Contacts of the helix formed by residues 78 - 87 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59O PRO* 4.3 9.6 - - + +
60O GLY* 3.6 28.5 - - - +
75O ARG* 5.0 1.8 - - - +
77O ARG* 1.3 74.2 - - - +
79O GLU* 1.3 65.1 + - - +
80O ALA* 3.4 11.8 - - - +
81O ASP* 3.0 31.9 + - - +
82O ILE* 2.9 27.1 + - - +
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Residues in contact with GLU 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O THR* 1.3 70.7 - - - +
80O ALA* 1.3 60.2 + - - +
82O ILE* 2.9 13.6 + - + +
83O GLU* 2.6 41.4 + - - +
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Residues in contact with ALA 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O THR* 3.4 11.9 - - - +
79O GLU* 1.3 79.8 - - - +
81O ASP* 1.3 63.5 + - - +
83O GLU* 3.2 8.2 - - - +
84O LEU* 2.9 33.4 - - + +
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Residues in contact with ASP 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O ARG* 3.0 35.6 + - - -
77O ARG* 3.6 19.5 + - + -
78O THR* 3.0 39.6 + - - +
79O GLU 3.0 0.2 - - - -
80O ALA* 1.3 77.3 - - - +
82O ILE* 1.3 67.1 + - - +
83O GLU 3.0 1.0 + - - -
84O LEU* 3.4 1.0 + - - -
85O GLY 3.2 16.8 + - - -
140O VAL* 4.0 18.2 - - - +
145O GLY 5.1 1.1 - - - +
158O SER* 3.4 23.0 + - - -
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Residues in contact with ILE 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77O ARG* 3.8 28.5 - - + +
78O THR 2.9 16.8 - - - +
79O GLU* 2.9 13.2 + - + +
81O ASP* 1.3 72.9 - - - +
83O GLU* 1.3 65.3 + - - +
85O GLY 3.5 0.5 + - - -
86O ARG* 3.2 50.7 + - - +
111O ASP* 3.9 0.5 - - - +
119O ALA 3.6 14.4 - - - +
120O GLY 3.1 30.7 - - - +
121O GLU* 4.2 8.7 - - + +
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Residues in contact with GLU 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O GLU* 2.6 20.3 + - - +
80O ALA* 3.2 15.5 - - - +
81O ASP 3.0 0.8 - - - -
82O ILE* 1.3 77.7 - - - +
84O LEU* 1.3 71.6 + - + +
86O ARG* 2.9 13.5 + - - +
87O SER* 3.2 13.6 + - - -
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Residues in contact with LEU 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O ALA* 2.9 31.3 + - + +
81O ASP* 4.1 1.6 - - - +
83O GLU* 1.3 88.0 - - + +
85O GLY* 1.3 62.7 + - - +
87O SER* 2.7 26.0 + - - +
88O VAL* 3.5 14.7 + - + +
144O PHE 5.1 11.7 - - - +
145O GLY* 5.5 6.3 - - - -
158O SER* 4.1 12.6 - - - +
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Residues in contact with GLY 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77O ARG* 4.6 0.9 - - - -
81O ASP 3.2 9.8 + - - -
83O GLU 3.0 1.8 + - - -
84O LEU* 1.3 77.8 - - - +
86O ARG* 1.3 58.9 + - - +
87O SER 3.5 0.2 + - - -
88O VAL* 3.6 7.2 + - - +
111O ASP* 3.4 28.2 + - - +
157O ASP* 5.9 0.4 - - - -
158O SER* 3.6 11.9 + - - -
159O ALA* 4.9 1.8 - - - -
161O ARG* 3.0 31.5 + - - -
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Residues in contact with ARG 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O ILE* 3.2 29.6 - - - +
83O GLU* 2.9 7.5 + - - +
85O GLY* 1.3 73.4 - - - +
87O SER* 1.3 58.5 + - - +
88O VAL 3.2 12.4 + - - +
111O ASP* 3.0 30.9 + - + -
112O GLN* 3.4 42.9 + - - +
115O THR* 4.8 0.6 + - - -
117O ASP 5.3 0.2 + - - -
118O GLU 3.4 23.4 + - - -
119O ALA* 4.2 6.3 + - - +
120O GLY* 3.8 13.5 - - - -
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Residues in contact with SER 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O GLU* 3.2 12.0 + - - -
84O LEU* 2.7 31.8 + - - +
86O ARG* 1.3 76.8 - - - +
88O VAL* 1.3 63.3 + - - +
89O GLN* 3.8 5.1 + - - +
92O GLN* 4.7 3.3 - - - +
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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