Contacts of the helix formed by residues 439 - 446 (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 HIS 439 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432O TRP* 3.5 60.8 + + + +
433O PHE* 5.8 0.2 - - - -
434O ASP* 5.8 1.6 - - + +
437O SER 3.8 3.0 + - - +
438O VAL* 1.3 80.7 - - - +
440O ALA* 1.3 67.9 + - + +
441O ILE* 3.1 46.1 + - + +
442O GLU* 3.4 10.0 + - - +
443O ARG* 3.2 22.2 + - - +
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Residues in contact with ALA 440 (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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439O HIS* 1.3 85.9 + - + +
441O ILE* 1.3 66.6 + - - +
442O GLU 3.1 1.6 - - - -
443O ARG* 3.4 9.9 + - - +
444O ARG* 2.9 40.6 + - + +
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Residues in contact with ILE 441 (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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432O TRP* 3.7 36.1 - - + +
439O HIS* 3.1 19.9 - - + +
440O ALA* 1.3 75.7 - - - +
442O GLU* 1.3 57.1 + - - +
444O ARG* 3.3 32.8 + - - +
445O ALA* 2.9 27.7 + - + +
503O PHE* 4.3 2.9 - - + -
507O TRP* 3.8 42.0 - - + +
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Residues in contact with GLU 442 (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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432O TRP* 3.2 23.5 - - + -
433O PHE* 4.0 11.6 - - - -
434O ASP 5.7 0.2 + - - -
437O SER 4.7 1.4 - - - +
438O VAL* 3.1 34.7 - - + +
439O HIS 3.8 12.7 + - - +
440O ALA 3.1 0.4 - - - -
441O ILE* 1.3 74.0 - - - +
443O ARG* 1.3 61.3 + - - +
445O ALA 2.9 2.1 + - - -
446O LEU* 2.8 33.3 + - + +
450O PHE* 4.4 2.5 - - - -
462O TYR* 3.0 35.0 + - + +
466O ARG* 3.8 12.0 + - - -
503O PHE* 3.4 26.6 - - + -
504O LEU* 5.7 0.3 - - - +
509O LEU* 5.4 0.2 - - - +
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Residues in contact with ARG 443 (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* 3.5 36.5 + - + +
439O HIS 3.2 17.2 + - - +
440O ALA* 3.4 9.8 + - - +
442O GLU* 1.3 75.3 - - - +
444O ARG* 1.3 62.1 + - + +
447O PRO* 3.6 22.0 - - - +
450O PHE* 3.6 40.6 - - + +
459O PRO* 5.1 6.5 - - - +
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Residues in contact with ARG 444 (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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439O HIS* 5.8 0.2 + - - -
440O ALA* 2.9 27.4 + - + +
441O ILE* 3.6 36.5 - - - +
442O GLU 3.0 0.4 - - - -
443O ARG* 1.3 79.8 - - + +
445O ALA* 1.3 64.7 + - - +
447O PRO* 3.8 8.5 - - - +
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Residues in contact with ALA 445 (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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441O ILE* 2.9 10.5 + - + +
442O GLU 2.9 2.3 + - - +
444O ARG* 1.3 78.3 - - - +
446O LEU* 1.3 66.1 + - + +
447O PRO* 3.2 9.5 - - - +
503O PHE* 3.4 39.5 - - + -
507O TRP* 5.5 0.9 - - - +
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Residues in contact with LEU 446 (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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442O GLU 2.8 14.1 + - - +
443O ARG 3.9 3.1 - - - -
445O ALA* 1.3 84.6 - - + +
447O PRO* 1.3 64.1 - - - +
448O GLU* 3.2 7.0 + - + +
449O PHE* 3.7 15.3 + - + -
450O PHE* 3.1 22.3 - - + -
462O TYR* 3.5 31.0 - - + -
499O ARG* 3.9 34.8 - - + +
500O VAL* 3.9 22.9 - - + -
503O PHE* 4.0 22.2 - - + -
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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