Contacts of the helix formed by residues 50 - 62 (chain B) in PDB entry 4XYN
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 GLU 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ILE* 3.7 5.0 - - - +
49B LYS* 1.3 85.9 - - + +
51B GLN* 1.3 66.8 + - - +
52B GLU* 3.8 18.0 - - + +
53B VAL* 3.0 37.2 + - + +
54B VAL* 3.4 6.6 + - - -
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Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 4.1 8.5 - - - +
34B LYS* 6.1 0.3 - - - +
49B LYS 4.0 2.0 + - - -
50B GLU* 1.3 72.5 + - - +
52B GLU* 1.3 72.6 + - - +
53B VAL 3.1 1.0 + - - -
54B VAL* 3.1 36.0 + - - +
55B ASP* 3.1 38.3 + - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLU* 3.2 17.1 - - + +
51B GLN* 1.3 88.0 + - - +
53B VAL* 1.3 61.8 + - + +
55B ASP* 3.7 13.2 + - - +
56B LYS* 3.5 29.9 + - - +
64D ASP* 3.3 40.2 - - + +
65D GLY* 5.4 1.9 - - - -
66D ASP* 5.4 4.4 + - - +
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLU 5.6 0.9 - - - +
48B ILE* 3.9 26.9 - - + -
49B LYS 5.4 1.1 - - - +
50B GLU* 3.0 28.4 + - + +
52B GLU* 1.3 78.2 - - + +
54B VAL* 1.3 65.4 + - - +
56B LYS* 3.2 18.4 + - + +
57B VAL* 3.3 18.7 + - + +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 3.6 45.5 - - + +
33B LEU* 5.2 3.4 - - + +
34B LYS* 4.2 22.0 - - + +
48B ILE* 3.5 29.6 - - + +
50B GLU 3.7 8.5 - - - +
51B GLN* 3.3 23.8 - - - +
53B VAL* 1.3 76.8 - - - +
55B ASP* 1.3 57.4 + - - +
57B VAL* 3.3 4.5 + - - +
58B MET* 2.9 27.8 + - + +
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Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 2.3 45.3 + - - +
51B GLN* 3.1 27.9 + - - +
52B GLU* 3.8 16.3 - - - +
54B VAL* 1.3 75.8 - - - +
56B LYS* 1.3 57.6 + - + +
58B MET* 3.3 0.7 + - - +
59B GLU* 2.7 54.2 + - - +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLU* 3.5 16.3 + - - +
53B VAL* 3.2 11.3 + - + +
55B ASP* 1.3 77.7 - - + +
57B VAL* 1.3 59.6 + - + +
59B GLU* 3.3 12.0 + - - +
60B THR* 2.7 34.9 + - - +
64D ASP* 5.0 20.4 + - - +
70D ASP* 5.5 0.8 + - - -
72D GLN* 3.3 27.6 + - - +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 4.0 11.9 - - + -
37B ILE* 4.2 12.3 - - + -
48B ILE* 4.5 18.2 - - + -
53B VAL* 3.3 19.4 + - + +
54B VAL* 3.8 5.4 - - - +
56B LYS* 1.3 78.1 - - + +
58B MET* 1.3 59.0 + - - +
60B THR* 2.9 10.1 + - - -
61B LEU* 2.8 48.4 + - + +
77B PHE* 4.5 9.6 - - + -
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Residues in contact with MET 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU 3.4 24.7 - - - +
29B LYS 3.7 2.5 - - - +
30B LYS* 3.5 43.5 - - + +
33B LEU* 3.9 20.6 - - + +
54B VAL 2.9 17.3 + - - +
55B ASP 4.0 2.2 - - - +
57B VAL* 1.3 76.7 - - - +
59B GLU* 1.3 56.4 + - + +
61B LEU* 4.2 1.6 - - - +
62B ASP* 2.6 43.6 + - + +
67B GLY* 3.5 22.2 - - - +
68B GLU 3.6 22.4 - - - +
69B CYS* 3.6 12.3 - - + +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 5.0 8.5 + - - +
55B ASP* 2.7 41.1 + - + +
56B LYS* 3.6 10.8 - - - +
58B MET* 1.3 74.0 - - + +
60B THR* 1.3 62.5 + - - +
62B ASP* 3.6 14.0 - - - +
63B ASN* 5.3 0.2 - - - +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 2.7 22.0 + - - +
57B VAL* 3.2 11.6 - - - -
59B GLU* 1.3 76.1 - - - +
61B LEU* 1.3 74.8 + - + +
63B ASN* 3.9 9.7 - - - +
80B MET* 4.5 19.0 - - + +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 4.1 15.3 - - + -
57B VAL* 2.8 33.6 + - + +
58B MET* 4.1 3.8 - - - +
60B THR* 1.3 77.6 - - + +
62B ASP* 1.3 66.2 + - - +
63B ASN* 3.1 11.4 + - - +
69B CYS* 4.4 24.0 - - + -
73B GLU* 3.2 25.3 - - - +
76B ALA* 5.6 0.7 - - + -
77B PHE* 3.5 47.6 - - + +
80B MET* 3.6 31.6 - - + -
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B MET* 2.6 31.6 + - + +
59B GLU* 3.6 14.3 - - - +
61B LEU* 1.3 71.2 - - - +
63B ASN* 1.3 62.2 + - - +
64B ASP* 3.0 11.3 + - - +
65B GLY* 3.4 11.9 + - - -
66B ASP* 3.0 5.5 + - - +
67B GLY* 2.6 32.5 + - - -
68B GLU 3.5 11.4 - - - +
73B GLU* 3.7 2.7 - - - -
501B CA 2.4 26.8 - - - -
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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