Contacts of the helix formed by residues 105 - 114 (chain D) in PDB entry 1KTD
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 VAL 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C PHE* 5.3 1.1 - - + -
6D ALA* 3.6 11.9 - - + +
7D TYR 3.8 19.7 - - - +
8D LEU* 3.9 23.8 - - + -
42D CYS* 4.6 6.1 - - - -
101D GLU* 2.9 36.2 + - + +
103D ASP 2.8 2.8 + - - -
104D THR* 1.3 88.0 - - - +
106D CYS* 1.3 61.3 - - - +
107D ARG 3.5 0.4 - - - -
108D HIS* 3.8 1.1 - - - -
109D ASN* 2.6 57.4 + - - +
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Residues in contact with CYS 106 (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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7C ILE* 5.5 0.2 - - - -
42D CYS* 2.0 55.6 - - + -
44D PHE* 3.2 13.3 - - + -
51D VAL* 3.8 17.5 - - + -
53D LEU* 4.0 25.1 - - - -
101D GLU 3.1 8.0 + - - -
102D VAL* 2.9 18.8 - - - +
105D VAL* 1.3 80.4 - - - +
107D ARG* 1.3 55.2 + - - +
109D ASN* 3.7 2.1 - - - +
110D TYR 2.8 25.5 + - - -
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Residues in contact with ARG 107 (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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44D PHE* 4.3 0.9 - - - -
48D THR* 2.7 53.5 + - + +
49D GLN 2.9 19.2 + - - -
50D ARG* 4.5 0.2 - - - +
51D VAL* 3.7 21.0 + - + +
102D VAL* 3.1 24.1 + - - +
103D ASP* 2.8 45.2 + - + +
106D CYS* 1.3 78.3 - - - +
108D HIS* 1.3 66.6 + - - +
110D TYR* 3.2 10.3 + - - +
111D GLU* 3.1 26.4 + - - +
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Residues in contact with HIS 108 (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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3D ASP* 4.6 15.9 - - + -
4D LEU* 2.9 23.9 + - - +
6D ALA* 3.8 15.3 + - + +
103D ASP 3.0 18.2 + - - +
104D THR* 3.5 12.3 - - - +
105D VAL 3.4 6.7 - - - +
106D CYS 3.2 0.2 - - - -
107D ARG* 1.3 79.8 - - - +
109D ASN* 1.3 78.8 + - - +
111D GLU* 3.3 23.6 + - - +
112D ILE* 3.6 10.7 + - + +
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Residues in contact with ASN 109 (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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7C ILE* 4.3 5.7 - - + +
24C PHE* 3.9 9.6 - - + -
5D ILE* 3.1 18.5 - - - +
6D ALA 2.7 49.0 + - - -
42D CYS* 5.9 0.6 - - - -
105D VAL* 2.6 36.1 + - - +
106D CYS* 4.0 2.4 - - - +
108D HIS* 1.3 77.0 - - - +
110D TYR* 1.3 65.0 + - - +
112D ILE* 3.1 8.9 + - - +
113D PHE* 3.0 43.6 + - + -
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Residues in contact with TYR 110 (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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3C GLU* 3.6 16.5 - - - +
5C HIS* 3.5 31.0 - + + -
7C ILE* 4.2 8.2 - - + +
26C PHE* 5.1 4.5 - + - -
44D PHE* 3.3 49.6 - + + -
47D GLY* 3.8 19.4 - - - -
48D THR* 3.3 21.5 - - + -
106D CYS 2.8 13.0 + - - +
107D ARG 3.2 5.6 + - - +
109D ASN* 1.3 71.8 - - - +
111D GLU* 1.3 55.0 + - + +
113D PHE* 3.0 4.9 + - + +
114D ASP* 2.7 51.6 + - + +
118D VAL* 3.8 23.9 - - + +
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Residues in contact with GLU 111 (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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3D ASP* 5.4 3.8 - - - +
48D THR* 4.6 11.9 - - + +
107D ARG* 3.1 27.6 + - - +
108D HIS* 3.4 12.7 + - - +
109D ASN 3.2 0.4 - - - -
110D TYR* 1.3 83.1 - - + +
112D ILE* 1.3 61.1 + - + +
114D ASP* 3.7 11.3 + - - +
115D ASN* 3.2 20.6 + - - +
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Residues in contact with ILE 112 (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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51C PHE 3.7 8.9 - - - +
52C ALA* 3.6 28.3 - - + -
1D ALA 5.6 1.1 - - - +
3D ASP* 3.2 44.6 - - + +
4D LEU 3.4 25.4 - - - +
5D ILE* 4.0 11.4 - - + +
108D HIS* 3.6 16.3 + - + +
109D ASN* 3.1 13.1 + - - +
111D GLU* 1.3 79.4 - - + +
113D PHE* 1.3 68.8 + - + +
114D ASP 3.5 0.2 + - - -
115D ASN* 3.5 12.7 + - - +
116D PHE* 3.1 23.3 - - + -
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Residues in contact with PHE 113 (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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7C ILE* 3.3 38.1 - - + -
24C PHE* 4.1 8.3 - + - -
26C PHE* 4.4 10.1 - + + -
31C ILE* 3.4 33.2 - - + -
5D ILE* 3.8 33.2 - - + -
109D ASN* 3.0 28.9 + - + -
110D TYR* 3.0 7.9 + - + +
112D ILE* 1.3 77.0 - - + +
114D ASP* 1.3 55.6 + - - +
115D ASN 3.0 7.4 + - - -
116D PHE* 3.9 15.9 - + - -
117D LEU* 2.9 54.8 + - + -
118D VAL* 3.2 7.3 + - + -
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Residues in contact with ASP 114 (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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3C GLU* 5.0 1.6 - - - +
110D TYR* 2.7 35.6 + - + +
111D GLU* 4.1 9.0 - - - +
112D ILE 3.3 1.2 - - - -
113D PHE* 1.3 72.2 - - - +
115D ASN* 1.3 64.0 + - - +
116D PHE 3.4 0.7 - - - -
118D VAL* 3.4 33.4 - - + +
119D PRO* 3.3 16.1 - - - +
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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