Contacts of the helix formed by residues 410 - 421 (chain A) in PDB entry 1D7K
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 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PHE* 5.2 0.7 - - - -
14A LEU* 4.1 25.2 - - - +
18A PHE 5.8 0.2 - - - -
44A ASP* 4.9 2.8 + - - -
46A GLY* 5.3 0.4 - - - -
409A MET* 1.3 78.1 - - - +
411A GLY* 1.4 55.7 + - - +
412A PRO* 3.6 12.1 - - - +
413A ALA* 3.1 26.7 + - - +
414A TRP* 2.8 34.8 + - - +
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Residues in contact with GLY 411 (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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13A PHE* 5.3 6.5 - - - +
14A LEU 4.8 7.4 + - - -
409A MET 3.9 0.6 + - - -
410A SER* 1.4 69.6 - - - +
412A PRO* 1.3 65.3 - - - +
414A TRP* 3.1 11.5 + - - +
415A GLN* 2.9 34.8 + - - +
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Residues in contact with PRO 412 (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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410A SER* 3.4 13.9 - - - +
411A GLY* 1.3 88.9 - - - +
413A ALA* 1.3 58.0 + - - +
415A GLN* 3.4 7.7 + - + +
416A LEU* 3.0 27.4 + - - +
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Residues in contact with ALA 413 (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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46A GLY* 3.6 32.3 - - - +
49A LEU* 4.2 5.1 - - + +
50A LYS* 6.5 1.1 - - - -
409A MET* 3.6 11.6 - - + +
410A SER* 3.1 25.0 + - - +
412A PRO* 1.3 71.9 - - - +
414A TRP* 1.3 66.0 + - - +
415A GLN 3.3 0.2 + - - -
416A LEU* 3.4 10.5 + - - +
417A MET* 3.1 23.2 + - - +
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Residues in contact with TRP 414 (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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13A PHE* 3.8 36.2 - + + -
409A MET* 3.9 19.8 - - - +
410A SER 2.8 18.5 + - - +
411A GLY* 3.1 10.1 + - - +
413A ALA* 1.3 71.2 - - - +
415A GLN* 1.3 85.6 + - + +
417A MET* 3.2 9.1 + - - +
418A GLN* 3.0 69.8 + - + +
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Residues in contact with GLN 415 (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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411A GLY 2.9 23.5 + - - +
412A PRO* 3.9 6.5 - - + +
414A TRP* 1.3 93.1 - - - +
416A LEU* 1.3 68.5 + - - +
418A GLN* 3.4 10.7 + - - +
419A GLN* 3.0 32.8 + - + +
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Residues in contact with LEU 416 (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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49A LEU* 3.6 38.1 - - + +
50A LYS* 5.8 0.4 - - - -
53A LEU* 4.3 21.1 - - + -
412A PRO 3.0 18.2 + - - +
413A ALA* 3.7 6.1 - - - +
415A GLN* 1.3 75.2 - - - +
417A MET* 1.3 63.3 + - - +
419A GLN* 2.9 30.8 + - + +
420A PHE* 3.0 35.8 + - + -
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Residues in contact with MET 417 (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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45A LEU* 5.7 0.2 - - + -
49A LEU* 3.5 14.3 - - + +
79A THR* 3.1 39.5 - - + +
82A ALA* 4.1 24.2 - - + -
83A THR* 3.9 13.5 - - - +
409A MET* 3.1 39.7 - - + +
413A ALA 3.1 11.5 + - - +
414A TRP* 3.3 13.9 - - - +
415A GLN 3.1 0.2 - - - -
416A LEU* 1.3 76.3 - - - +
418A GLN* 1.3 61.9 + - - +
420A PHE* 3.2 6.0 + - - +
421A GLN* 2.5 35.7 + - - +
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Residues in contact with GLN 418 (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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414A TRP* 3.0 78.8 + - + +
415A GLN* 3.6 12.8 - - - +
417A MET* 1.3 80.6 - - - +
419A GLN* 1.3 66.0 + - + +
420A PHE 3.3 0.4 - - - -
421A GLN* 3.3 39.6 + - + +
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Residues in contact with GLN 419 (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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415A GLN* 3.0 22.9 + - - +
416A LEU* 2.9 29.1 + - + +
418A GLN* 1.3 73.0 - - + +
420A PHE* 1.3 60.2 + - - +
421A GLN 4.6 1.0 - - - +
424A ASP* 5.2 2.3 - - - +
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Residues in contact with PHE 420 (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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49A LEU* 4.0 18.4 - - + -
52A HIS* 3.7 19.3 - + + -
53A LEU* 3.4 33.7 - - + -
56A LEU* 3.9 18.2 - - + -
82A ALA 3.9 0.4 - - - -
83A THR* 3.5 30.3 - - + +
416A LEU* 3.0 37.0 + - + -
417A MET 3.4 5.2 - - - +
419A GLN* 1.3 72.7 - - - +
421A GLN* 1.3 69.9 - - - +
422A ASN* 3.1 15.3 - - - +
424A ASP* 3.6 5.5 - - - +
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Residues in contact with GLN 421 (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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82A ALA* 3.2 36.2 - - + +
417A MET* 2.5 22.5 + - - +
418A GLN* 3.3 42.6 + - - +
419A GLN 4.6 1.0 - - - +
420A PHE* 1.3 69.0 - - - +
422A ASN* 1.3 57.8 + - - +
423A PRO* 2.9 11.5 - - + +
424A ASP* 2.7 19.2 - - - +
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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