Contacts of the helix formed by residues 58 - 67 (chain C) in PDB entry 6A5T
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 ALA 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785B TYR* 5.2 4.5 + - - +
854B LEU* 4.5 16.2 - - + -
969B ARG* 3.4 16.6 - - - +
53C ASN* 4.0 3.1 + - - -
56C VAL 4.1 1.0 + - - -
57C LEU* 1.3 84.4 - - - +
59C ASP* 1.3 67.4 + - - +
60C GLU* 3.2 24.0 - - - +
61C PHE* 3.7 20.5 - - + +
62C ILE* 3.9 6.9 + - - +
1J MET* 5.6 1.8 - - + +
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Residues in contact with ASP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948B ILE* 5.5 6.6 - - - +
969B ARG* 3.5 10.4 + - - +
50C ILE* 3.4 28.3 - - + +
53C ASN* 2.8 31.8 + - - +
58C ALA* 1.3 69.5 - - - +
60C GLU* 1.3 68.7 + - - +
61C PHE 2.8 10.4 + - - -
62C ILE* 2.9 15.7 + - - +
63C SER* 2.9 14.3 + - - -
62L ARG* 4.3 14.0 + - - -
67L ILE* 5.4 4.0 - - - +
69L PHE* 3.6 15.5 - - + -
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B TYR* 3.5 15.3 + - - +
854B LEU* 3.4 11.3 - - - +
969B ARG* 2.4 36.0 + - - -
971B THR* 3.6 12.0 + - + +
58C ALA* 3.2 12.3 - - - +
59C ASP* 1.3 85.1 + - - +
61C PHE* 1.3 56.1 + - - +
63C SER* 3.1 13.7 - - - -
64C HIS* 2.7 32.9 + - - +
69L PHE* 3.8 23.8 - - + -
71L ALA* 5.0 1.2 - - - -
72L ARG 5.6 2.4 - - - +
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Residues in contact with PHE 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B TYR* 3.4 49.6 - + - +
798B TYR* 3.5 25.8 - + - -
854B LEU* 5.4 0.4 - - + -
57C LEU* 4.4 20.4 - - + -
58C ALA* 3.7 25.8 - - + +
59C ASP 2.8 1.2 + - - -
60C GLU* 1.3 78.8 - - - +
62C ILE* 1.3 63.9 + - - +
64C HIS* 2.9 21.2 + - - +
65C ARG* 3.0 40.5 + - + +
1J MET* 3.4 38.1 - - + -
2J ILE* 4.6 1.6 - - + -
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C VAL* 6.4 0.7 - - + -
50C ILE* 5.8 3.8 - - + -
53C ASN* 5.4 2.7 - - - +
55C SER* 4.8 5.2 - - - +
57C LEU* 4.1 31.2 - - + -
58C ALA 4.2 7.4 - - - +
59C ASP* 2.9 10.3 + - - +
61C PHE* 1.3 76.2 - - + +
63C SER* 1.3 66.9 + - - +
65C ARG* 4.4 4.3 - - - +
66C LEU* 3.0 44.6 + - + +
144C LEU* 4.0 20.2 - - + +
145C CYS* 4.1 9.6 - - + -
153C LEU* 4.0 28.5 - - + -
155C ILE* 4.6 13.7 - - + -
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C VAL* 3.2 28.8 - - - +
50C ILE* 4.8 0.5 - - - +
59C ASP 2.9 8.8 + - - -
60C GLU* 3.1 15.9 - - - -
62C ILE* 1.3 78.4 - - - +
64C HIS* 1.3 63.7 + - - +
66C LEU* 3.8 1.6 - - - +
67C GLY 2.9 18.9 + - - -
69L PHE* 3.2 31.2 - - - -
71L ALA* 3.0 24.1 - - - +
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Residues in contact with HIS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B TYR* 4.8 7.6 - + + -
798B TYR* 3.2 29.7 + + - -
847B ASP 3.8 20.3 + - - -
848B ARG 4.6 0.9 - - - -
849B GLY* 4.0 21.6 - - - -
852B ARG* 4.3 13.0 + - - -
60C GLU 2.7 16.9 + - - +
61C PHE* 2.9 13.2 + - - +
63C SER* 1.3 72.0 - - - +
65C ARG* 1.3 67.0 + - - +
67C GLY* 2.9 14.6 + - - -
68C LEU* 3.6 26.6 + - + +
167C HIS* 5.9 0.9 - + - -
5J VAL* 6.1 0.7 - - + -
71L ALA* 3.1 26.4 - - - +
72L ARG* 3.7 18.6 - - - +
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Residues in contact with ARG 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B TYR* 3.6 26.9 + - - +
61C PHE* 3.0 37.2 + - + +
62C ILE* 4.1 4.5 - - - +
64C HIS* 1.3 75.8 - - - +
66C LEU* 1.3 65.3 + - - +
68C LEU* 2.7 21.7 + - - +
69C ILE* 3.6 6.7 + - - +
142C ILE* 5.5 2.2 - - - +
143C LEU* 3.9 18.9 + - - +
144C LEU* 4.0 29.3 + - + +
2J ILE* 3.2 37.6 + - - +
3J ILE* 2.3 31.3 + - - +
4J PRO* 4.0 5.4 + - - +
5J VAL* 3.9 23.7 - - + +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 3.0 35.9 + - + +
48C VAL* 4.4 9.2 - - + -
62C ILE* 3.0 27.0 + - + +
63C SER 3.9 2.2 - - - +
65C ARG* 1.3 76.2 - - - +
67C GLY* 1.3 62.2 + - - +
68C LEU 3.0 1.6 + - - -
69C ILE* 3.4 35.3 + - + +
118C LEU* 4.2 14.4 - - + -
144C LEU* 3.5 27.4 - - + -
155C ILE* 3.6 31.2 - - + -
157C CYS* 4.0 16.2 - - - -
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA* 4.3 4.7 - - - +
45C ILE* 3.6 16.7 - - - +
63C SER 2.9 10.7 + - - -
64C HIS 2.9 7.0 + - - -
65C ARG 2.9 0.2 + - - -
66C LEU* 1.3 76.8 - - - +
68C LEU* 1.3 63.2 + - - +
169C LYS* 3.0 28.3 - - - +
71L ALA* 3.6 22.9 - - - -
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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