Contacts of the helix formed by residues 446 - 456 (chain D) in PDB entry 3B60
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 SER 446 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445D TYR* 1.3 82.5 - - - +
447D ARG* 1.3 64.7 + - - +
448D GLU* 2.8 16.1 + - - -
449D GLN* 2.9 43.3 + - - +
450D ILE* 3.5 12.0 + - - +
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Residues in contact with ARG 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D ALA* 4.1 15.6 - - - +
445D TYR 3.8 1.8 + - - -
446D SER* 1.3 72.8 - - - +
448D GLU* 1.3 65.9 + - - +
450D ILE* 3.0 21.2 - - - +
451D GLU* 2.9 45.6 + - + +
470D LEU* 4.3 18.1 - - - +
471D ASP* 2.7 40.8 + - - +
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Residues in contact with GLU 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D SER* 2.8 10.5 - - - -
447D ARG* 1.3 83.9 + - - +
449D GLN* 1.3 69.0 + - - +
451D GLU* 2.7 11.5 + - - +
452D GLU* 2.6 38.4 + - + +
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Residues in contact with GLN 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D TYR* 4.0 15.2 - - + +
446D SER* 2.9 47.0 + - - +
448D GLU* 1.3 78.9 - - - +
450D ILE* 1.3 52.3 + - - +
452D GLU* 3.4 15.4 - - - +
453D ALA* 2.6 37.4 + - - +
496D LEU* 3.3 26.0 - - + +
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Residues in contact with ILE 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D ALA* 4.1 24.9 - - + +
437D ILE* 4.2 16.3 - - + +
438D ALA* 4.7 6.5 - - + +
445D TYR* 5.4 4.3 - - + -
446D SER 3.6 6.7 - - - +
447D ARG* 3.0 51.4 - - - +
449D GLN* 1.3 72.5 - - + +
451D GLU* 1.3 69.3 + - - +
453D ALA* 3.7 6.2 - - - +
454D ALA* 2.7 29.0 + - - +
470D LEU* 3.7 19.7 - - + -
496D LEU* 3.5 26.0 - - + -
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Residues in contact with GLU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D ARG* 2.9 35.2 + - + +
448D GLU* 2.7 18.9 + - - +
450D ILE* 1.3 75.9 - - - +
452D GLU* 1.3 62.2 - - - +
455D ARG* 3.1 32.7 + - - +
460D MET* 3.1 28.4 - - - +
464D ASN* 5.3 3.3 + - - +
470D LEU* 3.6 28.5 - - + +
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Residues in contact with GLU 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D GLU* 2.6 20.3 + - + +
449D GLN* 3.4 15.7 - - - +
451D GLU* 1.3 73.0 - - - +
453D ALA* 1.3 55.4 + - - +
455D ARG* 2.7 24.5 + - - +
456D MET* 2.6 77.5 + - + +
495D LEU* 5.7 1.4 - - - +
496D LEU* 5.9 1.9 - - - +
526D LEU* 5.4 7.4 - - - +
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Residues in contact with ALA 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437D ILE* 4.7 3.1 - - + -
449D GLN 2.6 22.2 + - - +
450D ILE* 3.0 6.3 + - - +
452D GLU* 1.3 80.7 - - - +
454D ALA* 1.3 57.5 + - - +
456D MET* 3.6 3.4 - - - +
457D ALA* 2.8 30.5 + - - +
492D ALA* 4.1 11.2 - - - +
495D LEU* 4.5 5.6 - - + +
496D LEU* 3.6 35.9 - - + +
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Residues in contact with ALA 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437D ILE* 4.5 16.1 - - + +
450D ILE 2.7 19.5 + - - +
453D ALA* 1.3 73.7 - - - +
455D ARG* 1.3 58.3 + - - +
457D ALA* 3.6 3.9 - - - -
458D TYR 3.6 2.3 + - - -
459D ALA* 2.9 32.3 + - + +
460D MET* 3.0 38.3 + - + +
463D ILE* 4.6 6.1 - - + -
470D LEU* 5.5 0.9 - - + -
492D ALA* 4.4 7.2 - - + +
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Residues in contact with ARG 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D GLU* 3.1 24.6 + - - +
452D GLU* 2.7 30.0 + - - +
454D ALA* 1.3 75.9 - - - +
456D MET* 1.3 85.7 + - + +
457D ALA 2.6 5.4 + - - -
458D TYR* 2.6 26.7 + - - -
459D ALA 4.6 0.2 - - - +
460D MET* 3.1 19.2 - - + +
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Residues in contact with MET 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D GLU* 2.6 49.0 + - + +
453D ALA 3.6 3.8 - - - +
455D ARG* 1.3 113.6 - - - +
457D ALA* 1.3 56.7 + - - +
458D TYR 3.6 0.4 - - - -
495D LEU* 3.0 24.7 - - + +
519D ILE* 5.4 1.2 - - - +
522D ALA* 3.8 27.0 - - + +
526D LEU* 6.0 3.1 - - + -
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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