Contacts of the helix formed by residues 407 - 417 (chain I) in PDB entry 1DFJ
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 407 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69E GLN* 3.6 19.0 + - - +
406I GLY* 1.3 71.9 - - - +
408I PRO* 1.3 74.3 - - + +
409I GLY 3.0 0.9 + - - -
410I VAL* 3.1 3.9 + - - +
411I LEU* 2.9 33.6 + - + +
433I TYR 4.0 0.3 - - - +
434I TRP* 3.1 33.1 - - - +
435I THR* 2.9 24.1 + - - +
438I VAL* 3.5 18.5 - - + +
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Residues in contact with PRO 408 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E GLN* 4.9 3.1 - - - +
379I ASN* 3.7 25.4 - - + +
406I GLY* 3.8 0.4 - - - -
407I ASP* 1.3 94.1 - - + +
409I GLY* 1.3 59.0 - - - +
411I LEU* 3.9 14.0 - - + +
412I GLN* 2.8 42.1 + - - +
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Residues in contact with GLY 409 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379I ASN* 3.4 18.1 + - - -
382I CYS* 3.5 36.2 - - - +
405I VAL* 4.3 1.1 - - - -
406I GLY 3.3 6.6 + - - -
407I ASP 3.0 1.0 + - - -
408I PRO* 1.3 76.0 - - - +
410I VAL* 1.3 65.4 + - - +
412I GLN* 2.9 15.4 + - - +
413I LEU* 3.1 9.2 + - - +
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Residues in contact with VAL 410 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405I VAL* 4.2 12.2 - - + +
406I GLY 3.2 15.0 + - - +
407I ASP 3.1 4.8 + - - +
409I GLY* 1.3 72.4 - - - +
411I LEU* 1.3 52.9 + - - +
413I LEU* 2.5 35.1 + - + +
414I LEU* 2.7 45.8 + - + -
427I LEU* 6.1 0.4 - - + -
429I LEU* 4.4 12.6 - - + -
432I THR* 4.8 0.2 - - + -
434I TRP* 3.6 32.1 - - + -
438I VAL* 4.0 16.2 - - + -
442I LEU* 4.9 7.2 - - + -
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Residues in contact with LEU 411 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407I ASP* 2.9 31.4 + - + +
408I PRO* 3.9 10.1 - - + +
410I VAL* 1.3 74.9 - - - +
412I GLN* 1.3 59.1 + - + +
414I LEU* 3.3 12.8 + - + +
415I GLY* 2.9 25.3 + - - -
438I VAL* 4.2 26.5 - - + -
441I ARG* 4.6 17.5 - - + +
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Residues in contact with GLN 412 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379I ASN* 3.3 26.1 + - - +
380I SER* 5.1 1.0 - - - +
382I CYS 4.4 9.2 - - - +
383I SER* 3.1 29.1 - - - -
386I ALA* 3.3 21.9 - - + +
408I PRO* 2.8 31.5 + - + +
409I GLY* 2.9 8.2 + - - +
411I LEU* 1.3 74.5 - - + +
413I LEU* 1.3 67.6 + - - +
415I GLY* 3.8 5.3 + - - +
416I SER* 3.8 5.7 + - - -
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Residues in contact with LEU 413 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382I CYS* 4.2 19.5 - - + +
385I LEU* 4.0 22.0 - - + -
386I ALA 4.4 1.1 - - - +
389I LEU* 3.5 26.9 - - + +
398I LEU* 5.1 1.1 - - + -
400I LEU* 4.4 15.3 - - + -
405I VAL* 5.6 0.9 - - + -
409I GLY 3.1 12.1 + - - +
410I VAL* 2.5 23.9 + - + +
412I GLN* 1.3 72.9 - - - +
414I LEU* 1.3 64.9 + - + +
416I SER* 3.0 16.3 + - - -
417I LEU* 3.1 18.2 + - + +
427I LEU* 3.9 34.8 - - + -
429I LEU* 4.6 12.1 - - + -
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Residues in contact with LEU 414 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410I VAL* 2.7 43.0 + - + +
411I LEU* 3.7 12.8 - - + +
413I LEU* 1.3 70.3 - - + +
415I GLY* 1.3 67.4 + - - +
417I LEU* 2.8 23.5 + - + -
418I GLU* 2.7 35.9 + - - +
427I LEU* 5.4 2.7 - - + -
438I VAL* 4.7 7.2 - - + -
441I ARG* 4.2 34.3 - - + +
442I LEU* 4.2 19.5 - - + +
445I LEU* 4.1 14.6 - - + -
454I VAL* 5.6 0.7 - - + -
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Residues in contact with GLY 415 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390I LEU* 5.5 0.2 - - - -
411I LEU 2.9 15.4 + - - -
412I GLN* 4.3 3.6 - - - -
413I LEU 3.3 0.8 - - - -
414I LEU* 1.3 75.8 - - - +
416I SER* 1.3 58.1 + - - +
418I GLU* 3.7 8.1 + - - +
419I GLN* 3.3 26.9 + - - +
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Residues in contact with SER 416 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386I ALA* 2.9 40.0 + - - +
389I LEU* 3.9 17.8 - - - +
390I LEU* 3.7 25.2 - - - +
412I GLN 3.8 1.6 + - - -
413I LEU 3.0 10.5 + - - -
415I GLY* 1.3 74.2 - - - +
417I LEU* 1.3 63.2 + - - +
419I GLN* 3.5 11.9 - - - +
422I CYS* 3.5 16.3 - - - +
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Residues in contact with LEU 417 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389I LEU* 3.9 24.0 - - + -
413I LEU* 3.2 12.8 - - + +
414I LEU* 2.8 31.1 + - + +
416I SER* 1.3 70.5 - - - +
418I GLU* 1.3 64.3 + - - +
419I GLN 3.0 6.0 + - - +
422I CYS* 3.8 22.0 - - - -
424I LEU* 4.2 13.9 - - + -
427I LEU* 3.8 23.6 - - + -
445I LEU* 3.6 16.4 - - + -
449I LYS* 3.2 28.2 + - - +
452I LEU* 4.3 14.6 - - + -
454I VAL* 4.7 9.9 - - + -
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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