Contacts of the helix formed by residues 55 - 67 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D LYS 4.3 1.8 + - - +
52D GLU 3.1 15.3 + - - +
53D ASN 4.1 2.0 - - - -
54D LYS* 1.3 80.9 - - + +
56D GLU* 1.3 63.2 + - - +
57D LYS* 3.0 26.2 + - - +
58D VAL* 2.9 37.7 + - + +
59D ILE* 3.4 4.0 + - - +
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LYS* 2.6 42.5 + - + +
53D ASN 4.4 2.7 + - - -
54D LYS 4.1 1.6 + - - -
55D ASN* 1.3 72.5 + - - +
57D LYS* 1.3 59.7 + - + +
59D ILE* 3.4 9.8 + - + +
60D GLU* 3.0 33.2 + - - +
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Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ASN* 3.0 17.3 + - - +
56D GLU* 1.3 78.7 - - + +
58D VAL* 1.3 58.8 + - - +
60D GLU* 3.5 20.2 + - - +
61D HIS* 3.0 47.5 + - + +
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Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLU* 3.9 36.6 - - + +
55D ASN* 2.9 35.6 + - + +
57D LYS* 1.3 75.2 - - - +
59D ILE* 1.3 66.4 + - - +
61D HIS* 3.0 14.5 + - + +
62D ILE* 2.9 30.1 + - + +
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Residues in contact with ILE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 3.6 23.0 - - + -
38D LYS* 3.9 31.0 - - + -
41D VAL* 3.8 26.0 - - + -
49D LEU* 5.0 1.1 - - + -
52D GLU* 3.4 40.4 - - + +
53D ASN* 3.9 13.5 - - - +
55D ASN 3.4 6.0 + - - +
56D GLU* 3.6 9.6 - - + +
58D VAL* 1.3 74.9 - - - +
60D GLU* 1.3 62.3 + - - +
62D ILE* 3.3 14.4 + - + +
63D MET* 3.1 18.5 + - - +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLN* 3.8 22.3 + - - +
38D LYS* 2.5 38.7 + - - +
56D GLU* 3.0 27.7 + - - +
57D LYS* 3.5 23.8 - - - +
58D VAL 3.2 0.2 - - - -
59D ILE* 1.3 77.1 - - - +
61D HIS* 1.3 58.1 + - + +
63D MET* 3.4 6.5 + - - +
64D GLU* 3.0 42.6 + - - +
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Residues in contact with HIS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LYS* 3.0 36.5 + - + +
58D VAL* 3.0 13.9 + - + +
60D GLU* 1.3 74.2 - - + +
62D ILE* 1.3 62.2 + - + +
64D GLU* 3.2 22.6 + - - +
65D ASP* 2.9 42.8 + - - +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 3.9 13.5 - - + -
49D LEU* 4.9 11.9 - - + -
52D GLU* 4.2 15.5 - - + -
58D VAL* 2.9 34.7 + - + +
59D ILE* 3.6 19.3 - - + +
60D GLU 3.3 0.2 - - - -
61D HIS* 1.3 78.6 - - + +
63D MET* 1.3 64.1 + - - +
65D ASP* 3.4 7.1 + - - +
66D LEU* 3.0 42.0 + - + +
82D LEU* 4.3 14.6 - - + -
85D ARG* 6.3 0.4 - - - +
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Residues in contact with MET 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU 3.5 25.1 - - - +
34D GLN* 3.6 36.8 - - + +
37D PHE* 3.6 33.0 - - + -
59D ILE 3.1 9.1 + - - +
60D GLU* 3.8 8.3 - - - +
61D HIS 3.3 0.2 - - - -
62D ILE* 1.3 79.3 - - - +
64D GLU* 1.3 56.6 + - + +
66D LEU* 3.1 6.8 + - - +
67D ASP* 2.9 29.5 + - + +
72D LYS* 3.6 14.6 - - - +
73D GLN* 3.5 19.7 - - - -
74D LEU* 3.7 18.6 - - + -
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN* 2.9 22.7 + - - -
27A HIS* 5.8 0.2 - - - -
34D GLN* 5.1 6.6 + - - +
60D GLU* 3.0 37.3 + - - +
61D HIS* 3.2 25.4 + - - +
63D MET* 1.3 75.5 - - + +
65D ASP* 1.3 63.1 + - - +
67D ASP* 3.2 12.7 + - - +
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Residues in contact with ASP 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN* 3.4 15.8 + - - +
27A HIS* 3.0 50.5 + - + +
61D HIS* 2.9 29.3 + - - +
62D ILE* 3.7 8.5 - - - +
64D GLU* 1.3 79.2 - - - +
66D LEU* 1.3 62.3 + - + +
68D THR* 4.2 7.6 - - - +
85D ARG* 5.4 9.4 + - - +
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.3 7.0 - - + -
62D ILE* 3.0 36.6 + - + +
63D MET 3.1 4.0 + - - +
65D ASP* 1.3 75.7 - - - +
67D ASP* 1.3 58.6 + - - +
68D THR* 2.9 15.4 + - - +
74D LEU* 3.8 26.7 - - + -
78D GLU* 3.4 38.4 - - - +
79D PHE* 5.2 1.3 - - - -
81D MET* 4.3 6.1 - - + -
82D LEU* 3.7 37.5 - - + +
85D ARG* 3.6 28.0 - - - +
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Residues in contact with ASP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 2.9 13.7 + - - -
63D MET* 2.9 19.3 + - + +
64D GLU* 3.2 7.7 + - - +
65D ASP 3.2 2.0 - - - -
66D LEU* 1.3 72.3 - - - +
68D THR* 1.3 63.0 + - - +
69D ASN* 3.1 6.2 - - - +
70D ALA* 3.0 16.3 + - - -
71D ASP* 3.2 4.6 + - - +
72D LYS* 2.7 30.2 + - - +
73D GLN 3.6 7.6 - - - -
74D LEU* 3.7 13.2 - - + -
78D GLU* 3.9 2.0 - - - -
4501D CA 2.4 29.8 - - - -
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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