Contacts of the helix formed by residues 100 - 109 (chain A) in PDB entry 1U2X
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 LYS 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ASN* 3.1 20.3 + - - +
99A GLU* 1.3 87.1 + - + +
101A MSE 1.3 60.1 + - - +
102A ASN 3.2 1.4 + - - -
103A GLU* 3.5 32.8 + - - +
104A TRP* 4.0 5.0 + - - +
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Residues in contact with MSE 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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72A ILE* 3.7 14.1 - - + +
73A ASN* 2.8 42.6 - - - +
74A GLU* 3.1 15.3 - - - +
75A PRO* 3.8 26.9 - - - -
96A LEU* 3.6 11.2 - - + -
98A ASN* 3.1 23.0 + - - +
100A LYS* 1.3 76.1 - - - +
102A ASN* 1.3 64.1 + - - +
103A GLU 3.2 0.2 - - - -
104A TRP* 3.0 15.6 + - + -
105A PHE* 2.9 48.3 + - + -
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Residues in contact with ASN 102 (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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96A LEU* 4.3 5.8 - - - +
99A GLU* 3.0 18.5 + - - +
101A MSE 1.3 78.7 - - - +
103A GLU* 1.3 60.3 + - + +
105A PHE 3.4 0.3 + - - -
106A ASP* 3.0 35.7 + - - +
179A LEU* 2.9 51.1 + - + +
181A ILE* 4.2 7.7 - - - +
183A ARG* 2.9 33.2 + - - +
214A PHE* 3.6 18.1 - - - -
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Residues in contact with GLU 103 (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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99A GLU 5.7 0.6 - - - +
100A LYS* 3.5 24.7 + - - +
101A MSE 3.2 0.4 - - - -
102A ASN* 1.3 76.0 - - + +
104A TRP* 1.3 60.2 + - - +
106A ASP* 4.0 6.0 - - - +
107A LYS* 2.8 37.6 + - + +
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Residues in contact with TRP 104 (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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52A LEU* 3.8 22.0 - - + -
56A PHE* 4.3 9.6 - + - -
75A PRO* 3.8 38.3 - - + +
78A PHE* 3.5 35.0 - + + -
100A LYS 4.0 2.1 + - - +
101A MSE 3.0 28.0 + - - +
103A GLU* 1.3 77.2 - - - +
105A PHE* 1.3 96.8 + + - +
107A LYS* 3.1 23.3 + - - +
108A THR* 2.8 48.7 + - + -
109A PHE* 4.3 3.1 - + - -
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Residues in contact with PHE 105 (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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72A ILE* 4.8 2.2 - - + -
78A PHE* 3.9 39.0 - + + -
96A LEU* 4.2 13.9 - - + -
101A MSE 2.9 42.4 + - + -
102A ASN 3.7 0.9 - - - +
104A TRP* 1.3 95.9 - + - +
106A ASP* 1.3 58.8 + - - +
109A PHE* 3.0 51.6 + + - -
111A TYR* 3.6 4.4 + - - +
183A ARG* 3.1 50.3 - - - +
185A PHE* 4.0 7.0 - + - -
210A VAL* 4.2 15.0 - - + -
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Residues in contact with ASP 106 (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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102A ASN* 3.0 24.8 + - - +
103A GLU* 4.0 6.1 - - - +
105A PHE* 1.3 76.0 - - - +
107A LYS* 1.3 59.3 + - - +
109A PHE 3.1 18.5 - - - +
111A TYR* 2.6 33.5 + - + -
145A ARG* 2.8 39.5 + - - +
179A LEU* 4.7 2.1 - - - +
181A ILE* 4.3 1.7 - - - +
183A ARG* 2.8 13.2 + - - -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A GLU* 2.8 25.3 + - + +
104A TRP* 3.7 22.0 - - - +
106A ASP* 1.3 76.7 - - - +
108A THR* 1.3 64.7 + - - +
109A PHE 4.8 0.3 - - - +
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Residues in contact with THR 108 (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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52A LEU* 4.1 17.9 - - + -
104A TRP* 2.8 46.7 + - + -
105A PHE 3.9 2.5 - - - -
107A LYS* 1.3 78.5 - - - +
109A PHE* 1.4 86.5 + - + +
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Residues in contact with PHE 109 (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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42A VAL* 4.0 18.2 - - + -
44A LEU* 4.6 5.8 - - + -
48A THR* 3.9 30.1 - - + -
49A ILE* 6.4 0.2 - - - -
52A LEU* 3.8 24.5 - - + -
78A PHE* 3.6 33.0 - + - -
104A TRP* 4.3 1.8 - + - -
105A PHE* 3.0 37.2 + + + +
106A ASP 3.1 18.2 - - - +
107A LYS 4.8 0.4 - - - +
108A THR* 1.4 93.1 - - + +
110A ARG* 1.3 67.5 + - - +
111A TYR* 4.2 12.9 - + + -
185A PHE* 3.9 17.5 - + - -
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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