Contacts of the helix formed by residues 439 - 450 (chain A) in PDB entry 1OFD
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 ASP 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A PHE* 4.2 1.3 - - - +
438A ASN* 1.3 84.4 + - - +
440A ALA* 1.3 62.3 + - - +
441A GLN* 3.0 16.4 - - + +
442A THR* 3.1 35.2 + - - +
443A VAL* 3.3 15.2 + - - +
675A GLN* 5.7 0.7 - - - -
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Residues in contact with ALA 440 (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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438A ASN 3.7 3.6 + - - -
439A ASP* 1.3 71.5 - - - +
441A GLN* 1.3 55.8 + - - +
442A THR 3.3 0.2 - - - -
443A VAL* 3.8 10.9 - - + +
444A LEU* 3.0 41.3 + - + +
675A GLN* 4.6 13.3 + - + +
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Residues in contact with GLN 441 (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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439A ASP* 3.0 11.7 - - + +
440A ALA* 1.3 75.3 - - - +
442A THR* 1.3 62.3 + - - +
444A LEU* 3.6 5.7 + - - +
445A GLN* 3.1 37.3 + - + +
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Residues in contact with THR 442 (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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437A PHE* 3.8 20.0 - - + -
439A ASP* 3.1 30.9 + - - +
441A GLN* 1.3 78.3 - - - +
443A VAL* 1.3 66.9 + - - +
445A GLN* 3.2 7.5 + - - +
446A GLN* 2.9 31.1 + - + +
608A ILE* 3.2 35.2 - - + -
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 3.5 27.8 - - + -
439A ASP 3.3 13.2 + - - +
440A ALA* 3.8 8.5 - - + +
441A GLN 3.4 0.2 - - - -
442A THR* 1.3 77.3 - - - +
444A LEU* 1.3 61.1 + - + +
446A GLN* 3.4 2.6 + - - +
447A GLN* 2.9 56.1 + - + +
668A LEU* 4.6 4.4 - - + +
671A GLU* 4.5 9.6 - - + +
672A SER* 5.1 0.2 - - - -
675A GLN* 3.7 46.2 - - + +
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Residues in contact with LEU 444 (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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440A ALA* 3.0 33.8 + - + +
441A GLN* 3.9 5.4 - - - +
443A VAL* 1.3 80.3 - - + +
445A GLN* 1.3 57.1 + - - +
447A GLN* 3.4 15.5 + - - +
448A ALA* 3.0 29.3 + - - +
778A LYS 4.7 10.5 - - - +
779A LYS* 4.2 8.5 - - - -
780A LEU* 3.7 45.2 - - + +
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Residues in contact with GLN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN* 3.1 26.7 + - + +
442A THR* 3.2 6.8 + - - +
444A LEU* 1.3 73.1 - - - +
446A GLN* 1.3 70.8 + - - +
448A ALA* 3.5 4.1 + - - -
449A ALA* 3.1 23.6 + - - +
772A ALA* 3.1 31.4 + - + +
773A PHE* 3.6 34.3 - - + +
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Residues in contact with GLN 446 (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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437A PHE* 4.6 6.5 - - + -
442A THR* 2.9 23.5 + - + +
443A VAL* 3.8 4.0 - - - +
445A GLN* 1.3 77.4 + - - +
447A GLN* 1.3 65.9 + - - +
449A ALA* 3.4 2.0 + - - -
450A PHE* 3.0 51.8 + - + +
608A ILE* 3.5 35.4 - - + +
609A LEU* 3.0 37.2 + - - +
667A TYR* 5.6 1.0 + - - -
668A LEU* 3.7 20.9 - - + -
773A PHE* 4.6 10.7 - - - -
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Residues in contact with GLN 447 (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 VAL* 2.9 31.3 + - + +
444A LEU* 3.5 32.7 - - - +
445A GLN 3.3 0.2 - - - -
446A GLN* 1.3 77.5 - - - +
448A ALA* 1.3 60.7 + - - +
451A GLY 3.2 4.9 + - - -
452A TYR* 2.9 53.9 + - + +
457A VAL* 4.6 12.8 - - - +
668A LEU* 3.7 11.2 - - + +
672A SER* 2.9 31.9 + - - +
675A GLN* 5.9 0.6 - - - +
780A LEU* 3.8 14.4 - - + +
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Residues in contact with ALA 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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444A LEU 3.0 16.8 + - - +
445A GLN* 3.8 6.3 - - - +
446A GLN 3.4 0.2 - - - -
447A GLN* 1.3 76.0 - - - +
449A ALA* 1.3 62.1 + - - +
451A GLY* 3.1 11.1 + - - -
452A TYR 4.1 4.5 - - - -
768A PHE* 3.6 20.5 - - - +
771A MET* 4.8 11.4 - - + +
772A ALA* 3.8 21.1 - - + +
780A LEU* 3.6 16.5 - - + +
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Residues in contact with ALA 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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445A GLN 3.1 18.8 + - - +
446A GLN* 3.9 5.4 - - - +
447A GLN 3.3 0.2 - - - -
448A ALA* 1.3 77.1 - - - +
450A PHE* 1.3 61.2 + - + +
451A GLY 3.5 0.7 + - - -
609A LEU* 3.8 16.6 - - + -
615A PHE* 3.5 17.3 - - - -
765A VAL 4.8 0.5 - - - +
768A PHE* 3.7 18.4 - - - +
769A HIS* 4.6 3.5 + - - -
772A ALA* 3.6 17.0 - - + +
773A PHE* 3.7 20.6 - - + -
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Residues in contact with PHE 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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446A GLN* 3.0 51.2 + - + +
447A GLN 4.3 1.3 - - - +
449A ALA* 1.3 76.8 - - - +
451A GLY* 1.3 58.0 + - - +
452A TYR* 3.6 6.7 + - + -
567A LEU* 4.9 0.2 - - + -
602A ASP* 3.7 39.5 - - + -
609A LEU* 4.0 25.6 - - + -
615A PHE* 3.6 40.4 - + + -
645A ALA* 3.4 36.1 - - + +
646A GLN* 2.9 36.3 + - + +
648A TRP* 4.1 4.2 - - - -
667A TYR* 4.2 3.1 - + - -
668A LEU* 4.5 0.7 - - + -
768A PHE* 5.2 0.7 - - - -
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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