Contacts of the helix formed by residues 101 - 118 (chain A) in PDB entry 1TFR
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 TRP 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.8 23.3 - - + -
29A LEU* 3.7 33.9 - - + -
98A THR* 5.0 4.7 + - - -
99A TRP* 2.7 65.6 + + + +
100A ASP* 1.3 72.4 - - - +
102A GLU* 1.3 60.8 + - - +
105A PHE* 2.9 60.5 + + + +
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Residues in contact with GLU 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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100A ASP* 3.0 7.7 + - - +
101A TRP* 1.3 76.5 - - - +
103A GLY* 1.3 66.8 + - - +
105A PHE* 3.6 2.3 + - - +
106A GLU* 2.7 65.3 + - - +
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Residues in contact with GLY 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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38A ILE* 3.7 20.2 - - - -
100A ASP* 2.9 21.4 + - - -
102A GLU* 1.3 71.9 + - - +
104A TYR* 1.3 65.9 + - - +
106A GLU* 3.4 7.9 + - - +
107A SER* 2.7 32.3 + - - -
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Residues in contact with TYR 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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21A SER 4.6 1.2 + - - -
24A ALA* 3.3 15.4 - - - +
25A LEU* 3.2 51.4 + - + +
28A ALA* 3.5 26.7 - - + -
32A PHE* 4.2 2.2 - + - -
38A ILE* 3.8 11.1 - - + +
43A VAL* 3.7 29.8 - - + -
46A LEU* 5.3 2.0 - - + -
47A ILE* 4.4 2.4 - - + +
99A TRP* 3.8 17.7 - + + -
100A ASP 3.1 18.1 + - - +
101A TRP 3.8 4.0 - - - +
103A GLY* 1.3 78.1 - - - +
105A PHE* 1.3 71.1 + + - +
107A SER* 3.9 1.4 - - - -
108A SER* 2.8 57.4 + - - -
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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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25A LEU* 4.0 28.0 - - + -
101A TRP* 2.9 57.4 + + + +
102A GLU* 4.4 2.0 - - - +
104A TYR* 1.3 95.8 - + - +
106A GLU* 1.3 60.4 + - + +
108A SER* 3.6 5.4 - - - -
109A HIS* 2.6 54.3 + + + +
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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
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102A GLU* 2.7 53.5 + - + +
103A GLY* 3.8 7.0 - - - +
104A TYR 3.2 0.2 - - - -
105A PHE* 1.3 77.5 - - + +
107A SER* 1.3 63.0 + - - +
109A HIS* 3.2 15.2 + - - +
110A LYS* 3.3 11.6 + - - +
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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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38A ILE 4.3 1.6 + - - -
39A ASN 4.0 2.1 - - - -
40A LEU* 3.7 45.0 + - - +
43A VAL* 4.0 13.2 - - - -
103A GLY* 2.7 20.1 + - - -
104A TYR 3.9 1.1 - - - -
106A GLU* 1.3 73.8 - - - +
108A SER* 1.3 61.7 + - - +
110A LYS* 3.0 6.2 + - - +
111A VAL* 2.8 34.3 + - - +
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Residues in contact with SER 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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43A VAL* 3.8 11.6 - - - +
47A ILE* 4.5 7.2 - - - +
104A TYR* 2.8 50.3 + - - -
105A PHE* 3.1 15.6 + - - -
107A SER* 1.3 72.4 - - - +
109A HIS* 1.3 67.6 + - - +
111A VAL* 3.4 1.8 + - - +
112A ILE* 3.0 37.6 + - - +
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Residues in contact with HIS 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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71A ASP 5.3 6.3 + - - -
72A ASN* 5.7 4.6 + - - -
105A PHE* 2.6 47.7 + + + +
106A GLU* 3.2 6.2 + - - +
108A SER* 1.3 84.1 + - - +
110A LYS* 1.3 62.2 + - - +
112A ILE* 3.6 13.7 + - + +
113A ASP* 3.4 25.6 + - - +
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Residues in contact with LYS 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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40A LEU* 3.9 19.3 - - + -
44A ARG* 4.6 3.1 - - - +
106A GLU 3.3 9.8 + - - +
107A SER* 3.0 10.3 + - - +
109A HIS* 1.3 76.5 - - - +
111A VAL* 1.3 59.6 + - - +
113A ASP* 3.0 42.8 + - - +
114A GLU* 3.1 33.5 + - - +
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Residues in contact with VAL 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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40A LEU* 3.8 17.7 - - + -
43A VAL* 4.3 2.5 - - + -
44A ARG* 3.7 35.2 - - + +
47A ILE* 3.7 39.9 - - + -
48A LEU* 5.4 0.7 - - + -
107A SER 2.8 24.4 + - - +
108A SER 3.4 4.2 + - - +
110A LYS* 1.3 72.7 - - - +
112A ILE* 1.3 56.8 + - - +
114A GLU* 2.9 21.0 + - - +
115A LEU* 2.9 33.9 + - + +
289A TYR* 4.4 3.6 - - - +
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Residues in contact with ILE 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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20A PHE* 3.3 35.4 - - + -
21A SER* 5.5 0.4 - - - +
47A ILE* 5.1 2.5 - - + -
70A ILE* 3.5 27.6 - - + -
108A SER* 3.0 22.8 + - - +
109A HIS* 3.7 15.0 - - + +
110A LYS 3.2 0.2 - - - -
111A VAL* 1.3 75.2 - - - +
113A ASP* 1.3 62.7 + - - +
115A LEU* 3.4 14.7 + - + +
116A LYS* 3.1 33.2 + - - +
123A VAL* 4.3 8.2 - - + +
125A ASP* 4.0 20.9 - - - +
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Residues in contact with ASP 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 HIS 3.4 13.9 + - - +
110A LYS* 3.0 33.0 + - - +
112A ILE* 1.3 76.8 - - - +
114A GLU* 1.3 57.9 - - - +
116A LYS* 3.2 25.1 + - - +
117A ALA* 3.0 26.6 + - - +
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Residues in contact with GLU 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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44A ARG* 2.4 53.4 + - - +
110A LYS* 3.1 31.9 + - + +
111A VAL* 2.9 15.1 + - - +
113A ASP* 1.3 75.1 - - - +
115A LEU* 1.3 58.5 + - - +
117A ALA* 3.0 3.6 + - - -
118A TYR* 2.8 48.5 + - + +
289A TYR* 2.6 36.9 + - + +
293A ALA* 5.4 0.2 - - - +
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Residues in contact with LEU 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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20A PHE* 4.1 16.4 - - + -
47A ILE* 4.2 8.7 - - + -
48A LEU* 4.1 14.8 - - + -
51A ILE* 3.8 31.0 - - + -
68A LEU* 4.1 12.8 - - + -
111A VAL* 2.9 22.1 + - + +
112A ILE* 3.6 23.1 - - + +
114A GLU* 1.3 74.1 - - - +
116A LYS* 1.3 60.7 + - - +
119A MET* 2.9 56.9 + - + +
123A VAL* 4.4 16.3 - - + +
278A TYR* 4.9 0.2 + - - -
289A TYR* 4.8 2.9 - - - +
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Residues in contact with LYS 116 (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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112A ILE* 3.1 24.2 + - - +
113A ASP* 3.5 22.6 + - - +
114A GLU 3.2 0.2 - - - -
115A LEU* 1.3 80.3 - - - +
117A ALA* 1.3 59.8 + - - +
123A VAL* 3.7 31.0 - - + -
125A ASP* 2.5 38.2 + - - -
274A TYR* 4.4 8.7 - - - +
278A TYR* 3.7 23.7 + - + +
279A LYS 5.3 1.7 - - - +
281A PRO* 4.4 11.6 - - - +
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Residues in contact with ALA 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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113A ASP 3.0 13.1 + - - +
114A GLU* 3.0 8.5 + - - +
116A LYS* 1.3 77.9 - - - +
118A TYR* 1.3 82.2 + - + +
281A PRO* 3.3 4.4 - - - +
285A LYS* 2.7 32.7 + - - +
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Residues in contact with TYR 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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114A GLU* 2.8 36.4 + - + +
117A ALA* 1.3 96.9 - - + +
119A MET* 1.3 64.9 + - - +
120A PRO 4.0 0.2 - - - -
281A PRO* 3.4 11.9 - - - +
282A PRO 4.4 1.2 - - - +
283A ARG* 5.5 0.3 - - - -
285A LYS* 4.0 30.1 - - + +
286A ILE* 3.7 15.4 - - - +
288A SER* 5.8 0.4 - - - -
289A TYR* 3.3 52.7 - + + -
292A LYS* 3.4 29.1 + - - +
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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