Contacts of the helix formed by residues 49 - 61 (chain 1) in PDB entry 5IY8
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 49 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471 ALA 3.8 0.4 - - - -
481 GLU* 1.3 103.5 - - + +
501 VAL* 1.4 63.3 + - + +
511 ASN 3.3 0.3 + - - -
521 VAL* 3.3 13.1 + - - +
531 LEU* 3.0 19.9 - - + +
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Residues in contact with VAL 50 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331 PHE* 4.2 18.2 - - + -
341 ILE* 3.1 47.1 - - + -
471 ALA* 2.9 20.1 - - + +
481 GLU 3.2 1.0 - - - -
491 LEU* 1.4 78.4 - - + +
511 ASN* 1.4 53.1 + - - +
521 VAL 3.2 0.2 - - - -
531 LEU* 2.7 21.3 + - + -
541 GLN* 2.7 50.2 + - + +
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Residues in contact with ASN 51 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91 LEU* 2.9 56.0 - - + +
111 GLU* 3.0 22.6 - - - +
461 ILE* 3.2 15.2 - - - +
471 ALA* 3.2 6.4 - - - +
481 GLU 3.5 7.8 + - - +
491 LEU 3.2 1.4 - - - -
501 VAL* 1.4 75.8 - - - +
521 VAL* 1.3 63.7 + - + +
541 GLN* 3.8 4.8 - - - +
551 GLU* 3.0 26.3 + - - +
4042 THR* 3.6 11.7 - - + +
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Residues in contact with VAL 52 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481 GLU 5.5 1.8 - - - +
491 LEU 3.3 8.9 + - - +
511 ASN* 1.3 78.2 - - + +
531 LEU* 1.3 95.2 + - + +
551 GLU* 3.9 3.2 - - - +
561 ARG* 3.0 39.5 + - + +
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Residues in contact with LEU 53 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311 LYS* 5.8 12.3 - - + -
341 ILE* 6.0 0.9 - - + -
491 LEU* 3.0 16.8 - - + +
501 VAL* 2.7 24.4 + - + +
521 VAL* 1.3 100.4 - - + +
541 GLN* 1.3 55.0 + - - +
561 ARG* 3.7 4.8 - - - +
571 VAL* 2.7 39.7 + - + +
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Residues in contact with GLN 54 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 GLU* 4.2 12.1 - - - +
201 LEU* 6.0 0.3 - - - +
211 LEU* 3.2 49.6 + - + +
241 ASP* 2.5 25.6 - - - +
341 ILE* 2.8 41.0 - - + +
461 ILE* 3.5 11.4 - - + +
501 VAL* 2.7 34.0 + - + +
511 ASN* 3.8 4.5 - - - +
531 LEU* 1.3 72.8 - - - +
551 GLU* 1.3 62.0 + - - +
571 VAL* 2.7 21.2 - - - +
581 GLY* 3.0 7.4 + - - -
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Residues in contact with GLU 55 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511 ASN 3.0 17.7 + - - +
521 VAL* 3.9 4.5 - - - +
541 GLN* 1.3 78.0 - - - +
561 ARG* 1.3 76.8 + - + +
581 GLY* 3.2 3.0 + - - -
591 GLU* 3.0 21.0 + - + +
4022 ARG* 2.8 63.5 + - + +
4032 PHE 4.7 5.5 - - - +
4042 THR* 5.4 2.4 + - - -
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Residues in contact with ARG 56 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521 VAL* 3.0 30.7 + - + +
531 LEU* 3.8 4.7 - - - +
551 GLU* 1.3 91.6 + - + +
571 VAL* 1.3 62.2 + - - +
591 GLU* 3.0 12.5 + - - +
601 LEU* 2.9 33.4 + - + +
3992 ASP 5.6 1.8 + - - -
4022 ARG* 5.4 9.7 - - - +
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Residues in contact with VAL 57 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201 LEU* 5.7 1.8 - - + -
241 ASP* 2.7 27.4 - - - +
311 LYS* 4.4 14.4 - - - +
531 LEU* 2.7 21.6 + - + +
541 GLN* 2.7 27.1 - - - +
561 ARG* 1.3 73.1 - - - +
581 GLY* 1.3 58.9 + - - +
601 LEU* 3.2 9.2 + - + +
611 MET* 2.8 60.8 + - + +
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Residues in contact with GLY 58 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201 LEU* 4.6 12.6 - - - -
211 LEU* 6.2 0.9 - - - -
541 GLN 3.0 8.2 + - - -
551 GLU* 3.2 4.2 + - - -
571 VAL* 1.3 85.9 - - - +
591 GLU* 1.3 51.4 + - - +
611 MET* 2.7 33.8 + - - +
621 ASP 3.7 1.2 - - - +
519V TYR* 3.7 15.9 + - - -
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Residues in contact with GLU 59 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551 GLU* 3.0 13.1 + - + +
561 ARG* 3.2 15.9 + - - +
581 GLY* 1.3 75.9 - - - +
601 LEU* 1.3 68.7 + - + +
611 MET 2.9 12.3 - - - +
3992 ASP* 3.1 8.8 - - - +
4022 ARG* 1.7 60.0 + - - +
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Residues in contact with LEU 60 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561 ARG* 2.9 26.4 + - + +
571 VAL* 3.8 8.5 - - + +
591 GLU* 1.3 88.3 - - + +
611 MET* 1.3 64.7 + - + +
621 ASP 3.8 0.2 + - - -
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Residues in contact with MET 61 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201 LEU* 4.0 14.4 - - + -
241 ASP* 4.8 16.4 - - - +
311 LYS* 5.4 2.2 - - - +
571 VAL* 2.8 42.0 + - + +
581 GLY* 2.7 19.1 - - - +
591 GLU 2.9 10.6 - - - +
601 LEU* 1.3 78.9 - - + +
621 ASP* 1.3 69.4 + - - +
519V TYR* 4.9 1.6 - - - +
523V VAL* 3.7 29.2 - - + -
526V LYS* 5.4 7.9 - - - +
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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