Contacts of the helix formed by residues 104 - 115 (chain D) in PDB entry 1TLF
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 VAL 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D SER 5.6 0.2 - - - +
103D GLY* 1.3 70.4 - - - -
105D GLU* 1.3 62.8 + - + +
107D CYS* 3.6 6.4 - - - +
108D LYS* 2.5 57.7 + - - +
128D LEU* 3.9 9.6 - - - +
132D ASP* 3.1 62.6 - - + +
135D ALA* 4.2 6.1 - - + -
136D VAL* 3.7 8.5 - - + -
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Residues in contact with GLU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D SER* 6.4 0.4 - - - -
103D GLY 2.7 5.4 + - - +
104D VAL* 1.3 83.0 - - + +
106D ALA* 1.3 52.6 + - - +
108D LYS* 3.0 24.5 + - - +
109D ALA* 2.8 35.2 + - - +
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Residues in contact with ALA 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL* 3.2 15.4 - - + +
100D GLU* 3.2 49.1 - - + +
102D SER* 3.7 16.5 - - - +
103D GLY 2.6 15.1 + - - +
105D GLU* 1.3 76.0 - - - +
107D CYS* 1.3 58.6 + - - +
109D ALA* 3.6 6.0 - - - +
110D ALA* 3.5 14.0 + - - +
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Residues in contact with CYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ALA* 4.9 2.2 - - - -
99D VAL* 3.3 12.5 - - - +
103D GLY 3.1 2.4 + - - -
104D VAL* 3.6 7.2 - - - +
106D ALA* 1.3 77.8 - - - +
108D LYS* 1.3 63.5 + - - +
110D ALA* 3.3 5.0 + - - +
111D VAL* 3.0 27.5 + - - +
124D ILE* 4.0 11.0 - - - -
126D TYR* 3.3 45.8 - - + -
128D LEU* 3.9 27.6 - - + -
136D VAL* 4.3 8.7 - - + -
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Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL* 2.5 41.4 + - - +
105D GLU* 3.0 27.2 + - - +
107D CYS* 1.3 70.2 - - - +
109D ALA* 1.3 66.5 + - - +
111D VAL* 2.9 12.2 + - - +
112D HIS* 2.9 23.6 + - - +
135D ALA* 3.9 28.3 + - - +
136D VAL* 4.3 9.9 - - + -
139D ALA* 4.7 17.4 - - + +
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Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLU* 5.0 6.1 - - - +
105D GLU 2.8 16.3 + - - +
106D ALA* 3.6 9.6 - - - +
108D LYS* 1.3 74.5 - - - +
110D ALA* 1.3 63.1 + - - +
112D HIS* 2.9 17.5 + - - +
113D ASN* 2.9 25.6 + - - +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ALA* 4.3 9.6 - - + -
97D SER* 4.0 20.0 + - - +
98D MET 4.7 4.9 - - - +
99D VAL* 3.4 33.2 - - + -
106D ALA 3.5 3.2 + - - +
107D CYS 3.3 4.2 + - - +
108D LYS 3.2 0.4 - - - -
109D ALA* 1.3 75.5 - - - +
111D VAL* 1.3 70.3 + - - +
113D ASN* 3.3 7.7 + - - +
114D LEU* 3.1 24.8 + - - +
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ALA* 5.1 2.4 - - + +
107D CYS* 3.0 19.4 + - - +
108D LYS* 2.9 8.9 + - - +
110D ALA* 1.3 75.8 - - - +
112D HIS* 1.3 64.4 + - - +
114D LEU* 3.0 4.9 + - - +
115D LEU* 2.9 28.7 + - + +
122D LEU* 3.5 28.3 - - + -
124D ILE* 4.1 11.7 - - + -
136D VAL* 3.8 26.2 - - + +
139D ALA* 4.4 6.1 - - + +
140D CYS* 3.5 31.6 - - - +
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Residues in contact with HIS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D LYS 2.9 11.0 + - - +
109D ALA* 3.1 13.7 - - - +
111D VAL* 1.3 76.9 - - - +
113D ASN* 1.3 61.5 + - - +
115D LEU* 2.9 37.1 + - + +
116D ALA* 2.9 14.4 + - - +
139D ALA* 5.1 7.2 - - + -
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Residues in contact with ASN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C SER* 4.8 17.4 + - - -
94C VAL 5.3 3.8 + - - +
97D SER* 4.1 16.9 + - - +
109D ALA* 2.9 20.3 + - - +
110D ALA* 3.3 10.1 + - - +
112D HIS* 1.3 76.4 - - - +
114D LEU* 1.3 60.9 + - - +
116D ALA* 3.7 13.6 + - - +
117D GLN* 3.0 29.0 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C VAL* 5.7 1.3 - - + -
65D GLY* 3.6 21.5 - - - +
66D VAL 3.9 13.0 - - - +
67D ALA* 4.2 8.5 - - + +
95D VAL* 3.4 41.5 - - + +
96D VAL 4.7 0.4 - - - -
97D SER* 3.9 20.0 - - - -
110D ALA 3.1 16.6 + - - +
111D VAL 3.0 5.6 + - - +
113D ASN* 1.3 73.4 - - - +
115D LEU* 1.3 58.6 + - - +
116D ALA 3.0 1.1 - - - -
117D GLN* 2.8 27.3 + - - +
119D VAL* 3.0 23.9 - - + +
122D LEU* 3.5 27.6 - - + -
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D VAL* 2.9 24.7 + - + +
112D HIS* 2.9 19.9 + - + +
114D LEU* 1.3 74.9 - - - +
116D ALA* 1.3 57.6 + - - +
117D GLN 2.8 6.6 + - - -
118D ARG* 3.5 17.9 + - - +
119D VAL* 5.3 0.9 - - + -
122D LEU* 4.1 13.2 - - + -
139D ALA 3.2 27.6 - - - +
140D CYS* 3.5 12.3 - - - +
141D THR* 4.0 6.5 - - - +
143D VAL* 3.4 37.2 - - + -
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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