Contacts of the helix formed by residues 447 - 450 (chain O) in PDB entry 6LTJ
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 PRO 447 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443O ARG 3.6 14.3 - - - +
444O ARG 3.8 8.1 - - - +
445O ALA 3.2 13.9 - - - +
446O LEU* 1.3 85.5 - - - +
448O GLU* 1.3 55.6 + - + +
449O PHE 2.8 1.7 + - - -
450O PHE* 2.7 30.1 + - + -
451O ASN* 3.0 26.0 + - - +
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Residues in contact with GLU 448 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285M GLU* 3.0 21.2 - - - +
287M GLU* 3.5 7.6 - - - +
446O LEU* 4.6 6.6 - - + +
447O PRO* 1.3 81.3 - - + +
449O PHE* 1.3 87.9 + - + +
451O ASN* 3.8 20.3 + - - +
452O GLY 5.2 0.5 + - - -
454O ASN* 4.5 8.0 + - - +
457O LYS* 2.8 35.1 + - + +
496O ALA* 3.6 9.9 - - - +
499O ARG* 2.7 48.8 + - - +
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Residues in contact with PHE 449 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446O LEU* 3.9 19.1 - - + -
447O PRO 2.8 3.0 + - - -
448O GLU* 1.3 106.1 - - + +
450O PHE* 1.3 70.3 + + + +
451O ASN 3.6 0.9 - - - -
452O GLY* 4.4 4.4 + - - -
457O LYS* 2.9 45.5 - - + +
458O THR 3.7 14.8 - - - +
459O PRO* 3.3 16.5 - - - +
461O ILE* 4.5 0.7 - - + -
462O TYR* 3.6 27.4 - + + -
465O TYR* 4.1 24.0 - + - -
496O ALA* 4.0 12.1 - - + -
500O VAL* 3.6 31.4 - - + -
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Residues in contact with PHE 450 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438O VAL* 3.6 31.9 - - + -
442O GLU 4.3 2.2 - - - -
443O ARG* 3.6 49.1 - - + +
446O LEU* 3.1 32.1 - - + -
447O PRO* 2.7 15.1 + - + +
449O PHE* 1.3 78.2 - + + +
451O ASN* 1.3 62.6 + - - +
452O GLY* 3.1 2.2 - - - +
459O PRO* 3.6 39.0 - - + -
462O TYR* 3.7 21.5 - + - -
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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