Contacts of the helix formed by residues 45 - 57 (chain A) in PDB entry 2QDC
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PRO* 1.3 72.0 - - + +
47A ARG* 3.2 7.4 - - + +
48A GLU* 3.1 33.1 + - + +
49A VAL* 2.9 36.7 + - - +
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Residues in contact with PRO 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 1.3 87.1 - - + +
47A ARG* 1.3 57.7 + - - +
49A VAL* 3.8 8.5 - - + +
50A THR* 3.0 33.8 + - - -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 3.2 7.1 - - + -
46A PRO* 1.3 77.9 - - - +
48A GLU* 1.3 61.6 + - + +
50A THR* 3.3 13.1 + - - +
51A LEU* 3.0 50.3 + - + +
86A ASN* 2.9 38.1 + - - +
87A PHE 3.9 19.6 + - - -
88A VAL* 5.6 5.2 - - - +
92A ASP* 6.0 1.8 - - - -
110A ASN* 5.2 3.4 - - - +
112A GLN* 5.6 6.3 + - - +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 3.1 30.9 + - + +
47A ARG* 1.3 81.4 - - + +
49A VAL* 1.3 58.1 + - + +
51A LEU* 3.9 9.2 - - + +
52A HIS* 2.9 32.6 + - - +
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 2.9 28.0 + - - +
46A PRO* 3.8 9.2 - - + +
48A GLU* 1.3 74.1 - - + +
50A THR* 1.3 66.5 + - - +
52A HIS* 3.4 5.6 + - - +
53A PHE* 3.1 23.9 + - + +
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO 3.0 21.9 + - - -
47A ARG* 3.5 16.3 + - - +
49A VAL* 1.3 79.0 - - - +
51A LEU* 1.3 64.3 + - + +
53A PHE* 3.3 2.3 + - - +
54A LEU* 3.0 37.9 + - + +
84A PRO* 3.7 32.7 - - + +
86A ASN* 3.9 20.2 - - + +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 3.0 41.9 + - + +
48A GLU* 4.0 8.5 - - + +
50A THR* 1.3 77.0 - - + +
52A HIS* 1.3 57.4 + - - +
54A LEU* 3.9 2.8 - - - +
55A ARG* 3.0 67.0 + - - +
86A ASN* 4.3 18.2 - - - +
307A LEU* 3.8 23.1 - - + -
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Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLU 2.9 19.0 + - - +
49A VAL* 3.8 5.8 - - - +
51A LEU* 1.3 77.9 - - - +
53A PHE* 1.3 58.5 + - - +
55A ARG* 3.8 3.9 - - - +
56A THR* 2.7 62.9 + - + +
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 3.1 14.3 + - + +
50A THR 3.6 7.6 - - - +
52A HIS* 1.3 78.9 - - - +
54A LEU* 1.3 60.0 + - - +
56A THR* 3.2 3.5 + - - -
57A ALA* 2.7 59.8 + - + +
79A GLU 5.5 0.2 - - - -
82A LYS* 3.9 31.9 - - + -
83A ILE* 4.0 7.4 - - + -
84A PRO* 3.3 33.4 - - + -
299A LEU* 4.7 9.9 - - + -
303A CYS* 3.8 12.1 - - - -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 3.0 39.1 + - + +
51A LEU* 4.0 1.1 - - - +
53A PHE* 1.3 76.3 - - - +
55A ARG* 1.3 60.7 + - - +
56A THR 3.6 0.3 + - - -
57A ALA 4.4 2.4 + - - +
83A ILE* 3.9 10.3 - - + -
84A PRO* 3.8 30.1 - - + +
86A ASN* 3.8 21.5 - - + -
303A CYS* 3.3 46.6 - - + +
304A GLN* 3.6 11.8 + - - -
306A ARG* 4.0 5.2 - - + -
307A LEU* 3.8 34.1 - - + +
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.0 56.7 + - - +
52A HIS* 4.0 5.2 - - - +
53A PHE 3.2 0.2 - - - -
54A LEU* 1.3 75.9 - - - +
56A THR* 1.3 65.2 + - + +
57A ALA 5.3 0.4 - - - -
304A GLN* 4.4 11.9 + - - +
307A LEU* 4.0 22.0 - - + +
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A HIS* 2.7 52.0 + - + +
53A PHE* 3.8 2.8 + - - -
55A ARG* 1.3 87.9 - - + +
57A ALA* 1.3 67.7 + - - +
58A GLY* 3.6 1.6 + - - -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 2.7 57.3 + - + +
54A LEU 4.4 2.7 + - - +
55A ARG 5.3 0.3 - - - -
56A THR* 1.3 76.0 + - - +
58A GLY* 1.3 58.5 + - - +
297A ASP* 4.6 0.3 - - - +
299A LEU* 4.3 8.3 - - + -
300A GLY* 3.9 15.1 - - - -
303A CYS* 3.8 11.8 - - - -
304A GLN* 5.8 1.0 + - - -
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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