.5 8.3 - - - -
472A TYR* 3.9 17.8 - - + -
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Residues in contact with LYS 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 TYR 2.8 17.4 + - - +
451A ARG* 3.7 6.7 - - - +
452A PHE 3.3 0.2 - - - -
453A CYS* 1.3 76.8 - - - +
455A LEU* 1.3 65.0 + - + +
457A THR* 3.1 9.6 + - + -
458A GLU* 3.0 43.9 + - + +
470A GLY 4.9 0.4 + - - -
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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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59A GLU 3.8 16.8 - - - +
60A SER* 3.8 13.3 - - - +
61A GLY* 3.6 30.3 - - - +
321A ARG* 4.3 4.5 + - - -
451A ARG* 3.0 51.0 + - + +
452A PHE* 3.4 4.0 + - - +
454A LYS* 1.3 80.8 - - + +
456A ASP* 1.3 63.0 + - - +
458A GLU* 3.4 37.6 + - - +
459A LYS* 3.8 7.6 + - - +
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Residues in contact with ASP 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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61A GLY 4.2 0.3 - - - +
318A ASN* 3.1 22.9 + - - -
321A ARG* 2.8 53.1 + - - +
324A LEU* 4.0 11.8 - - + +
452A PHE 3.0 15.0 + - - +
453A CYS 3.8 2.7 - - - +
455A LEU* 1.3 74.9 - - - +
457A THR* 1.3 61.8 + - - +
459A LYS* 3.2 1.5 + - - -
460A TYR* 2.8 36.9 + - - +
467A THR* 4.3 3.4 - - + -
472A TYR* 2.2 35.8 + - - +
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Residues in contact with THR 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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453A CYS* 2.8 23.5 + - - -
454A LYS* 3.1 10.5 + - + +
456A ASP* 1.3 75.1 - - - +
458A GLU* 1.3 58.9 + - + +
459A LYS 2.9 5.6 - - - -
461A GLY* 2.8 45.4 + - - +
462A SER* 5.4 1.1 - - - -
467A THR* 3.3 26.5 + - - +
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Residues in contact with GLU 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 LYS* 3.0 44.3 + - + +
455A LEU* 3.7 30.5 - - - +
456A ASP 3.3 0.6 - - - -
457A THR* 1.3 77.4 - - + +
459A LYS* 1.3 59.1 + - + +
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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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321A ARG* 3.9 20.9 - - - +
325A ASP* 3.8 7.4 - - - -
455A LEU 4.2 7.9 - - - +
456A ASP* 3.2 6.9 + - - +
457A THR 2.9 0.2 - - - -
458A GLU* 1.3 84.7 - - + +
460A TYR* 1.3 105.0 + - + +
461A GLY 3.7 0.4 - - - -
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Residues in contact with TYR 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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321A ARG* 4.1 4.5 - - - -
324A LEU* 3.3 48.3 + - + -
325A ASP* 2.7 37.5 + - - -
327A TYR* 5.7 3.6 - - + -
456A ASP* 2.8 23.1 + - - +
459A LYS* 1.3 114.6 - - + +
461A GLY* 1.3 66.3 + - - +
462A SER 3.7 2.1 + - - +
463A VAL* 3.9 22.7 - - + +
467A THR* 5.5 0.4 - - + -
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Residues in contact with GLY 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 THR* 2.8 37.4 + - - -
459A LYS 3.7 1.0 - - - -
460A TYR* 1.3 83.2 - - - +
462A SER* 1.3 51.1 + - - -
463A VAL* 3.5 1.4 + - - +
467A THR* 2.7 24.3 + - - +
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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