Contacts of the helix formed by residues 51 - 60 (chain A) in PDB entry 4XK8
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A THR* 1.3 70.9 - - - +
52A THR* 1.3 68.1 + - - +
53A TRP 3.1 2.5 - - - -
54A ILE* 2.9 30.3 + - + +
55A TRP* 3.9 13.4 + - - -
720A THR* 3.6 26.5 - - + +
721A GLN 3.0 11.9 + - - +
722A PRO* 3.7 10.5 - - + -
723A ARG* 3.0 27.7 + - - +
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Residues in contact with THR 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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50A THR* 3.2 14.1 + - - -
51A THR* 1.3 78.8 + - - +
53A TRP* 1.3 64.6 + - - +
55A TRP* 3.0 27.7 + - + +
56A ASN* 3.0 30.2 + - - +
723A ARG* 3.6 20.7 - - - +
724A ALA 4.7 4.7 + - - -
726A SER* 5.6 12.8 - - - +
729A GLN* 6.1 0.2 - - - +
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Residues in contact with TRP 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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37A PRO* 3.6 38.4 - - + -
43A THR 5.0 1.1 - - - -
44A ILE* 2.6 53.7 + - + +
47A GLY* 3.2 30.9 + - - -
48A PRO* 3.6 26.9 - - + -
49A ASP 4.8 0.9 - - - +
50A THR* 3.5 17.6 + - - +
52A THR* 1.3 75.8 - - - +
54A ILE* 1.3 104.6 + - + +
56A ASN* 3.0 14.7 + - - +
57A LEU* 2.9 34.6 + - + +
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Residues in contact with ILE 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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48A PRO* 5.3 3.4 - - + -
50A THR 5.2 0.7 - - - +
51A THR* 3.2 23.3 - - - +
53A TRP* 1.3 105.6 - - + +
55A TRP* 1.3 80.0 + - + +
57A LEU* 3.0 11.7 + - + +
58A HIS* 2.8 37.3 + - + +
720A THR* 5.4 5.2 - - + -
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Residues in contact with TRP 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 THR* 3.9 22.7 + - - -
52A THR* 3.0 17.3 + - + +
54A ILE* 1.3 84.7 - - + +
56A ASN* 1.3 65.7 + - - +
58A HIS* 3.0 13.9 + + + +
59A ALA* 2.9 22.8 + - + +
723A ARG 5.4 2.4 + - - -
725A LEU* 3.5 22.7 - - + +
729A GLN* 3.2 43.7 - - - +
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Residues in contact with ASN 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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44A ILE* 3.9 17.6 - - + +
52A THR* 3.0 35.7 + - - +
53A TRP* 3.0 12.5 + - - +
55A TRP* 1.3 76.8 - - - +
57A LEU* 1.3 63.3 + - - +
59A ALA* 3.0 18.5 + - - +
60A ASP* 3.0 24.9 + - - +
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Residues in contact with LEU 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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37A PRO* 4.1 10.5 - - + -
38A GLY* 3.4 34.1 - - - +
40A PHE* 3.5 24.3 - - + -
44A ILE* 4.1 14.5 - - + +
53A TRP* 2.9 37.2 + - + +
54A ILE* 3.0 13.0 + - + +
56A ASN* 1.3 76.0 - - - +
58A HIS* 1.3 76.9 + - + +
61A ALA* 3.6 9.4 + - - +
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Residues in contact with HIS 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 ILE* 2.8 43.0 + - + +
55A TRP* 3.0 12.6 + + + +
57A LEU* 1.3 94.6 - - + +
59A ALA* 1.3 65.3 + - - +
60A ASP 3.4 0.8 + - - -
61A ALA* 3.6 15.4 + - - +
62A HIS 5.1 0.2 + - - -
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Residues in contact with ALA 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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55A TRP 2.9 15.4 + - - +
56A ASN* 3.0 9.4 + - - +
58A HIS* 1.3 80.8 - - - +
60A ASP* 1.3 68.4 + - - +
61A ALA 3.4 1.0 + - - -
62A HIS 4.9 1.7 + - - -
63A ASP* 4.9 4.0 + - - +
578A ARG* 4.2 21.5 + - - +
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Residues in contact with ASP 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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40A PHE* 3.6 13.3 - - + -
41A SER* 6.0 0.9 - - - -
44A ILE* 4.0 12.0 - - + +
56A ASN* 3.0 21.7 + - - +
59A ALA* 1.3 77.4 - - - +
61A ALA* 1.3 56.6 + - - +
62A HIS 3.3 3.1 - - - -
63A ASP* 3.3 17.2 + - + +
66A SER* 4.5 13.9 - - - +
67A HIS* 2.8 32.2 + - + +
578A ARG* 3.2 26.0 + - - -
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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