Contacts of the helix formed by residues 103 - 115 (chain A) in PDB entry 1TFZ
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 ASP 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TRP* 4.5 3.3 - - + -
101A SER 3.5 6.2 + - - +
102A PHE* 1.3 85.3 - - - +
104A HIS* 1.3 62.0 + - - +
105A GLY* 3.1 9.4 + - - -
106A SER* 2.7 43.4 + - - +
107A CYS* 2.8 32.2 + - - +
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Residues in contact with HIS 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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63A VAL* 2.8 38.1 + - + +
81A PRO* 3.2 22.4 - - + -
82A TYR 3.2 27.0 + - - -
83A SER 4.5 0.9 + - - -
84A PRO* 4.1 22.7 - - + +
87A SER* 3.6 24.2 - - - -
102A PHE* 3.7 8.5 - + - -
103A ASP* 1.3 73.0 + - - +
105A GLY* 1.3 58.0 + - - +
107A CYS* 3.2 1.4 + - - +
108A ARG* 2.9 45.7 + - - +
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Residues in contact with GLY 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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103A ASP* 3.1 8.4 + - - -
104A HIS* 1.3 79.4 - - - +
106A SER* 1.3 56.5 + - - +
108A ARG* 3.9 4.0 - - - +
109A SER* 2.9 31.8 + - - -
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Residues in contact with SER 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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32A TRP* 3.5 15.8 - - - -
103A ASP* 2.7 33.9 + - - +
105A GLY* 1.3 72.5 - - - +
107A CYS* 1.3 57.2 + - - +
109A SER* 3.7 5.4 - - - -
110A PHE* 2.8 32.1 + - - +
119A ARG* 4.9 8.3 - - - -
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Residues in contact with CYS 107 (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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32A TRP* 3.4 35.9 - - + +
33A CYS 4.5 6.1 - - - -
79A THR 4.7 1.8 - - - -
81A PRO* 3.5 30.1 - - + -
102A PHE* 3.6 25.1 - - + -
103A ASP 2.8 17.7 + - - +
104A HIS 3.5 4.0 - - - +
106A SER* 1.3 76.0 - - - +
108A ARG* 1.3 62.8 + - - +
110A PHE* 3.2 3.5 + - - +
111A PHE* 3.0 25.1 + - - +
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Residues in contact with ARG 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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81A PRO* 3.3 29.6 + - + +
82A TYR 3.3 29.3 + - - -
83A SER* 4.5 4.2 - - - +
84A PRO* 3.9 16.5 - - - +
104A HIS* 2.9 36.8 + - - +
105A GLY* 4.0 4.0 - - - +
107A CYS* 1.3 75.9 - - - +
109A SER* 1.3 58.2 + - - +
111A PHE* 3.4 4.6 + - - +
112A SER* 2.9 32.6 + - - -
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Residues in contact with SER 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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105A GLY 2.9 20.4 + - - -
106A SER* 3.7 6.5 - - - -
108A ARG* 1.3 74.7 - - - +
110A PHE* 1.3 65.5 + - - +
112A SER* 3.7 5.4 - - - -
113A SER* 3.0 28.9 + - - -
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Residues in contact with PHE 110 (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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32A TRP* 3.5 35.2 - + + -
106A SER 2.8 18.8 + - - +
107A CYS 3.5 3.4 - - - +
109A SER* 1.3 77.9 - - - +
111A PHE* 1.3 61.8 + - + +
113A SER* 4.7 0.4 - - - -
114A HIS* 2.8 57.1 + + + +
115A GLY 4.0 14.6 - - - -
117A GLY* 4.0 17.3 - - - -
118A VAL 3.5 28.3 - - - -
119A ARG* 4.0 7.9 - - - +
163A ASP* 3.6 44.9 - - + -
164A VAL* 4.8 2.5 - - + -
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Residues in contact with PHE 111 (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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32A TRP 3.4 19.3 - - - -
33A CYS* 3.6 16.6 - - - +
34A GLY* 3.3 30.1 - - - -
107A CYS* 3.0 17.2 + - - +
108A ARG* 3.9 4.7 - - - +
110A PHE* 1.3 79.8 - - + +
112A SER* 1.3 64.7 + - - +
115A GLY* 2.8 36.3 + - - +
116A LEU* 3.5 30.7 - - + -
367A ARG* 4.2 1.6 + - - -
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Residues in contact with SER 112 (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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108A ARG 2.9 20.2 + - - -
109A SER* 3.7 6.1 - - - -
111A PHE* 1.3 78.6 - - - +
113A SER* 1.3 61.6 + - - +
281A GLU* 4.6 3.3 - - - +
367A ARG* 3.3 15.1 + - - -
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Residues in contact with SER 113 (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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109A SER* 3.0 18.8 + - - -
110A PHE 3.7 2.0 - - - -
112A SER* 1.3 78.0 - - - +
114A HIS* 1.3 76.1 + - - +
163A ASP* 5.1 0.4 + - - -
281A GLU* 3.0 40.4 + - - +
367A ARG* 2.8 21.8 + - - -
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Residues in contact with HIS 114 (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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110A PHE* 2.8 57.3 + + + +
113A SER* 1.3 85.0 + - - +
115A GLY* 1.3 65.4 + - - +
116A LEU 5.0 0.7 - - - +
117A GLY* 6.3 0.9 - - - -
162A GLY* 6.0 0.4 - - - -
163A ASP* 2.7 31.6 + - + +
280A ASN* 2.7 49.4 + - - +
281A GLU 3.4 17.9 - - - -
282A GLY* 5.2 0.2 - - - -
283A ALA 4.6 11.4 - - - -
367A ARG* 3.0 24.3 + - - +
369A THR* 5.2 1.2 + - - -
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Residues in contact with GLY 115 (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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110A PHE* 4.0 12.0 - - - -
111A PHE* 2.8 42.5 + - - -
114A HIS* 1.3 77.5 - - - +
116A LEU* 1.3 66.1 + - - -
117A GLY* 3.3 3.1 + - - -
367A ARG* 3.7 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