Contacts of the helix formed by residues 447 - 459 (chain A) in PDB entry 4G84
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 LYS 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A ALA 5.4 8.9 + - - +
418A LYS* 4.9 15.6 - - - +
445A ASN 3.8 5.8 + - - +
446A PRO* 1.3 74.9 - - - +
448A LEU* 1.3 67.7 + - - +
449A LEU* 4.3 8.5 - - + +
450A ASN* 3.1 25.1 + - + +
451A GLN* 3.0 13.8 + - - +
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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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414A ALA* 4.4 13.9 - - + -
415A SER 4.5 9.2 + - - +
416A ALA* 4.0 26.3 + - + +
446A PRO 3.8 1.6 + - - -
447A LYS* 1.3 73.1 - - - +
449A LEU* 1.3 63.0 + - - +
451A GLN* 3.2 16.8 + - + +
452A LEU* 2.9 40.3 + - + +
463A VAL* 5.1 2.0 - - + -
465A ILE* 4.2 22.2 - - + -
479A ARG* 4.0 24.2 - - - +
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Residues in contact with LEU 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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447A LYS* 3.2 5.7 - - + +
448A LEU* 1.3 79.2 - - - +
450A ASN* 1.3 57.8 + - - +
452A LEU* 3.3 12.7 + - + +
453A GLN* 2.9 63.9 + - + +
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Residues in contact with ASN 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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441A LEU* 3.6 23.6 - - - +
443A LYS* 5.7 3.6 - - - +
446A PRO* 4.9 6.3 - - - +
447A LYS* 3.1 20.6 + - + +
449A LEU* 1.3 79.2 - - - +
451A GLN* 1.3 56.5 + - - +
453A GLN* 3.4 14.5 + - - +
454A TYR* 3.1 27.2 + - - +
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Residues in contact with GLN 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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412A LEU* 3.6 16.7 - - + +
413A VAL 4.2 2.9 - - - +
414A ALA* 3.1 32.6 - - + +
415A SER 3.1 22.8 + - - +
424A ARG* 4.8 1.7 + - - -
441A LEU* 3.6 29.5 + - + +
446A PRO* 3.4 23.7 + - + +
447A LYS 3.0 25.2 + - - +
448A LEU* 3.2 10.7 + - + +
450A ASN* 1.3 74.7 - - - +
452A LEU* 1.3 66.1 + - - +
454A TYR* 3.2 8.3 + - - +
455A CYS* 3.1 25.5 + - - -
463A VAL* 5.6 0.9 - - + -
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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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448A LEU* 2.9 39.3 + - + +
449A LEU* 3.7 12.8 - - + +
451A GLN* 1.3 76.4 - - - +
453A GLN* 1.3 56.3 + - - +
455A CYS* 3.2 5.6 + - - +
456A GLU* 2.9 41.3 + - - +
463A VAL* 3.8 29.6 - - + -
465A ILE* 5.9 0.7 - - + -
479A ARG* 3.6 38.1 - - - +
481A VAL* 4.7 11.2 - - + +
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Residues in contact with GLN 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 LEU* 2.9 53.2 + - + +
450A ASN* 3.8 16.0 - - - +
452A LEU* 1.3 76.3 - - + +
454A TYR* 1.3 64.1 + - - +
456A GLU* 3.3 17.7 + - - +
457A GLU* 3.0 25.5 + - - +
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Residues in contact with TYR 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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412A LEU* 4.2 14.8 - - + -
439A GLU* 2.8 28.5 + - - -
441A LEU* 4.1 27.6 - - + -
450A ASN* 3.1 15.7 + - - +
451A GLN* 3.4 11.9 - - - +
452A LEU 3.2 0.2 - - - -
453A GLN* 1.3 77.3 - - - +
455A CYS* 1.3 63.8 + - - +
457A GLU* 3.9 9.3 - - - +
458A ALA* 3.1 29.6 + - + +
460A ILE* 3.7 26.7 - - + -
88B GLY 5.7 0.2 + - - -
146B ASN* 6.2 2.0 - - - -
148B LYS* 5.1 2.4 - - - -
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Residues in contact with CYS 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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412A LEU* 3.4 45.5 - - - -
451A GLN 3.1 5.8 + - - -
452A LEU 3.5 7.9 - - - +
454A TYR* 1.3 81.3 - - - +
456A GLU* 1.3 56.9 + - - +
458A ALA 3.2 0.2 + - - -
459A GLY* 2.7 27.9 + - - -
460A ILE* 2.9 42.5 + - - +
463A VAL* 3.5 17.5 - - + -
481A VAL* 3.8 10.3 - - + -
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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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403A LYS* 3.2 16.8 + - - +
452A LEU* 2.9 29.7 + - - +
453A GLN* 3.3 19.4 + - - +
455A CYS* 1.3 77.2 - - - +
457A GLU* 1.3 62.6 + - - +
459A GLY* 3.5 7.4 + - - -
481A VAL* 3.6 27.7 - - + +
484A ARG* 4.6 14.4 + - - -
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Residues in contact with GLU 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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68A ARG* 4.9 8.0 + - - -
403A LYS* 3.8 20.8 + - - +
453A GLN 3.0 16.1 + - - +
454A TYR* 3.9 9.0 - - - +
456A GLU* 1.3 77.3 - - - +
458A ALA* 1.3 60.6 + - - +
459A GLY 3.7 0.2 + - - -
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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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403A LYS* 4.9 2.7 - - - -
405A ARG* 3.3 27.4 + - - +
406A THR* 5.1 1.6 + - - -
407A THR* 4.1 13.3 + - + +
439A GLU* 5.8 0.7 - - - +
454A TYR* 3.1 27.2 + - + +
457A GLU* 1.3 76.0 - - + +
459A GLY* 1.3 59.4 + - - +
460A ILE* 3.5 21.9 + - + -
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Residues in contact with GLY 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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403A LYS* 4.5 10.3 - - - +
405A ARG* 3.4 21.2 + - - -
455A CYS 2.7 6.7 + - - -
456A GLU* 3.5 7.5 + - - -
457A GLU 3.3 3.6 + - - -
458A ALA* 1.3 78.5 - - - +
460A ILE* 1.3 66.0 + - - +
461A PRO* 3.2 11.3 - - - +
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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