Contacts of the helix formed by residues 94 - 101 (chain A) in PDB entry 1DXK
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 GLY 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A SER* 3.3 10.5 + - - -
58A SER 3.4 4.0 + - - -
60A ASP 4.0 2.2 - - - -
61A ASP* 3.4 11.0 - - - -
64A THR* 3.3 23.0 - - - +
92A ILE 3.1 1.2 + - - -
93A GLY* 1.3 75.7 - - - +
95A ILE* 1.3 63.7 + - - +
96A LYS 3.2 3.4 - - - -
97A THR* 3.1 14.4 + - - -
98A LEU* 3.1 19.0 + - - +
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A SER* 4.4 0.4 + - - -
84A ILE* 5.1 2.9 - - + -
92A ILE* 3.0 31.1 + - + +
93A GLY 3.3 1.5 - - - +
94A GLY* 1.3 77.2 - - - +
96A LYS* 1.3 61.5 + - + +
98A LEU* 3.4 10.7 + - + -
99A LYS* 2.9 46.4 + - + +
105A ALA* 3.4 32.3 - - + -
120A TYR* 4.0 13.5 - - + -
121A GLU* 3.3 42.2 - - + +
123A PRO* 4.1 17.3 - - + -
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP* 3.5 24.0 - - - +
65A LYS* 6.1 2.2 - - - +
93A GLY 4.8 0.4 + - - -
94A GLY* 3.2 0.8 - - - -
95A ILE* 1.3 84.0 - - + +
97A THR* 1.3 62.0 + - - +
99A LYS* 3.9 1.4 - - - +
100A GLU* 3.1 43.0 + - - +
121A GLU* 3.7 29.8 + - + +
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Residues in contact with THR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP* 2.7 29.6 + - - +
64A THR* 4.1 7.6 - - + -
65A LYS* 3.0 41.6 + - + +
68A ILE* 4.1 17.0 - - + -
94A GLY 3.1 8.7 + - - -
96A LYS* 1.3 72.9 - - - +
98A LEU* 1.3 65.6 + - - +
100A GLU* 3.4 10.1 - - - +
101A ARG* 3.2 42.9 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 5.4 1.6 - - + -
57A SER* 4.4 10.8 - - - -
64A THR* 3.9 21.8 - - + -
68A ILE* 4.0 13.5 - - + -
82A VAL* 3.8 46.2 - - + -
84A ILE* 4.4 4.3 - - + -
94A GLY 3.1 12.9 + - - +
95A ILE* 3.7 15.5 - - + +
97A THR* 1.3 77.9 - - - +
99A LYS* 1.3 61.6 + - - +
101A ARG 3.4 0.2 + - - -
102A GLY 3.3 3.3 + - - -
103A ILE* 2.9 50.4 + - + +
105A ALA* 4.2 16.4 - - + -
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 2.9 37.6 + - + +
96A LYS 3.9 0.7 - - - +
98A LEU* 1.3 76.0 - - - +
100A GLU* 1.3 61.0 + - - +
102A GLY* 3.3 13.0 + - - -
103A ILE 4.6 4.9 - - - +
105A ALA* 4.7 9.0 - - + +
121A GLU* 3.5 26.0 + - - +
122A GLU* 3.1 35.7 + - - +
123A PRO* 5.3 0.4 - - + -
124A LEU* 6.4 1.6 - - - -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.7 25.5 + - - -
96A LYS* 3.1 45.3 + - - +
97A THR* 3.4 13.9 - - - +
99A LYS* 1.3 76.0 - - - +
101A ARG* 1.3 65.6 + - + +
102A GLY 3.3 0.8 + - - -
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.4 32.2 + - - +
68A ILE* 3.8 26.1 - - - +
69A GLU* 3.0 34.1 + - - +
72A GLU* 5.1 2.0 + - - -
78A ARG* 6.1 1.0 - - - +
97A THR* 3.2 31.6 + - - +
99A LYS 3.3 0.2 - - - -
100A GLU* 1.3 87.1 + - + +
102A GLY* 1.3 62.9 + - - +
103A ILE* 4.0 23.3 - - + +
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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