Contacts of the helix formed by residues 460 - 473 (chain A) in PDB entry 3U78
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 ARG 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A LYS* 5.3 1.4 - - - +
458A ASN 3.8 9.4 - - - +
459A VAL* 1.3 76.6 - - - +
461A PRO* 1.3 71.1 - - - +
462A GLY 3.5 2.0 - - - -
463A HIS* 3.2 55.1 + - + +
464A LEU* 2.9 24.8 + - - +
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Residues in contact with PRO 461 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A TRP* 3.8 15.2 - - + -
443A MET* 3.4 29.8 - - + -
455A ILE* 3.5 33.7 - - + -
459A VAL* 3.3 13.2 - - + +
460A ARG* 1.3 84.7 - - - +
462A GLY* 1.3 63.3 + - - +
464A LEU* 3.7 1.4 - - - +
465A ILE* 3.0 32.9 + - - +
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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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443A MET* 4.6 5.1 - - - +
460A ARG 3.5 0.6 - - - -
461A PRO* 1.3 80.8 - - - +
463A HIS* 1.3 61.1 + - - +
465A ILE* 3.8 9.0 + - - +
466A LYS* 3.3 20.4 + - - +
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Residues in contact with HIS 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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460A ARG* 3.2 57.8 + - + +
462A GLY* 1.3 73.6 - - - +
464A LEU* 1.3 69.5 + - - +
466A LYS* 2.8 17.5 + - + +
467A GLU* 2.9 49.5 + - + +
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Residues in contact with LEU 464 (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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404A TRP* 3.6 36.8 - - + +
407A ALA* 4.0 23.3 - - + +
408A LYS* 4.3 16.4 - - + +
411A LEU* 3.9 24.7 - - + -
439A LEU* 3.8 15.3 - - + -
459A VAL* 4.7 7.9 - - + -
460A ARG* 2.9 23.6 + - - +
461A PRO 3.7 2.9 - - - +
463A HIS* 1.3 73.4 + - - +
465A ILE* 1.3 65.5 + - - +
467A GLU* 3.0 9.0 + - - +
468A LEU* 2.9 30.7 + - + +
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Residues in contact with ILE 465 (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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404A TRP* 4.4 4.9 - - + -
436A HIS* 3.5 24.6 + - + +
439A LEU* 3.6 33.0 - - + +
440A LYS* 3.8 18.6 - - + +
443A MET* 3.6 33.0 - - + -
461A PRO 3.0 19.1 + - - +
462A GLY* 3.9 7.4 - - - +
463A HIS 3.2 0.2 - - - -
464A LEU* 1.3 75.5 - - - +
466A LYS* 1.3 56.2 + - - +
468A LEU* 3.6 8.0 + - - -
469A SER* 3.0 25.9 + - - -
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Residues in contact with LYS 466 (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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462A GLY 3.3 11.7 + - - +
463A HIS* 2.8 13.3 + - + +
465A ILE* 1.3 75.8 - - - +
467A GLU* 1.3 63.7 + - - +
468A LEU 3.1 1.6 - - - -
469A SER* 3.0 8.3 + - - -
470A LYS* 2.8 40.4 + - - +
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Residues in contact with GLU 467 (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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411A LEU* 3.6 27.1 - - + -
415A LYS* 4.0 15.3 + - - +
463A HIS* 2.9 53.9 + - + +
464A LEU* 3.5 6.5 - - - +
466A LYS* 1.3 76.6 - - - +
468A LEU* 1.3 57.1 + - - +
470A LYS* 3.2 35.8 + - - +
471A VAL* 3.1 32.1 + - - +
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Residues in contact with LEU 468 (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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407A ALA* 4.1 18.8 - - + +
410A LEU* 6.2 0.2 - - + -
411A LEU* 3.9 33.2 - - + +
432A VAL* 4.1 20.2 - - + -
435A LEU* 4.9 2.9 - - + -
436A HIS* 4.0 31.0 - - + +
439A LEU* 4.1 25.4 - - + -
464A LEU* 2.9 20.5 + - + +
465A ILE* 3.7 9.4 - - - +
467A GLU* 1.3 73.9 - - - +
469A SER* 1.3 66.6 + - - +
471A VAL* 3.2 5.1 + - + +
472A ILE* 2.9 30.5 + - - +
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Residues in contact with SER 469 (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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436A HIS* 3.7 21.4 - - - -
465A ILE* 3.0 17.0 + - - -
466A LYS* 3.4 11.4 - - - -
468A LEU* 1.3 75.6 - - - +
470A LYS* 1.3 63.1 + - - +
472A ILE* 3.4 5.6 + - - +
473A ARG* 3.1 21.5 + - - +
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Residues in contact with LYS 470 (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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466A LYS* 2.8 25.9 + - - +
467A GLU* 3.2 49.2 + - - +
469A SER* 1.3 70.8 - - - +
471A VAL* 1.3 57.1 + - + +
473A ARG* 2.5 35.4 + - - +
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Residues in contact with VAL 471 (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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411A LEU* 3.9 20.2 - - + -
414A LEU* 3.6 40.4 - - + +
415A LYS* 5.0 12.8 - - + +
418A ARG* 5.9 4.3 - - + -
432A VAL* 5.2 0.9 - - + -
467A GLU 3.1 20.0 + - - +
468A LEU* 3.7 5.6 - - + +
470A LYS* 1.3 77.9 - - + +
472A ILE* 1.3 64.6 + - + +
473A ARG 2.9 12.4 - - - +
474A ALA* 3.1 9.1 - - - +
475A ILE* 3.6 16.8 - - + +
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Residues in contact with ILE 472 (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 LEU* 5.7 0.4 - - + -
429A VAL* 5.6 3.1 - - + +
432A VAL* 3.7 19.3 - - + -
433A LYS* 3.4 55.4 - - + +
436A HIS* 4.0 20.9 - - + -
468A LEU 2.9 20.7 + - - +
469A SER* 3.8 4.9 - - - +
471A VAL* 1.3 78.6 - - + +
473A ARG* 1.3 54.4 + - - +
474A ALA 2.8 13.6 - - - +
475A ILE* 4.2 7.4 - - + +
476A GLU* 3.2 33.5 + - - +
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Residues in contact with ARG 473 (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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469A SER 3.1 12.9 + - - +
470A LYS* 2.5 30.9 - - - +
471A VAL* 2.9 3.6 - - - +
472A ILE* 1.3 71.9 - - - +
474A ALA* 1.3 70.8 + - - +
476A GLU* 4.1 6.5 - - - +
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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