Contacts of the helix formed by residues 410 - 423 (chain Z) in PDB entry 5IJO
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 LEU 410 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326Y LEU* 4.5 23.8 - - + -
327Y ARG 5.7 0.2 - - - +
406Z LEU 4.1 5.8 - - - +
407Z LEU* 2.9 20.9 - - - +
408Z SER* 2.7 13.9 - - - +
409Z PRO* 1.5 61.4 - - - +
411Z GLU* 1.5 54.5 - - - +
412Z GLU 3.7 1.3 - - - +
413Z LEU* 4.2 10.2 - - + +
414Z VAL* 3.2 30.7 + - - +
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Residues in contact with GLU 411 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407Z LEU 3.7 1.8 + - - -
408Z SER* 3.1 27.9 - - - +
409Z PRO 3.5 2.9 - - - -
410Z LEU* 1.5 66.6 - - - +
412Z GLU* 1.7 42.8 + - - -
414Z VAL* 4.8 4.7 - - - -
415Z LYS* 3.0 30.0 + - - +
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Residues in contact with GLU 412 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409Z PRO 2.8 19.8 + - - +
411Z GLU 1.7 52.5 + - - +
413Z LEU* 1.2 72.9 - - + +
414Z VAL 3.3 0.7 - - - -
415Z LYS 3.7 2.0 - - - -
416Z GLU* 3.0 34.2 + - - +
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Residues in contact with LEU 413 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326Y LEU 5.3 2.9 - - - +
327Y ARG 5.5 1.3 - - - +
329Y GLN* 4.4 26.8 - - + +
330Y LYS* 4.8 10.3 - - + -
333Y PRO* 6.3 2.0 - - + -
410Z LEU* 4.2 14.8 - - + +
412Z GLU* 1.2 89.8 - - + +
414Z VAL* 1.3 56.1 + - - +
416Z GLU* 4.2 3.3 - - - +
417Z GLN* 3.5 19.4 + - - +
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Residues in contact with VAL 414 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389X VAL* 6.6 0.2 - - + -
329Y GLN* 6.2 0.2 - - - +
410Z LEU 3.2 24.0 + - - +
411Z GLU* 4.5 4.3 - - - +
412Z GLU 3.3 0.4 - - - -
413Z LEU* 1.3 72.7 - - - +
415Z LYS* 1.4 53.4 + - - +
416Z GLU 2.9 7.8 + - - -
417Z GLN* 3.4 6.8 + - - +
418Z SER* 3.3 20.1 + - - -
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Residues in contact with LYS 415 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411Z GLU 3.0 22.5 + - - +
412Z GLU 3.7 3.3 + - - -
414Z VAL* 1.4 65.6 - - - +
416Z GLU* 1.4 62.6 + - - +
418Z SER* 3.9 11.7 - - - -
419Z GLY* 3.7 11.3 + - - -
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Residues in contact with GLU 416 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412Z GLU 3.0 21.2 + - - +
413Z LEU* 4.2 3.1 - - - +
414Z VAL 2.9 1.2 - - - -
415Z LYS* 1.4 84.5 - - - +
417Z GLN* 1.3 69.1 + - - +
418Z SER 3.0 0.2 - - - -
419Z GLY* 3.1 0.9 + - - -
420Z THR* 3.0 23.6 + - - -
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Residues in contact with GLN 417 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396X GLN* 5.0 15.7 - - + -
413Z LEU 3.5 14.2 + - - +
414Z VAL* 3.4 8.5 + - - +
416Z GLU* 1.3 80.1 - - - +
418Z SER* 1.3 58.5 - - - +
420Z THR* 3.7 5.6 - - - -
421Z ILE* 2.7 37.2 + - - +
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Residues in contact with SER 418 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396X GLN* 6.1 1.1 - - - +
414Z VAL 3.3 15.1 + - - -
415Z LYS* 3.9 13.0 - - - -
417Z GLN* 1.3 79.8 - - - +
419Z GLY* 1.3 63.4 + - - -
421Z ILE* 2.8 7.2 + - - +
422Z TYR* 2.7 23.8 + - - +
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Residues in contact with GLY 419 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415Z LYS 3.7 8.1 + - - -
416Z GLU 3.1 7.5 + - - -
418Z SER* 1.3 77.4 - - - +
420Z THR* 1.4 67.6 + - - +
422Z TYR* 3.2 13.4 + - - +
423Z LEU* 3.2 11.1 + - - +
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Residues in contact with THR 420 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416Z GLU* 3.0 17.4 + - - -
417Z GLN* 3.8 5.8 - - - -
418Z SER 2.9 0.4 - - - -
419Z GLY* 1.4 84.6 - - - +
421Z ILE* 1.4 44.9 - - - +
423Z LEU* 2.9 29.7 + - - +
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Residues in contact with ILE 421 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396X GLN* 6.0 9.2 - - + +
417Z GLN 2.7 19.9 + - - +
418Z SER* 3.6 5.4 - - - +
420Z THR* 1.4 72.7 - - - +
422Z TYR* 1.3 65.1 + - - +
424Z GLN* 2.9 24.8 - - - +
426Z ALA* 5.9 0.5 - - - -
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Residues in contact with TYR 422 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418Z SER 2.7 12.4 + - - +
419Z GLY* 3.6 11.2 - - - +
420Z THR 3.2 0.2 - - - -
421Z ILE* 1.3 77.5 - - - +
423Z LEU* 1.4 52.3 + - - +
424Z GLN 2.6 18.9 + - - +
425Z HIS 5.5 0.2 - - - -
426Z ALA* 5.7 2.1 - - - -
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Residues in contact with LEU 423 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419Z GLY 3.2 6.0 + - - +
420Z THR* 2.9 17.6 + - - +
422Z TYR* 1.4 75.1 - - - +
424Z GLN* 1.3 57.7 + - - +
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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