Contacts of the helix formed by residues 73 - 84 (chain C) in PDB entry 6B3I
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 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C GLU 5.1 1.6 + - - -
72C LEU* 1.3 78.0 + - - +
74C GLY* 1.3 68.7 + - - +
76C PHE* 3.6 10.3 + - - +
77C GLU* 3.1 18.5 + - - -
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Residues in contact with GLY 74 (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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73C SER* 1.3 80.9 - - - +
75C ASN* 1.3 63.2 + - - -
76C PHE 4.3 0.2 - - - -
77C GLU* 3.6 7.1 + - - +
78C LYS* 3.2 21.9 + - - +
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Residues in contact with ASN 75 (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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74C GLY* 1.3 70.8 - - - -
76C PHE* 1.3 59.9 + - - +
77C GLU 3.3 0.7 - - - -
78C LYS* 3.3 33.7 + - - +
79C THR* 2.8 34.7 + - - -
265C GLU* 2.3 45.1 + - - +
266C GLU 5.3 0.2 - - - +
269C ILE* 4.1 9.2 - - + -
307C PHE* 3.4 26.6 - - + +
402C EDO 5.3 3.6 + - - -
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Residues in contact with PHE 76 (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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34C GLU* 4.3 17.9 - - + -
37C ILE* 5.0 9.4 - - + -
38C ILE* 3.6 37.5 - - + -
41C LEU* 6.0 0.7 - - + -
72C LEU* 3.5 42.2 - - + -
73C SER 3.6 7.4 + - - +
74C GLY 3.3 0.6 - - - -
75C ASN* 1.3 77.9 - - - +
77C GLU* 1.3 57.1 + - - +
79C THR* 4.2 2.6 - - - -
80C ALA* 3.1 28.2 + - + +
306C ASP* 3.4 51.4 - - + -
307C PHE* 4.0 12.3 - - - +
310C LEU* 4.0 16.5 - - + +
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Residues in contact with GLU 77 (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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68C LEU 4.2 7.0 - - - +
69C LYS* 3.7 16.1 - - - +
72C LEU* 3.5 28.9 - - + +
73C SER* 3.1 32.1 + - - +
74C GLY 3.7 6.9 + - - +
75C ASN 3.3 0.2 - - - -
76C PHE* 1.3 76.9 - - - +
78C LYS* 1.3 65.0 + - - +
80C ALA* 3.7 3.7 - - + +
81C LEU* 3.0 55.3 + - + +
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Residues in contact with LYS 78 (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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74C GLY 3.2 15.0 + - - +
75C ASN* 3.3 28.7 + - - +
76C PHE 3.4 0.2 - - - -
77C GLU* 1.3 82.3 + - - +
79C THR* 1.3 57.4 + - - +
81C LEU* 3.9 4.9 - - - +
82C ALA* 3.0 27.9 + - - +
90C TYR* 4.3 15.4 - - + +
94C GLN* 5.4 0.2 - - - +
97C LYS* 3.9 12.9 - - - +
266C GLU* 2.4 48.1 + - - +
269C ILE* 4.4 10.6 - - + +
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Residues in contact with THR 79 (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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75C ASN 2.8 19.1 + - - -
78C LYS* 1.3 75.1 - - - +
80C ALA* 1.3 64.6 + - - +
82C ALA* 3.5 1.4 - - - +
83C LEU* 3.0 25.8 + - + +
269C ILE* 3.3 23.4 - - + +
273C VAL* 4.4 4.5 - - + -
307C PHE* 3.2 20.1 - - - -
310C LEU* 3.6 25.1 - - + -
311C LEU* 4.3 9.4 - - + -
314C LEU* 4.1 22.0 - - + -
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Residues in contact with ALA 80 (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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41C LEU* 3.6 28.6 - - + +
68C LEU* 4.3 8.1 - - + -
72C LEU* 4.1 20.2 - - + -
76C PHE* 3.1 21.2 + - + +
77C GLU 3.7 4.0 - - - +
79C THR* 1.3 77.6 - - - +
81C LEU* 1.3 62.7 + - + +
83C LEU* 3.3 5.9 + - - +
84C LEU* 3.2 27.3 + - - +
310C LEU* 4.2 4.2 - - + +
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Residues in contact with LEU 81 (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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65C GLU* 3.7 45.1 - - + +
68C LEU* 4.3 14.8 - - + -
69C LYS* 3.6 22.4 - - + -
77C GLU* 3.0 46.8 + - + +
78C LYS* 4.2 4.0 - - - +
80C ALA* 1.3 73.9 - - + +
82C ALA* 1.3 65.9 + - - +
84C LEU* 3.2 12.6 + - + +
85C ASP* 3.3 21.0 + - - +
90C TYR* 5.5 0.2 - - - -
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Residues in contact with ALA 82 (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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78C LYS 3.0 19.7 + - - +
79C THR* 3.2 9.2 + - - +
81C LEU* 1.3 78.3 - - - +
83C LEU* 1.3 60.1 + - - +
85C ASP* 3.4 19.5 + - - +
86C HIS 5.2 0.3 - - - +
90C TYR* 3.5 46.5 - - + +
269C ILE* 4.2 1.3 - - + -
273C VAL* 3.7 22.7 - - + +
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Residues in contact with LEU 83 (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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41C LEU* 3.8 36.3 - - + +
49C ARG* 2.4 60.8 + - - +
50C GLN* 4.9 0.7 + - - -
79C THR* 3.0 24.6 + - + +
80C ALA 3.7 5.2 - - - +
81C LEU 3.2 0.4 - - - -
82C ALA* 1.3 74.7 - - - +
84C LEU* 1.3 61.7 + - - +
85C ASP 3.2 3.0 + - - +
273C VAL* 4.0 29.4 - - + +
276C ALA* 5.9 4.3 - - + -
310C LEU* 4.4 5.6 - - + -
314C LEU* 3.9 33.0 - - + -
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Residues in contact with LEU 84 (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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41C LEU* 3.8 25.1 - - + -
49C ARG* 4.7 17.9 - - + +
50C GLN* 2.9 8.5 + - - +
53C LYS* 2.6 42.5 + - + -
64C LEU* 3.8 26.5 - - + -
65C GLU* 3.7 31.2 - - + +
68C LEU* 3.7 28.0 - - + -
80C ALA 3.2 11.8 + - - +
81C LEU* 3.2 10.4 + - + +
83C LEU* 1.3 78.5 - - - +
85C ASP* 1.3 55.1 + - - +
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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