Contacts of the helix formed by residues 444 - 449 (chain A) in PDB entry 1D6M
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 ALA 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A ALA* 3.5 7.7 - - - +
441A LEU* 3.6 25.9 - - + +
442A ALA 4.1 0.8 - - - -
443A GLU* 1.3 71.5 - - - +
445A GLY* 1.3 66.6 + - - +
446A TRP 3.3 0.5 + - - -
447A ARG* 2.9 19.5 + - - +
448A THR* 3.9 30.5 - - + +
455A ARG* 4.5 7.2 - - - -
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Residues in contact with GLY 445 (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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363A VAL* 3.8 21.6 - - - +
415A CYS* 5.2 0.2 - - - -
416A PRO* 3.4 19.7 - - - -
417A ASP 4.2 6.5 - - - -
443A GLU* 3.4 3.2 - - - +
444A ALA* 1.3 74.1 - - - +
446A TRP* 1.3 63.5 + - - +
448A THR* 2.4 31.0 + - - -
449A LEU* 5.6 0.2 - - - +
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Residues in contact with TRP 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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286A GLU* 3.0 52.8 + - - +
287A SER* 3.4 3.0 - - - -
288A ALA* 3.2 41.6 - - + +
289A PRO* 3.9 26.0 - - + -
412A MET* 3.8 27.6 - - + +
415A CYS* 3.6 22.5 - - + +
416A PRO 2.9 15.2 + - - +
418A ALA* 3.6 9.7 - - - +
444A ALA 3.3 0.6 + - - -
445A GLY* 1.3 67.9 - - - +
447A ARG* 1.3 83.8 + - + +
448A THR 2.9 7.3 + - - -
449A LEU* 3.1 23.2 + - - +
450A LEU* 3.6 23.5 + - + -
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Residues in contact with ARG 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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286A GLU* 2.7 30.0 + - - -
418A ALA* 3.6 16.2 - - + -
420A PHE* 3.9 9.1 - - - -
441A LEU* 3.9 12.6 - - + -
444A ALA* 2.9 14.9 + - - +
445A GLY 2.9 3.4 + - - -
446A TRP* 1.3 92.9 - - + +
448A THR* 1.3 59.6 + - - +
449A LEU 3.2 0.7 - - - -
450A LEU* 3.2 35.8 + - + +
454A GLU 2.9 17.4 + - - -
455A ARG* 2.8 57.7 + - + +
457A GLU* 4.2 14.5 + - - +
458A GLU* 3.4 24.3 + - - +
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Residues in contact with THR 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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361A GLN* 4.5 13.6 - - - +
363A VAL* 3.2 33.2 - - + +
444A ALA* 3.8 19.1 + - + +
445A GLY 2.4 38.7 + - - -
447A ARG* 1.3 69.6 - - - +
449A LEU* 1.3 56.4 + - - +
450A LEU 2.9 15.8 - - - +
455A ARG* 4.8 8.3 + - - +
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Residues in contact with LEU 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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358A LEU* 4.4 24.5 - - + +
361A GLN* 4.0 27.1 - - + +
363A VAL* 6.2 0.7 - - + -
364A VAL* 4.6 1.6 - - + -
408A ARG* 3.3 29.4 + - + +
411A LEU* 3.7 21.8 - - + -
412A MET* 3.3 46.4 - - + +
415A CYS* 3.7 14.4 - - - -
446A TRP 3.3 10.1 - - - +
448A THR* 1.3 72.7 - - - +
450A LEU* 1.3 62.8 + - - +
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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