Contacts of the helix formed by residues 104 - 122 (chain A) in PDB entry 1TU3
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 ASN 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.9 14.3 + - - -
29A SER 6.0 0.2 + - - -
31A VAL* 6.0 0.4 - - - +
101A ASP* 2.6 22.1 + - + +
102A ILE 3.4 0.4 - - - -
103A THR* 1.3 81.0 + - - +
105A GLU* 1.3 62.7 + - - +
106A GLU* 3.3 20.5 + - - +
107A SER* 2.8 40.8 + - - +
108A PHE 3.3 3.5 + - - -
143A VAL* 4.1 3.9 - - - +
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Residues in contact with GLU 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 THR 4.0 2.0 + - - -
104A ASN* 1.3 72.5 + - - +
106A GLU* 1.3 63.3 + - - +
108A PHE* 3.2 19.7 + - + +
109A ALA* 3.2 12.5 + - - +
142A ALA* 2.9 26.9 - - + +
143A VAL* 3.0 35.1 - - - +
147A GLU* 4.2 16.6 - - - +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.0 26.6 - - - +
104A ASN* 3.2 10.8 + - - +
105A GLU* 1.3 80.2 - - - +
107A SER* 1.3 56.4 + - - +
109A ALA* 3.3 11.3 + - - +
110A ARG* 3.0 28.6 + - - +
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Residues in contact with SER 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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28A GLU* 3.3 27.9 + - - +
31A VAL* 3.8 20.6 - - - -
99A VAL 4.8 1.0 - - - +
100A TYR* 3.3 9.0 - - - +
101A ASP 2.9 24.8 + - - -
104A ASN* 2.8 31.2 + - - +
106A GLU* 1.3 78.9 - - - +
108A PHE* 1.3 58.0 + - - +
110A ARG* 3.3 3.5 + - - +
111A ALA* 3.0 20.8 + - - +
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Residues in contact with PHE 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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100A TYR* 3.4 53.8 - + + -
104A ASN 3.3 3.8 + - - +
105A GLU* 3.2 16.8 + - - +
106A GLU 3.1 0.2 - - - -
107A SER* 1.3 78.0 + - - +
109A ALA* 1.3 66.7 + - - +
111A ALA* 3.0 14.3 + - + +
112A LYS* 3.2 46.0 + - - +
130A LEU* 4.5 9.9 - - + -
143A VAL* 4.1 15.3 - - + -
147A GLU* 4.3 22.9 - - - -
148A ALA* 3.8 29.2 - - + -
151A TYR* 4.3 11.7 - + - -
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Residues in contact with ALA 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 GLU 3.2 9.0 + - - +
106A GLU* 3.5 17.9 - - - +
108A PHE* 1.3 81.1 - - - +
110A ARG* 1.3 63.1 + - - +
112A LYS* 3.2 28.2 + - + +
113A ASN* 3.7 13.7 + - - +
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Residues in contact with ARG 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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28A GLU* 3.8 31.6 - - + +
80A GLU* 3.1 22.5 + - - -
83A HIS* 3.1 39.0 + - - +
106A GLU* 3.0 23.9 + - - +
107A SER* 3.5 9.6 - - - +
108A PHE 3.1 0.2 - - - -
109A ALA* 1.3 76.0 - - - +
111A ALA* 1.3 62.1 + - - +
113A ASN* 3.5 19.8 + - - +
114A TRP* 3.2 58.0 + - + +
117A GLU* 5.6 0.2 + - - -
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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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27A GLY* 6.0 0.4 - - - -
28A GLU 5.9 0.4 - - - +
98A VAL* 3.5 25.5 - - + +
99A VAL 4.5 3.1 - - - +
100A TYR* 4.2 19.3 - - + -
107A SER 3.0 13.6 + - - +
108A PHE* 3.0 12.9 + - + +
110A ARG* 1.3 76.4 - - - +
112A LYS* 1.3 65.4 + - - +
114A TRP* 3.1 8.1 + - - +
115A VAL* 2.9 27.5 + - - +
130A LEU* 4.6 5.6 - - + -
151A TYR* 5.6 0.9 - - + -
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Residues in contact with LYS 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 PHE* 3.2 46.4 + - + +
109A ALA* 3.2 15.9 + - - +
111A ALA* 1.3 76.5 - - - +
113A ASN* 1.3 60.7 + - - +
115A VAL* 3.3 4.9 + - - +
116A LYS* 2.9 26.7 + - - +
147A GLU* 5.2 5.7 + - - +
151A TYR* 3.4 47.9 + - + +
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Residues in contact with ASN 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 ALA* 3.7 14.6 + - - +
110A ARG* 3.5 22.9 + - - +
111A ALA 3.3 0.2 - - - -
112A LYS* 1.3 75.9 - - - +
114A TRP* 1.3 60.1 + - - +
115A VAL 3.2 0.2 - - - -
116A LYS* 3.6 22.9 + - + +
117A GLU* 2.8 30.6 + - - +
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Residues in contact with TRP 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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26A LEU* 3.9 33.2 - - + -
27A GLY* 3.8 35.9 - - - +
28A GLU* 4.1 0.8 - - - +
76A THR* 6.0 0.4 - - - -
78A GLY* 5.6 8.5 + - - -
83A HIS* 3.7 20.4 - + - -
86A ALA* 3.6 33.0 - - + -
90A TYR* 4.6 1.6 - + - -
98A VAL* 4.1 15.3 - - + -
110A ARG* 3.2 52.7 + - + +
111A ALA* 3.1 11.2 + - - +
113A ASN* 1.3 76.2 - - - +
115A VAL* 1.3 61.4 + - - +
117A GLU* 3.4 31.1 + - + +
118A LEU* 3.1 30.4 + - + +
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Residues in contact with VAL 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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98A VAL* 4.2 19.1 - - + -
111A ALA 2.9 19.7 + - - +
112A LYS 3.3 1.6 - - - +
114A TRP* 1.3 72.3 - - - +
116A LYS* 1.3 68.3 + - - +
118A LEU* 3.2 10.6 + - - +
119A GLN* 2.9 52.7 + - + +
128A ILE* 4.6 7.2 - - + -
130A LEU* 4.9 3.8 - - + -
151A TYR* 3.2 28.0 - - + +
155A ASN* 4.6 1.8 - - - +
157A LEU* 3.9 29.2 - - + -
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Residues in contact with LYS 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 LYS 2.9 16.6 + - - +
113A ASN* 3.6 23.3 + - + +
115A VAL* 1.3 76.4 - - - +
117A GLU* 1.3 65.0 + - + +
119A GLN* 3.3 15.7 + - - +
120A ARG* 3.2 45.4 + - + +
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Residues in contact with GLU 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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83A HIS* 2.7 34.2 + - - -
87A PRO* 4.1 8.3 - - - +
90A TYR* 2.6 31.0 + - + +
110A ARG* 5.6 0.2 + - - -
113A ASN 2.8 21.0 + - - +
114A TRP* 3.5 23.3 - - + +
115A VAL 3.3 0.2 - - - -
116A LYS* 1.3 76.4 - - + +
118A LEU* 1.3 57.7 + - - +
120A ARG* 3.4 15.1 + - - +
121A GLN* 2.8 52.6 + - - +
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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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26A LEU* 3.9 12.3 - - + -
90A TYR* 3.8 33.9 - - + -
96A ALA* 3.7 23.8 - - + -
98A VAL* 3.9 20.6 - - + -
114A TRP 3.1 20.5 + - - +
115A VAL* 3.6 6.1 - - - +
117A GLU* 1.3 72.0 - - - +
119A GLN* 1.3 62.2 + - - +
120A ARG 3.1 1.8 - - - -
122A ALA* 2.8 51.0 + - + +
123A SER 5.0 0.2 - - - +
126A ILE* 4.3 10.0 - - + +
128A ILE* 4.2 21.1 - - + -
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Residues in contact with GLN 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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115A VAL* 2.9 34.2 + - + +
116A LYS* 3.3 14.5 + - - +
118A LEU* 1.3 75.4 - - - +
120A ARG* 1.3 59.1 + - - +
122A ALA 4.9 3.1 - - - +
124A PRO* 5.9 2.3 - - - +
126A ILE* 6.0 1.1 - - - -
128A ILE* 4.1 14.3 - - + +
155A ASN* 3.4 41.3 + - - +
157A LEU* 4.3 2.4 - - - +
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Residues in contact with ARG 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 LYS* 3.2 34.3 + - + +
117A GLU* 3.8 15.3 - - - +
118A LEU 3.1 0.4 - - - -
119A GLN* 1.3 78.1 - - - +
121A GLN* 1.3 95.6 + - - +
122A ALA 4.9 1.5 - - - +
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Residues in contact with GLN 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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87A PRO* 4.3 11.1 - - - +
90A TYR* 3.0 30.0 + - + +
91A ARG* 6.1 0.3 - - - -
117A GLU* 2.8 26.2 + - - +
120A ARG* 1.3 125.5 + - - +
122A ALA* 1.3 63.6 + - - +
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Residues in contact with ALA 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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90A TYR* 4.1 17.0 - - + +
91A ARG* 5.9 1.1 - - - +
118A LEU* 2.8 51.1 + - + +
119A GLN 4.9 2.3 - - - +
120A ARG 4.9 1.7 - - - -
121A GLN* 1.3 79.5 + - - +
123A SER* 1.3 67.9 + - - +
124A PRO* 3.3 5.0 - - - +
126A ILE* 4.0 19.5 - - + -
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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