Contacts of the helix formed by residues 433 - 444 (chain A) in PDB entry 5IJ7
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 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A SER* 5.4 0.2 - - - -
432A TRP* 1.4 72.2 - - - +
434A GLY* 1.3 60.3 + - - +
435A ALA* 3.9 7.3 + - - +
436A GLU* 2.7 39.9 + - - +
437A ALA* 2.9 31.3 + - - +
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Residues in contact with GLY 434 (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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269A ALA 3.3 19.0 + - - -
270A LYS 3.2 7.1 - - - +
271A SER* 3.5 23.6 - - - -
433A SER* 1.3 71.3 - - - +
435A ALA* 1.4 51.7 + - - +
438A SER* 2.8 40.7 + - - -
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Residues in contact with ALA 435 (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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264A ILE* 3.3 43.8 - - + +
269A ALA* 4.0 12.7 + - + -
433A SER* 3.2 7.5 + - - +
434A GLY* 1.4 74.2 - - - +
436A GLU* 1.4 59.3 + - + +
439A MET* 3.2 28.8 + - - +
654S ARG* 4.3 13.3 - - - +
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Residues in contact with GLU 436 (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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432A TRP* 3.5 19.7 + - + -
433A SER* 2.7 44.3 + - - +
435A ALA* 1.4 74.3 - - + +
437A ALA* 1.3 60.2 + - - +
439A MET* 3.7 4.9 + - - +
440A PHE* 3.1 26.7 + - - +
458A ILE* 4.0 11.4 - - + +
460A THR* 2.9 31.8 + - - +
461A LYS* 2.8 36.7 + - + +
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Residues in contact with ALA 437 (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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271A SER* 3.5 12.6 - - - +
432A TRP* 4.2 3.8 - - + +
433A SER 2.9 16.2 + - - +
434A GLY 3.8 2.0 - - - +
436A GLU* 1.3 75.5 - - - +
438A SER* 1.4 64.3 + - - +
440A PHE* 3.1 13.9 + - - +
441A ARG* 3.1 42.1 + - - +
469A PHE* 3.9 23.1 - - + -
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Residues in contact with SER 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 3.9 14.6 - - - -
270A LYS 2.7 26.7 + - - -
272A VAL* 2.8 28.2 + - - +
277A SER* 3.8 18.2 + - - -
434A GLY 2.8 16.8 + - - -
437A ALA* 1.4 70.9 - - - +
439A MET* 1.4 60.8 + - - +
441A ARG* 3.4 5.1 + - - +
442A VAL* 3.1 28.3 + - - +
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Residues in contact with MET 439 (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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264A ILE* 3.7 23.0 - - + +
435A ALA 3.2 19.5 + - - +
436A GLU* 3.8 5.6 - - - +
438A SER* 1.4 74.7 - - - +
440A PHE* 1.4 55.8 + - - +
442A VAL* 3.4 7.9 + - - +
443A LEU* 2.8 45.6 + - + +
458A ILE* 4.1 11.4 - - + -
654S ARG* 3.7 37.0 - - + +
657S MET* 3.3 42.6 - - + -
658S LEU* 3.9 16.8 - - + -
661S VAL* 5.6 0.2 - - - -
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Residues in contact with PHE 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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432A TRP* 4.2 8.7 - + + -
436A GLU 3.1 14.8 + - - +
437A ALA 3.1 9.3 + - - +
439A MET* 1.4 75.2 - - - +
441A ARG* 1.4 67.5 + - + +
443A LEU* 3.0 4.8 + - - +
444A ILE* 2.9 71.8 + - + +
451A PHE* 4.6 1.1 - + - -
454A ILE* 4.4 4.3 - - + -
458A ILE* 4.0 12.1 - - + +
466A VAL* 3.9 36.1 - - + -
469A PHE* 3.4 30.7 - + + -
470A ARG* 3.6 31.6 - - + -
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Residues in contact with ARG 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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271A SER* 2.7 30.8 + - - -
272A VAL* 3.4 30.9 + - - +
273A GLN* 4.0 20.3 + - + +
274A ARG* 3.2 29.8 - - + +
437A ALA* 3.1 31.0 + - - +
438A SER 3.7 8.5 - - - +
440A PHE* 1.4 83.2 - - + +
442A VAL* 1.4 58.7 + - - +
444A ILE* 3.3 27.3 - - + +
445A GLY 4.0 0.5 + - - -
469A PHE* 4.2 12.1 - - - -
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Residues in contact with VAL 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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274A ARG* 2.7 52.2 + - + +
277A SER* 3.7 27.6 - - - -
278A LEU* 4.5 3.4 - - + -
438A SER 3.1 17.4 + - - +
439A MET* 3.6 14.1 - - - +
441A ARG* 1.4 74.4 - - - +
443A LEU* 1.4 60.1 + - - +
445A GLY* 3.0 14.0 + - - -
446A THR* 3.8 1.6 + - - -
658S LEU* 3.9 20.9 - - + -
661S VAL* 3.7 25.1 - - + -
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Residues in contact with LEU 443 (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 MET* 2.8 27.2 + - + +
440A PHE 3.9 0.4 - - - +
442A VAL* 1.4 72.5 - - - +
444A ILE* 1.4 52.8 + - - +
446A THR* 3.2 2.8 + - - +
447A TYR* 2.8 50.6 + - + +
454A ILE* 3.8 35.9 - - + +
457A LEU* 3.7 44.6 - - + -
458A ILE* 3.9 14.1 - - + -
657S MET* 3.8 18.2 - - + -
661S VAL* 4.5 20.2 - - + -
674S ILE* 5.6 0.7 - - + -
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Residues in contact with ILE 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 PHE* 2.9 64.6 + - + +
441A ARG* 3.3 25.1 - - + +
443A LEU* 1.4 74.8 - - - +
445A GLY* 1.3 56.8 + - - +
446A THR 3.2 0.2 - - - -
448A TYR* 3.1 42.2 + - - +
451A PHE* 4.7 4.9 - - + -
454A ILE* 3.6 19.7 - - + -
470A ARG* 5.2 7.4 - - - -
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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