Contacts of the helix formed by residues 55 - 67 (chain L) in PDB entry 1XK4
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 ASN 55 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51L LYS 5.3 1.3 - - - +
52L GLU 3.0 15.7 + - - +
53L ASN 3.1 2.2 - - - -
54L LYS* 1.3 80.7 - - + +
56L GLU* 1.3 64.4 + - - +
57L LYS* 3.1 24.7 + - - +
58L VAL* 3.0 39.9 + - + +
59L ILE* 3.3 3.9 + - - +
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Residues in contact with GLU 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L LYS* 2.7 40.7 + - + +
53L ASN 4.7 2.5 + - - -
54L LYS 4.1 1.0 + - - -
55L ASN* 1.3 73.8 + - - +
57L LYS* 1.3 58.4 + - + +
59L ILE* 3.2 9.7 + - - +
60L GLU* 3.0 33.2 + - - +
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Residues in contact with LYS 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L ASN* 3.1 16.7 + - - +
56L GLU* 1.3 76.7 - - + +
58L VAL* 1.3 66.0 + - - +
60L GLU* 3.5 19.0 + - - +
61L HIS* 3.1 22.7 + - - +
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Residues in contact with VAL 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L GLU* 3.8 37.9 - - + +
55L ASN* 3.0 39.4 + - + +
57L LYS* 1.3 76.7 - - - +
59L ILE* 1.3 62.7 + - - +
61L HIS* 3.2 7.3 + - - +
62L ILE* 3.0 28.7 + - + +
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Residues in contact with ILE 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L PHE* 3.7 22.4 - - + -
38L LYS* 4.1 28.9 - - + +
41L VAL* 3.8 27.1 - - + -
49L LEU* 4.9 0.7 - - + -
52L GLU* 3.6 42.8 - - + +
53L ASN* 3.8 11.9 - - - +
55L ASN 3.3 5.8 + - - +
56L GLU* 3.2 11.1 + - - +
58L VAL* 1.3 75.3 - - - +
60L GLU* 1.3 64.8 + - - +
62L ILE* 3.2 14.3 + - + +
63L MET 3.0 18.2 + - - -
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Residues in contact with GLU 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L GLN* 3.7 22.8 + - - +
37L PHE* 5.9 0.2 - - - -
38L LYS* 2.6 40.1 + - - +
56L GLU* 3.0 21.1 + - - +
57L LYS* 3.7 20.7 - - - +
59L ILE* 1.3 78.4 - - - +
61L HIS* 1.3 57.9 + - - +
63L MET* 3.3 7.4 + - - +
64L GLU* 2.9 44.4 + - - +
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Residues in contact with HIS 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I HIS* 4.5 8.5 + - - -
57L LYS 3.1 18.2 + - - +
58L VAL* 3.2 7.6 + - - +
60L GLU* 1.3 72.7 - - - +
62L ILE* 1.3 67.8 + - + +
64L GLU* 3.6 20.6 + - + +
65L ASP* 2.9 66.0 + - - +
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Residues in contact with ILE 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L PHE* 3.9 19.1 - - + -
49L LEU* 4.8 12.8 - - + -
52L GLU* 4.2 15.0 - - + -
58L VAL* 3.0 32.3 + - + +
59L ILE* 3.2 19.9 + - + +
61L HIS* 1.3 78.9 - - + +
63L MET* 1.3 64.3 + - - +
65L ASP* 3.3 8.4 + - - +
66L LEU* 3.1 32.8 + - + +
82L LEU* 4.5 13.9 - - + -
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Residues in contact with MET 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L LEU 3.4 25.8 - - - +
33L ASN 3.8 6.5 - - - +
34L GLN* 3.6 31.2 - - + +
37L PHE* 3.6 31.1 - - + -
59L ILE 3.0 8.5 + - - +
60L GLU* 3.6 10.5 - - - +
61L HIS 3.3 0.2 - - - -
62L ILE* 1.3 77.6 - - - +
64L GLU* 1.3 57.8 + - + +
66L LEU* 3.1 5.6 + - - +
67L ASP* 2.9 30.1 + - + +
72L LYS* 3.7 22.9 - - - +
73L GLN 3.9 2.9 - - - -
74L LEU* 3.7 28.4 - - + +
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Residues in contact with GLU 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I ASN* 2.8 22.5 + - - -
34L GLN* 5.2 5.4 + - - +
60L GLU* 2.9 39.9 + - - +
61L HIS* 3.6 22.4 + - + +
63L MET* 1.3 76.1 - - + +
65L ASP* 1.3 63.5 + - - +
67L ASP* 3.2 13.9 + - - +
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Residues in contact with ASP 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I ASN* 3.3 16.3 + - - +
27I HIS* 3.2 48.4 + - + +
61L HIS* 2.9 50.0 + - - +
62L ILE* 3.8 6.9 - - - +
63L MET 3.2 0.4 - - - -
64L GLU* 1.3 80.2 - - - +
66L LEU* 1.3 60.3 + - - +
68L THR* 4.2 6.8 - - - +
85L ARG* 5.3 10.8 + - - +
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Residues in contact with LEU 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L PHE* 4.1 6.3 - - + -
62L ILE* 3.1 33.4 + - + +
63L MET 3.1 2.2 + - - +
65L ASP* 1.3 74.9 - - + +
67L ASP* 1.3 60.0 + - - +
68L THR* 2.8 15.8 + - - +
74L LEU* 3.7 33.0 - - + -
78L GLU* 3.3 36.7 - - - +
79L PHE* 5.1 0.4 - - - -
81L MET* 4.3 4.3 - - + -
82L LEU* 3.7 37.0 - - + +
85L ARG* 3.6 29.2 - - - +
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Residues in contact with ASP 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I ASN* 3.0 14.4 + - - -
63L MET* 2.9 19.0 + - + +
64L GLU* 3.6 9.9 - - - +
65L ASP 3.2 2.2 - - - -
66L LEU* 1.3 74.3 - - - +
68L THR* 1.3 56.7 + - - +
69L ASN* 3.0 8.7 - - - +
70L ALA* 3.0 21.3 + - - -
71L ASP* 3.1 7.8 + - - +
72L LYS* 2.7 31.3 + - - +
73L GLN 3.1 8.0 - - - +
74L LEU* 3.8 9.9 - - + -
78L GLU* 3.9 1.6 - - - -
4521L CA 2.4 30.7 - - - -
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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