Contacts of the helix formed by residues 77 - 84 (chain 2) 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 LYS 77 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602 LEU* 5.1 7.3 + - - +
762 LYS* 1.3 72.1 - - - +
782 GLU* 1.3 97.1 + - + +
802 SER* 3.3 5.0 + - - -
812 LYS* 2.8 36.7 + - - +
962 TRP* 3.5 49.9 - - + +
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Residues in contact with GLU 78 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762 LYS* 3.3 0.4 - - - +
772 LYS* 1.3 102.9 - - + +
792 PHE* 1.3 64.8 + - - +
812 LYS* 2.7 52.5 + - - +
822 ALA* 3.1 2.4 + - - +
932 LEU* 5.1 0.2 - - - -
962 TRP* 3.1 36.5 - - + -
1252 GLY 4.6 0.3 - - - +
1262 GLY* 3.2 21.3 - - - +
1292 TRP* 2.7 47.1 - - + +
1302 SER* 4.6 0.9 - - - -
1322 ASP* 4.7 0.8 - - + +
1332 THR* 4.2 8.3 - - - -
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Residues in contact with PHE 79 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762 LYS* 3.2 40.2 + - + +
782 GLU* 1.3 81.2 - - - +
802 SER* 1.3 68.2 + - - +
822 ALA* 3.2 15.8 + - + +
832 GLN* 4.2 14.5 + - + +
1292 TRP* 4.7 17.7 - + - +
1322 ASP* 4.5 17.0 - - - -
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Residues in contact with SER 80 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 LYS 3.0 15.8 + - - -
772 LYS* 3.8 5.2 - - - -
792 PHE* 1.3 83.8 - - - +
812 LYS* 1.3 63.4 + - - +
822 ALA 3.2 0.5 + - - -
832 GLN* 3.4 19.1 + - - +
842 GLU* 4.3 4.9 + - - +
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Residues in contact with LYS 81 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772 LYS* 2.8 19.0 + - - +
782 GLU* 2.7 59.7 + - + +
802 SER* 1.3 76.5 - - - +
822 ALA* 1.3 71.2 + - - +
842 GLU* 2.8 24.5 + - - +
892 LEU* 2.9 42.4 - - + +
932 LEU* 2.9 40.2 - - + -
1322 ASP* 4.6 11.3 + - - -
1332 THR* 4.8 5.5 - - - +
1362 LEU* 4.8 4.0 - - - -
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Residues in contact with ALA 82 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782 GLU 3.1 6.2 + - - +
792 PHE* 3.4 14.1 - - + +
802 SER 3.1 1.0 - - - -
812 LYS* 1.3 87.8 - - - +
832 GLN* 1.3 67.9 + - + +
842 GLU 3.2 9.0 - - - +
892 LEU* 3.5 12.0 - - - +
1322 ASP* 4.0 21.3 - - - +
1362 LEU* 5.5 8.4 - - + +
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Residues in contact with GLN 83 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792 PHE* 4.9 15.6 - - + +
802 SER* 3.4 12.0 + - - +
812 LYS 3.1 0.6 - - - -
822 ALA* 1.3 83.2 - - + +
842 GLU* 1.3 64.0 + - + +
852 GLU* 3.8 4.3 + - - +
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Residues in contact with GLU 84 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432 ALA* 5.7 7.4 - - - +
802 SER 4.8 4.3 - - - +
812 LYS* 2.8 19.3 + - - +
822 ALA 3.2 9.0 - - - +
832 GLN* 1.3 83.4 - - + +
852 GLU* 1.3 79.3 + - - +
862 SER 3.5 1.0 + - - -
892 LEU* 3.4 10.9 - - + +
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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