Contacts of the helix formed by residues 45 - 60 (chain A) in PDB entry 2XKE
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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43A SER 5.4 1.6 - - - +
44A MET* 1.3 77.7 - - - +
46A GLU* 1.3 65.3 + - - +
47A ALA* 3.5 9.3 + - - +
48A GLU* 2.9 38.5 + - - +
49A LYS* 2.9 23.8 + - - +
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Residues in contact with GLU 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 74.3 - - - +
47A ALA* 1.3 58.0 + - - +
49A LYS* 3.3 21.1 + - - +
50A GLN* 2.9 30.3 + - - +
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Residues in contact with ALA 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* 3.1 9.3 + - - +
46A GLU* 1.3 80.0 - - - +
48A GLU* 1.3 61.3 + - + +
50A GLN* 3.7 6.3 + - - +
51A MET* 3.3 22.0 + - - +
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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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43A SER 4.3 3.8 - - - +
44A MET* 3.1 34.2 - - + +
45A THR* 2.9 43.9 + - - +
47A ALA* 1.3 78.8 - - + +
49A LYS* 1.3 57.3 + - - +
51A MET* 3.7 5.4 + - - +
52A LEU* 3.1 19.1 + - - +
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Residues in contact with LYS 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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41A TYR* 3.9 34.4 + - + +
44A MET* 3.4 31.2 + - + -
45A THR 2.9 22.0 + - - +
46A GLU* 3.3 22.1 + - - +
48A GLU* 1.3 74.4 - - - +
50A GLN* 1.3 60.8 + - - +
52A LEU* 3.3 3.8 + - + +
53A VAL* 2.9 35.3 + - + +
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Residues in contact with GLN 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 GLU 2.9 17.0 + - - +
47A ALA* 3.9 7.4 - - - +
49A LYS* 1.3 76.7 - - - +
51A MET* 1.3 58.2 + - - +
53A VAL* 3.5 12.0 + - - +
54A SER* 3.1 30.5 + - - +
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Residues in contact with MET 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 ALA 3.3 14.4 + - - +
48A GLU* 4.0 7.0 - - - +
50A GLN* 1.3 77.3 - - - +
52A LEU* 1.3 61.0 + - - +
54A SER* 3.7 7.0 - - - -
55A GLU* 3.1 39.2 + - + +
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Residues in contact with LEU 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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39A LEU* 5.1 17.3 - - + -
41A TYR* 4.5 11.0 - - + -
44A MET* 3.7 24.9 - - + -
48A GLU 3.1 18.1 + - - +
49A LYS* 3.5 7.4 - - + +
50A GLN 3.2 0.4 - - - -
51A MET* 1.3 75.0 - - - +
53A VAL* 1.3 61.8 + - + +
55A GLU* 3.3 17.2 + - - +
56A VAL* 3.0 44.4 + - + +
82A LEU* 3.7 28.0 - - + -
84A ILE* 5.7 0.7 - - + -
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Residues in contact with VAL 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 LYS* 2.9 23.4 + - + +
50A GLN* 3.8 14.8 - - - +
52A LEU* 1.3 76.5 - - + +
54A SER* 1.3 62.7 + - - +
56A VAL* 3.9 6.2 - - - +
57A ASN* 3.1 39.1 + - - +
73A ARG* 5.5 4.5 - - - +
82A LEU* 6.6 0.4 - - + -
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Residues in contact with SER 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 GLN* 3.1 25.8 + - - +
51A MET* 3.7 9.0 - - - -
52A LEU 3.2 0.2 - - - -
53A VAL* 1.3 75.3 - - - +
55A GLU* 1.3 66.0 + - - +
56A VAL 3.3 0.2 + - - -
57A ASN* 3.3 6.3 + - - +
58A LEU* 3.2 37.4 + - - +
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Residues in contact with GLU 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 MET* 3.1 27.3 + - + +
52A LEU* 3.6 18.7 - - + +
54A SER* 1.3 76.5 + - - +
56A VAL* 1.3 63.7 + - + +
58A LEU* 3.4 11.0 + - + +
59A LEU* 3.2 28.6 + - + +
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Residues in contact with VAL 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 LEU* 3.0 34.3 + - + +
53A VAL* 3.9 6.7 - - - +
54A SER 3.2 0.2 - - - -
55A GLU* 1.3 74.8 - - + +
57A ASN* 1.3 66.2 + - - +
59A LEU* 3.3 21.9 + - + +
60A ARG* 3.2 19.2 + - + +
72A ASP 5.7 0.4 - - - +
73A ARG* 4.0 38.8 - - + +
82A LEU* 4.3 10.8 - - + -
84A ILE* 4.2 27.8 - - + -
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Residues in contact with ASN 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 VAL* 3.1 31.8 + - - +
54A SER* 3.9 5.8 - - - +
56A VAL* 1.3 75.8 - - - +
58A LEU* 1.3 66.5 + - + +
59A LEU 3.4 0.2 - - - -
60A ARG* 3.6 21.6 + - - +
61A GLU* 4.0 14.0 + - - +
73A ARG* 2.9 30.5 + - - +
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Residues in contact with LEU 58 (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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54A SER* 3.2 26.4 + - - +
55A GLU* 3.8 9.9 - - + +
56A VAL 3.2 0.4 - - - -
57A ASN* 1.3 79.4 - - + +
59A LEU* 1.3 66.0 + - - +
60A ARG 3.2 0.4 + - - -
61A GLU* 3.4 18.4 + - - +
62A LEU* 3.8 12.9 + - - +
130A ARG* 5.7 0.3 + - - -
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Residues in contact with LEU 59 (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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37A LYS* 6.2 1.6 - - - +
55A GLU* 3.2 20.4 + - + +
56A VAL* 3.4 24.0 - - + +
58A LEU* 1.3 77.4 - - - +
60A ARG* 1.3 61.7 + - + +
61A GLU 3.2 0.9 + - - -
62A LEU* 3.3 27.2 + - + +
70A TYR* 3.9 48.3 - - + +
84A ILE* 4.6 22.7 - - + -
159A ASP 4.6 5.6 - - - +
160A PHE* 4.3 20.6 - - + -
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Residues in contact with ARG 60 (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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56A VAL* 3.2 18.1 + - + +
57A ASN* 3.8 23.3 + - - +
58A LEU 3.2 0.8 - - - -
59A LEU* 1.3 77.7 - - + +
61A GLU* 1.3 61.4 + - + +
62A LEU 3.4 0.2 - - - -
63A LYS* 3.1 21.7 - - - -
69A ARG* 3.3 10.2 + - - +
70A TYR* 3.9 17.0 - - + +
71A TYR 3.2 25.6 + - - +
72A ASP* 3.3 28.9 + - - +
73A ARG* 3.2 40.6 - - - +
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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