Contacts of the helix formed by residues 110 - 127 (chain A) in PDB entry 5TWF
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 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLU* 4.2 19.0 - - - +
84A CYS 3.4 18.4 - - - -
85A PRO* 3.7 6.5 + - - -
109A CYS* 1.3 77.4 - - - +
111A ALA* 1.3 55.7 + - - +
112A PRO* 3.8 10.8 - - - +
113A LYS* 3.3 20.6 + - - +
114A TYR* 2.7 32.6 + - - +
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Residues in contact with ALA 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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72A TYR* 4.5 0.2 - - - -
79A CYS* 4.1 0.2 - - - -
84A CYS* 3.5 21.9 + - + -
87A MET* 3.9 26.3 - - + +
109A CYS 3.7 1.4 + - - -
110A SER* 1.3 71.1 - - - +
112A PRO* 1.3 67.0 - - + +
114A TYR* 2.9 8.5 + - - -
115A ILE* 2.7 35.2 + - - +
161A HIS* 3.6 25.4 - - + +
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Residues in contact with PRO 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.8 12.5 - - + +
79A CYS* 3.5 21.8 - - - +
80A THR* 3.4 38.4 - - - +
81A GLU* 3.9 2.5 - - + +
84A CYS* 3.9 2.5 - - + -
110A SER* 3.6 8.7 - - - +
111A ALA* 1.3 92.9 - - + +
113A LYS* 1.3 61.1 + - - +
115A ILE* 3.6 1.4 + - + +
116A ASP* 3.0 25.1 + - - +
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Residues in contact with LYS 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 CYS* 4.3 10.3 - - + -
110A SER* 3.3 27.4 + - - +
112A PRO* 1.3 78.4 - - - +
114A TYR* 1.3 58.4 + - - +
116A ASP* 3.3 5.1 + - - +
117A TYR* 2.8 50.9 + - + -
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Residues in contact with TYR 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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87A MET* 3.3 36.1 - - + -
95A TYR* 3.4 35.0 - - + +
96A HIS 3.8 11.4 + - - -
97A TRP* 3.8 27.2 - + + -
109A CYS* 4.6 11.1 - - - +
110A SER 2.7 21.2 + - - +
111A ALA* 2.9 4.9 + - - +
113A LYS* 1.3 73.2 - - - +
115A ILE* 1.3 59.0 + - + +
117A TYR* 3.1 9.6 + - - +
118A LEU* 2.8 53.7 + - + +
157A ARG* 2.4 42.7 + - + -
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Residues in contact with ILE 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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72A TYR* 3.8 41.7 - - + +
87A MET* 3.5 33.7 - - + -
111A ALA* 2.7 25.6 + - + +
112A PRO 4.2 1.6 - - - +
114A TYR* 1.3 76.1 - - + +
116A ASP* 1.3 56.6 + - - +
118A LEU* 4.3 2.7 - - - -
119A MET* 2.8 57.2 + - + +
158A VAL* 4.0 36.6 - - + +
161A HIS* 5.1 0.9 - - + -
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Residues in contact with ASP 116 (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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112A PRO 3.0 19.7 + - - +
113A LYS* 3.5 6.6 - - - +
115A ILE* 1.3 75.2 - - - +
117A TYR* 1.3 64.6 + - + +
119A MET* 4.0 3.4 - - - +
120A THR* 2.7 42.2 + - - -
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Residues in contact with TYR 117 (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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97A TRP* 3.1 44.5 + + + +
103A ILE* 5.9 1.8 - - + -
107A ILE* 4.9 9.4 - - + +
109A CYS* 4.8 11.8 - - + +
113A LYS* 2.8 42.9 + - + +
114A TYR* 3.2 9.4 - - - +
116A ASP* 1.3 81.4 - - + +
118A LEU* 1.3 64.8 + - - +
120A THR* 3.2 5.4 + - - -
121A TRP* 3.0 19.2 + - - +
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Residues in contact with LEU 118 (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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97A TRP* 3.5 30.7 - - + -
114A TYR* 2.8 42.2 + - + +
115A ILE* 4.1 6.1 - - - +
117A TYR* 1.3 74.3 - - - +
119A MET* 1.3 78.7 + - - +
121A TRP* 2.9 2.3 + - - +
122A VAL* 2.7 51.8 + - + +
154A ARG* 3.3 37.0 - - + +
155A LEU* 4.5 3.6 - - + -
157A ARG* 5.1 0.7 - - + -
158A VAL* 4.1 15.0 - - + -
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Residues in contact with MET 119 (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 PHE* 3.5 47.6 - - + +
68A ILE* 4.1 5.4 - - + -
69A ASN* 3.8 35.7 - - - +
72A TYR* 6.4 0.4 - - - -
115A ILE* 2.8 39.5 + - + +
116A ASP* 4.0 3.6 - - - +
118A LEU* 1.3 90.7 - - - +
120A THR* 1.3 58.7 + - - +
123A GLN* 3.0 27.7 + - - +
155A LEU* 3.5 27.1 - - + -
158A VAL* 4.6 3.1 - - - -
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Residues in contact with THR 120 (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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116A ASP* 2.7 30.6 + - - -
117A TYR* 3.5 7.6 - - - -
119A MET* 1.3 74.0 - - - +
121A TRP* 1.3 59.8 + - - +
123A GLN* 3.2 9.0 + - + +
124A ASP* 2.9 46.9 + - - +
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Residues in contact with TRP 121 (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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97A TRP* 3.7 27.4 - + + +
99A ASP* 4.1 31.2 + - + +
100A GLY* 5.9 0.4 - - - -
117A TYR 3.0 7.9 + - - +
118A LEU 2.9 9.0 + - - +
120A THR* 1.3 76.5 - - - +
122A VAL* 1.3 87.8 + - + +
124A ASP* 3.0 11.9 + - + +
125A GLN* 2.8 63.0 + - + +
147A VAL* 5.0 2.7 - - + -
150A THR* 3.8 22.7 - - + -
151A ILE* 3.9 26.7 - - + -
154A ARG* 4.1 24.0 - - + -
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Residues in contact with VAL 122 (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 PHE* 3.4 30.1 - - + -
118A LEU* 2.7 41.4 + - + +
119A MET 3.9 4.0 - - - +
121A TRP* 1.3 92.3 - - + +
123A GLN* 1.3 62.4 - - - +
125A GLN* 3.3 5.7 + - - +
126A LEU* 3.0 29.9 + - + +
151A ILE* 3.6 35.7 - - + +
154A ARG* 5.1 2.7 - - + -
155A LEU* 4.7 7.4 - - + -
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Residues in contact with GLN 123 (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 PHE* 3.4 28.9 - - + -
69A ASN* 5.3 1.2 + - - -
119A MET 3.0 16.0 + - - +
120A THR* 3.4 13.2 - - + +
121A TRP 3.2 0.2 - - - -
122A VAL* 1.3 77.6 - - - +
124A ASP* 1.3 53.0 + - - +
126A LEU* 3.0 12.7 + - - +
127A ASP* 2.7 61.4 + - - +
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Residues in contact with ASP 124 (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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120A THR* 2.9 32.2 + - - +
121A TRP* 3.0 13.0 + - + +
123A GLN* 1.3 76.4 - - - +
125A GLN* 1.3 70.4 + - - +
127A ASP* 3.1 18.8 + - - +
128A ASP* 3.1 18.8 + - - +
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Residues in contact with GLN 125 (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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121A TRP* 2.8 68.4 + - + +
122A VAL 3.3 10.1 + - - +
124A ASP* 1.3 80.5 - - - +
126A LEU* 1.3 61.4 + - - +
127A ASP 3.2 0.3 + - - -
128A ASP* 3.3 12.5 + - - +
131A LEU* 3.8 22.0 - - + +
132A PHE* 2.9 18.7 - - + -
147A VAL* 3.7 25.8 - - + +
151A ILE* 3.6 20.0 - - + -
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Residues in contact with LEU 126 (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 THR* 4.4 8.5 - - + -
62A VAL* 3.8 34.8 - - + -
65A PHE* 3.6 43.5 - - + -
122A VAL* 3.0 20.0 + - + +
123A GLN* 3.4 11.4 - - - +
125A GLN* 1.3 74.4 - - - +
127A ASP* 1.3 63.0 + - - +
128A ASP 3.4 1.0 + - - -
129A GLU* 5.4 0.5 - - - +
132A PHE* 3.6 44.5 - - + +
151A ILE* 4.4 8.5 - - + -
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Residues in contact with ASP 127 (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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123A GLN* 2.7 44.2 + - - +
124A ASP* 3.1 13.2 + - - +
126A LEU* 1.3 75.6 - - - +
128A ASP* 1.3 58.0 + - - +
129A GLU* 3.9 14.3 + - - +
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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