Contacts of the helix formed by residues 57 - 63 (chain E) in PDB entry 1KXT
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 PRO 57 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E GLU* 4.8 0.2 - - - +
51E VAL* 3.6 15.7 - - + -
54E PRO* 3.3 23.8 - - + +
55E SER 3.6 0.2 - - - -
56E ARG* 1.3 94.5 - - - +
58E TRP* 1.3 64.6 + - - +
59E TRP* 3.6 52.9 - - + +
60E GLU* 3.3 20.4 - - - +
72E ARG* 4.4 3.6 + - - -
357E TRP* 3.3 20.0 - - + +
359E GLY* 4.2 1.8 - - - +
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Residues in contact with TRP 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E PHE* 4.2 14.0 - + + -
18E GLU* 3.4 25.2 - - - +
57E PRO* 1.3 73.5 - - - +
59E TRP* 1.3 104.5 + + + +
60E GLU 3.2 1.2 + - - -
61E ARG* 3.4 14.6 + - - +
62E TYR* 4.3 12.9 - + - -
299E HIS* 3.9 29.4 - + - -
300E ASP* 4.0 22.9 - - - -
303E ARG* 3.3 26.8 - - + +
342E TYR* 3.4 20.0 - - - +
356E ASP* 2.7 27.2 + - - -
357E TRP* 3.0 32.7 + - - +
358E ILE 3.5 7.0 - - - -
359E GLY* 3.8 4.4 - - - -
360E PRO* 4.9 0.2 - - - -
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Residues in contact with TRP 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E VAL* 4.0 15.0 - - + -
53E ASN 4.4 2.5 - - - -
54E PRO* 3.8 24.0 - - + -
57E PRO* 3.6 29.8 - - + +
58E TRP* 1.3 122.4 - + + +
60E GLU* 1.3 65.8 + - - +
61E ARG 2.9 2.9 - - - -
62E TYR* 2.9 25.5 + - + +
63E GLN* 4.0 24.4 + - - +
357E TRP* 3.6 20.3 - - + +
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ASN* 3.2 27.9 + - - +
49E ILE 3.6 12.0 - - - +
51E VAL* 2.9 56.0 + - + +
56E ARG* 2.7 44.2 + - - -
57E PRO* 3.3 19.3 + - + +
58E TRP 3.2 0.2 - - - -
59E TRP* 1.3 83.1 - - - +
61E ARG* 1.3 64.3 + - + +
62E TYR 3.0 5.4 + - - -
63E GLN* 3.1 19.7 + - - +
72E ARG* 3.8 10.6 - - - +
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Residues in contact with ARG 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E GLU* 2.7 49.1 + - - +
21E TRP* 4.1 2.8 - - - -
43E SER* 3.6 21.5 - - - -
44E PRO* 2.7 60.4 + - + +
46E ASN* 5.1 1.2 + - - +
48E ASN* 3.8 26.0 + - - +
58E TRP 3.6 13.0 - - - +
59E TRP 2.9 1.2 - - - -
60E GLU* 1.3 85.4 - - + +
62E TYR* 1.3 62.3 + - + +
63E GLN 3.3 2.9 + - - -
64E PRO* 5.1 1.9 - - - +
71E THR* 3.2 21.0 + - - -
72E ARG* 5.1 11.6 - - - +
73E SER* 2.8 35.4 + - - +
98E VAL* 4.4 1.7 - - - +
367E ILE* 5.8 0.8 - - - +
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Residues in contact with TYR 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E HIS* 5.1 4.0 + - - -
17E PHE* 5.2 6.0 - + - -
43E SER* 5.1 2.6 + - - -
44E PRO* 3.8 17.5 - - + +
58E TRP* 4.3 14.4 - + - -
59E TRP* 2.9 25.2 + - + +
61E ARG* 1.3 83.6 - - + +
63E GLN* 1.3 62.7 + - + +
64E PRO* 3.3 6.2 - - - +
96E ASP* 2.5 31.7 + - - -
98E VAL* 3.7 14.6 - - + -
101E HIS* 2.9 35.7 - - + -
165E LEU* 4.8 2.3 - - + +
195E ARG* 3.8 2.5 - - - -
197E ASP* 3.5 27.8 - - - +
299E HIS* 3.7 32.5 + + - -
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Residues in contact with GLN 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ASN* 3.2 4.1 - - - +
49E ILE* 2.8 52.3 + - + +
51E VAL* 4.5 6.3 - - - +
59E TRP* 4.0 33.1 + - - +
60E GLU 3.1 7.6 + - - +
61E ARG 3.3 0.6 - - - -
62E TYR* 1.3 83.9 - - + +
64E PRO* 1.3 63.7 - - - +
102E MET 4.4 0.2 - - - -
103E CYS* 3.6 13.1 - - - +
104E GLY* 2.9 25.7 + - - +
107E ALA* 5.1 3.1 - - - +
165E LEU* 4.2 16.4 - - + +
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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