Contacts of the helix formed by residues 82 - 89 (chain D) in PDB entry 2QJA
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 GLY 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A TYR* 5.9 3.9 - - - -
59B ASN* 3.3 18.9 + - - +
62B ILE* 3.6 15.4 - - - +
80D LEU 3.1 0.8 + - - -
81D GLU* 1.3 71.7 - - - +
83D SER* 1.3 63.8 + - - +
84D ASP 3.3 2.9 - - - -
85D PHE* 3.0 30.7 + - - +
86D GLN* 3.4 14.9 + - - +
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D HIS* 3.2 34.6 + - - -
78D LEU* 4.7 4.7 - - - -
79D GLY 3.5 14.3 + - - -
80D LEU* 3.0 22.9 + - - +
81D GLU 3.3 1.8 + - - -
82D GLY* 1.3 75.0 - - - +
84D ASP* 1.3 70.8 + - - +
86D GLN* 4.5 7.4 - - - +
87D CYS* 3.0 31.0 + - - +
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Residues in contact with ASP 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.7 24.2 - - + -
91A TYR* 3.4 11.6 - - - -
101A LYS* 3.3 17.7 + - - -
103A TYR* 3.1 26.6 + - + +
82D GLY 3.3 1.4 - - - -
83D SER* 1.3 81.8 + - - +
85D PHE* 1.3 68.5 + - + +
87D CYS* 5.3 0.7 - - - -
88D ARG* 3.3 33.5 + - - +
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 5.2 2.0 - + - -
28A TRP* 3.4 41.4 - + + -
31A TRP* 4.1 19.7 - + - -
32A ILE* 4.5 1.6 - - + -
89A MET* 4.0 18.8 - - + -
103A TYR* 3.9 22.4 - + - -
106A MET* 3.9 32.8 - - + -
59B ASN* 4.8 3.4 - - - -
62B ILE* 4.0 7.6 - - + -
63B VAL* 4.1 13.9 - - + -
66B LEU* 3.6 25.1 - - + +
82D GLY* 3.0 23.7 + - - +
84D ASP* 1.3 79.2 - - + +
86D GLN* 1.3 58.1 + - - +
88D ARG* 4.0 1.6 - - - +
89D ASP* 3.1 23.2 + - - +
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE* 3.3 29.8 - - + -
50B PRO* 3.3 11.4 - - + +
51B LEU* 3.0 49.1 + - - +
62B ILE* 3.6 35.2 - - + +
65B THR* 5.7 0.7 - - - +
66B LEU* 4.4 0.4 - - - -
78D LEU* 3.5 28.1 - - + +
79D GLY 5.4 2.8 + - - +
81D GLU 5.6 0.4 + - - -
82D GLY 3.4 17.1 + - - +
83D SER* 4.4 1.3 - - - +
84D ASP 3.4 0.2 - - - -
85D PHE* 1.3 74.4 - - - +
87D CYS* 1.3 66.4 + - - +
88D ARG 3.4 0.3 + - - -
89D ASP 3.5 1.9 + - - -
99D ILE* 3.3 21.7 - - - +
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Residues in contact with CYS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D HIS* 4.3 13.9 - - + -
78D LEU* 3.3 17.0 - - - -
83D SER 3.0 18.0 + - - +
84D ASP* 4.5 1.6 - - - +
86D GLN* 1.3 78.3 - - - +
88D ARG* 1.3 63.5 + - + +
99D ILE* 3.8 18.5 - - - +
100D GLU* 5.4 0.7 - - - -
101D CYS* 2.0 54.5 - - + -
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 5.2 0.4 - - + -
30A ASP* 5.0 3.0 + - - -
31A TRP* 3.4 70.8 - - + +
92A LEU* 5.1 12.5 + - - +
93A ASP 5.4 5.3 + - - -
96A GLU* 5.7 2.8 + - - -
84D ASP* 3.3 24.3 + - - +
85D PHE 4.2 1.8 - - - +
86D GLN 3.2 0.8 - - - -
87D CYS* 1.3 79.7 - - + +
89D ASP* 1.3 75.9 + - - +
90D THR 5.2 0.3 - - - -
99D ILE* 5.0 0.2 - - - -
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Residues in contact with ASP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 3.0 23.5 + - - -
49B PHE* 3.9 7.4 - - - -
66B LEU* 3.6 8.2 - - - +
85D PHE 3.1 13.6 + - - -
86D GLN 3.5 3.5 + - - -
87D CYS 3.4 2.0 - - - -
88D ARG* 1.3 84.8 - - - +
90D THR* 1.3 84.2 + - - +
91D PRO* 4.3 1.7 - - - +
97D ARG* 2.8 55.7 + - - +
98D SER* 4.8 0.2 - - - -
99D ILE* 3.7 23.1 + - + +
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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