Contacts of the helix formed by residues 103 - 113 (chain X) in PDB entry 1DT7
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 SER 103 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99X GLY 4.2 6.3 - - - -
100X GLN* 3.0 15.2 + - - +
101X SER* 2.5 7.6 + - - -
102X THR* 1.3 74.7 - - - +
104X ARG* 1.3 51.8 + - - -
105X HIS* 2.9 11.6 - - - -
106X LYS* 2.6 43.7 + - - +
107X LYS* 3.5 2.1 + - - +
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Residues in contact with ARG 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 5.9 3.2 - - - +
45A GLU* 3.0 50.0 + - - +
46A GLU 2.5 34.5 + - - -
47A ILE* 3.2 31.0 - - - +
48A LYS* 4.5 10.3 - - - +
52A VAL* 4.0 18.7 - - - +
101X SER* 2.7 20.3 + - - +
102X THR* 2.7 13.8 + - - +
103X SER* 1.3 74.6 - - - +
105X HIS* 1.3 75.4 + - - +
107X LYS* 2.9 32.3 + - - +
108X LEU* 3.6 13.3 + - - +
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Residues in contact with HIS 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.9 28.0 - - + -
55A LYS* 3.6 39.0 - - + +
102X THR* 2.4 43.2 + - + +
103X SER* 2.7 17.6 + - - -
104X ARG* 1.3 85.0 - - - +
106X LYS* 1.3 87.2 + - + +
108X LEU* 3.0 18.1 + - - +
109X MET* 3.1 17.6 + - + +
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Residues in contact with LYS 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X SER* 2.6 27.7 + - - +
105X HIS* 1.3 96.1 - - + +
107X LYS* 1.3 61.6 + - - +
109X MET* 2.9 25.2 + - + +
110X PHE* 3.5 4.5 + - - +
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Residues in contact with LYS 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 2.9 29.9 + - - -
87A PHE* 6.6 0.2 - - + -
103X SER 3.5 2.0 + - - +
104X ARG* 2.9 21.4 + - - +
106X LYS* 1.3 80.3 - - - +
108X LEU* 1.3 59.0 + - - +
110X PHE* 2.7 31.6 - - + +
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Residues in contact with LEU 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 5.6 8.1 - - + -
56A VAL* 5.0 11.9 - - + -
76A PHE* 3.8 32.5 - - + -
79A MET* 5.6 4.0 - - + -
80A VAL* 4.6 22.9 - - + -
83A ALA* 5.7 2.0 - - + -
104X ARG* 3.6 12.0 + - - +
105X HIS* 3.0 12.1 + - - +
107X LYS* 1.3 76.3 - - - +
109X MET* 1.3 72.4 + - + +
110X PHE* 3.0 16.4 - - + -
111X LYS* 2.9 29.4 + - + +
112X THR* 3.9 2.2 + - + +
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Residues in contact with MET 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS* 2.7 42.6 - - + +
56A VAL* 4.7 18.4 - - + -
59A THR* 5.1 7.9 - - - +
105X HIS* 3.1 22.3 + - + +
106X LYS* 2.9 25.4 + - + +
108X LEU* 1.3 80.3 - - + +
110X PHE* 1.3 63.0 + - - +
111X LYS 2.8 6.1 - - - -
112X THR* 2.4 49.7 + - + +
113X GLU* 3.1 3.6 + - - -
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Residues in contact with PHE 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA* 3.8 13.5 - - + -
86A GLU* 5.7 6.1 - - + -
87A PHE* 6.1 2.7 - + - -
106X LYS 3.5 4.3 + - - +
107X LYS* 2.7 29.9 + - + +
108X LEU* 3.0 16.7 + - + -
109X MET* 1.3 77.7 - - - +
111X LYS* 1.3 111.8 + - + +
113X GLU* 2.9 27.2 - - - +
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Residues in contact with LYS 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A MET* 3.2 55.7 - - + +
80A VAL 4.7 0.2 - - - +
82A THR* 3.7 13.9 + - + +
83A ALA* 3.1 30.4 - - - +
86A GLU* 4.5 4.6 + - - -
71B GLN* 6.4 0.2 - - + -
108X LEU* 3.1 20.0 - - + +
109X MET 2.8 0.8 + - - -
110X PHE* 1.3 122.4 - - + +
112X THR* 1.3 65.0 + - - +
113X GLU* 3.2 15.8 + - + +
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Residues in contact with THR 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 4.5 20.2 - - + +
79A MET* 4.4 17.5 - - + -
108X LEU* 4.5 1.3 - - + +
109X MET* 2.4 64.1 + - + +
111X LYS* 1.3 73.9 - - - +
113X GLU* 1.3 60.2 + - - -
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Residues in contact with GLU 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLN* 3.6 28.2 - - - +
109X MET 3.1 4.8 + - - -
110X PHE* 2.9 21.5 - - - +
111X LYS* 3.4 12.1 - - + +
112X THR* 1.3 88.4 + - - +
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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