Contacts of the helix formed by residues 55 - 62 (chain J) in PDB entry 5IYB
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 55 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735B VAL* 4.0 26.7 - - + -
738B THR* 4.0 17.3 - - + -
740B PHE* 5.7 0.2 - - + -
754B PRO* 5.4 4.5 - - + -
771B GLU* 4.0 22.0 - - + +
772B LEU* 3.6 34.5 - - + -
773B PRO* 5.7 0.4 - - + -
1J MET* 3.7 28.3 - - + +
53J VAL* 3.1 10.4 + - + +
54J ASP* 1.3 69.9 - - - +
56J ILE* 1.3 65.4 + - - +
57J GLU 3.0 4.3 + - - -
58J LYS* 3.0 25.4 + - + +
59J LEU* 3.4 14.0 + - + +
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Residues in contact with ILE 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 4.3 17.9 - - + -
59C LEU* 5.2 5.4 - - + -
151C VAL* 4.8 6.5 - - + -
152C LYS* 4.0 38.4 - - + +
1J MET* 4.0 7.1 - - + +
2J ILE* 3.9 36.8 - - + +
54J ASP* 3.3 23.6 - - - +
55J LEU* 1.3 76.9 - - - +
57J GLU* 1.3 76.0 + - - +
59J LEU* 3.0 16.1 + - + +
60J LEU* 2.8 31.3 + - + +
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Residues in contact with GLU 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C THR* 5.7 0.9 - - - +
152C LYS* 2.8 29.9 + - - +
54J ASP* 2.9 34.3 - - + +
55J LEU 3.0 0.6 + - - -
56J ILE* 1.3 81.1 - - - +
58J LYS* 1.3 69.3 + - + +
60J LEU* 3.8 17.7 - - - +
61J ASN* 3.1 22.2 + - - +
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Residues in contact with LYS 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ASP* 4.3 15.3 + - - +
172B CYS* 5.5 3.6 - - - -
178B PRO* 5.0 14.2 - - + +
179B LEU* 5.3 9.6 - - + +
738B THR* 4.4 24.0 - - + +
771B GLU* 3.2 30.2 + - + +
54J ASP 5.6 1.3 - - - +
55J LEU* 3.0 20.0 + - + +
57J GLU* 1.3 79.9 - - + +
59J LEU* 1.3 63.3 + - - +
61J ASN* 3.1 25.2 - - + +
62J TYR* 3.5 14.8 - - + -
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Residues in contact with LEU 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738B THR* 3.5 27.6 - - - +
740B PHE* 4.7 11.2 - - + -
741B HIS* 4.1 20.7 + - + +
58C VAL* 3.5 48.1 - - + +
59C LEU* 5.8 0.9 - - + -
1J MET* 4.5 26.2 - - + -
55J LEU* 3.4 9.3 + - + +
56J ILE* 3.0 24.1 + - + +
58J LYS* 1.3 79.9 - - - +
60J LEU* 1.3 62.5 + - - +
61J ASN 3.2 0.5 + - - -
62J TYR* 3.3 22.5 + - - +
64J PRO* 5.0 2.8 - - - +
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Residues in contact with LEU 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 3.8 22.2 - - + -
112C THR* 4.0 13.9 - - + +
152C LYS* 3.6 50.9 - - + +
153C LEU 4.4 0.2 - - - -
154C ARG* 3.0 60.2 + - + +
157C GLN* 4.0 8.7 - - - +
56J ILE* 2.8 22.3 + - + +
57J GLU* 3.8 21.1 - - - +
58J LYS 3.4 0.2 - - - -
59J LEU* 1.3 72.1 - - - +
61J ASN* 1.3 58.9 + - - +
62J TYR 3.3 0.7 + - - +
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Residues in contact with ASN 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ASP* 4.3 8.0 - - - +
169B ARG* 5.2 8.7 - - - +
172B CYS* 3.3 36.5 - - - +
173B GLU* 5.5 0.5 - - - -
154C ARG* 4.8 4.9 + - - +
57J GLU 3.1 14.3 + - - +
58J LYS* 3.1 21.2 - - + +
59J LEU 3.1 0.8 - - - -
60J LEU* 1.3 72.3 - - - +
62J TYR* 1.3 66.3 + - - +
63J ALA* 4.6 0.5 - - - -
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Residues in contact with TYR 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B CYS* 3.1 37.5 - - + -
175B ASN* 3.8 23.1 - - - +
176B GLU 4.3 4.0 - - - -
177B CYS* 3.3 13.3 - - - -
178B PRO* 3.8 3.9 - - + +
738B THR* 2.8 30.5 + - - -
739B ASN* 3.1 35.8 + - + +
741B HIS* 3.6 15.5 - + - +
154C ARG* 3.1 17.5 + - - -
58J LYS* 3.5 23.3 - - + -
59J LEU* 3.3 13.7 + - - +
60J LEU 3.2 2.7 - - - +
61J ASN* 1.3 83.7 - - - +
63J ALA* 1.3 56.5 + - - +
64J PRO* 2.2 38.3 - - + +
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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