Contacts of the helix formed by residues 78 - 88 (chain C) in PDB entry 2QJK
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 THR 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C PRO* 4.3 9.0 - - + +
60C GLY* 3.6 28.9 - - - +
75C ARG* 5.1 1.6 - - - +
77C ARG* 1.3 74.2 - - - +
79C GLU* 1.3 63.9 + - - +
80C ALA* 3.4 10.6 - - - +
81C ASP* 3.0 32.0 + - - +
82C ILE* 2.9 26.3 + - - +
121C GLU* 5.8 0.4 - - - -
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Residues in contact with GLU 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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78C THR* 1.3 70.3 - - - +
80C ALA* 1.3 67.3 + - - +
82C ILE* 2.9 12.2 + - + +
83C GLU* 2.7 27.1 + - - +
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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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78C THR* 3.4 11.4 + - - +
79C GLU* 1.3 81.1 - - - +
81C ASP* 1.3 63.4 + - - +
83C GLU* 3.4 4.9 + - - +
84C LEU* 2.8 34.2 + - + +
83L GLU* 4.6 21.3 - - + +
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Residues in contact with ASP 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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75C ARG* 2.9 34.3 + - - -
77C ARG* 3.6 18.2 + - + -
78C THR* 3.0 39.3 + - - +
80C ALA* 1.3 80.6 - - - +
82C ILE* 1.3 65.3 + - - +
83C GLU 3.1 1.2 + - - -
84C LEU* 3.5 2.8 + - - +
85C GLY 3.2 15.9 + - - -
140C VAL* 3.6 21.9 - - - +
145C GLY 4.8 3.3 - - - +
158C SER* 3.4 22.5 + - - -
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Residues in contact with ILE 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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77C ARG* 3.8 24.0 - - + +
78C THR 2.9 18.2 - - - +
79C GLU* 2.9 10.6 + - + +
81C ASP* 1.3 74.8 - - - +
83C GLU* 1.3 65.2 + - - +
85C GLY* 3.5 1.2 + - - -
86C ARG* 3.2 49.9 + - - +
111C ASP* 3.9 0.2 - - - +
119C ALA 3.9 8.7 - - - +
120C GLY 3.2 33.9 - - - +
121C GLU* 4.1 14.8 - - + +
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Residues in contact with GLU 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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79C GLU 2.7 15.9 + - - +
80C ALA* 3.4 12.3 - - - +
81C ASP 3.1 0.2 - - - -
82C ILE* 1.3 71.2 - - - +
84C LEU* 1.3 70.8 + - + +
86C ARG* 2.7 24.5 + - - +
87C SER* 3.0 11.5 + - - -
80L ALA* 4.3 23.9 - - - +
83L GLU* 4.4 15.9 - - + -
84L LEU* 4.3 20.2 - - + +
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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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80C ALA* 2.8 28.0 + - + +
81C ASP* 3.9 2.2 - - - +
83C GLU* 1.3 83.7 - - + +
85C GLY* 1.3 64.4 + - - +
87C SER* 3.0 28.1 + - - +
88C VAL* 3.4 10.5 + - + +
144C PHE 4.4 18.4 - - - +
145C GLY* 4.8 9.4 - - - +
158C SER* 3.8 14.4 - - - +
83L GLU* 4.2 17.7 - - + +
84L LEU* 5.4 5.8 - - + +
87L SER* 3.9 31.9 - - - +
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Residues in contact with GLY 85 (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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77C ARG* 4.6 1.1 - - - -
81C ASP 3.2 8.2 + - - -
83C GLU 2.7 6.1 + - - -
84C LEU* 1.3 76.9 - - - +
86C ARG* 1.3 58.3 + - - -
88C VAL* 3.9 6.6 + - - +
111C ASP* 3.4 28.7 + - - +
157C ASP* 5.9 0.2 - - - -
158C SER* 3.6 10.5 + - - -
159C ALA* 4.9 1.6 - - - -
161C ARG* 3.0 31.6 + - - -
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Residues in contact with ARG 86 (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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82C ILE* 3.2 29.6 - - - +
83C GLU* 2.7 17.0 + - - +
85C GLY* 1.3 70.9 - - - -
87C SER* 1.3 68.3 + - - +
88C VAL 4.1 3.8 - - - +
111C ASP* 3.3 29.6 + - + -
112C GLN* 3.6 37.2 + - - +
115C THR* 5.0 0.2 + - - -
118C GLU 3.5 22.4 + - - -
119C ALA* 3.8 16.0 + - - +
120C GLY* 3.8 7.3 - - - -
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Residues in contact with SER 87 (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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83C GLU* 3.0 9.8 + - - -
84C LEU* 3.0 21.0 + - - +
86C ARG* 1.3 83.4 - - - +
88C VAL* 1.3 81.0 + - - +
89C GLN* 3.6 10.7 + - - +
84L LEU* 3.7 35.6 - - - +
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Residues in contact with VAL 88 (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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84C LEU* 3.4 9.1 + - + +
85C GLY 4.2 3.8 - - - +
86C ARG 3.5 4.6 - - - +
87C SER* 1.3 92.4 + - - +
89C GLN* 1.3 74.4 + - - +
90C LEU 3.8 2.1 + - - -
92C GLN* 4.2 14.1 - - + +
93C LEU* 4.0 27.8 - - + +
157C ASP* 5.9 0.4 - - + -
161C ARG* 3.9 18.0 + - - +
163C ARG* 3.4 33.9 - - - +
172H ALA 4.9 0.7 - - - +
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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