Contacts of the helix formed by residues 119 - 130 (chain D) in PDB entry 1TF6
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 HIS 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D TYR* 3.1 42.4 - + + +
118D LYS* 1.3 69.9 - - - +
120D ASN* 1.3 77.4 + - - +
122D LEU* 2.8 36.8 + - + +
123D LYS* 3.0 42.5 + - + +
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Residues in contact with ASN 120 (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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118D LYS* 5.1 2.5 - - + +
119D HIS* 1.3 95.1 + - - +
121D GLN* 1.3 73.9 + - - +
123D LYS* 2.9 19.7 + - - +
124D VAL* 3.0 18.1 + - + +
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Residues in contact with GLN 121 (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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116D PHE* 3.5 34.4 - - + -
117D LYS* 5.0 4.3 - - + -
118D LYS* 2.9 64.0 + - + +
119D HIS 3.1 0.2 - - - -
120D ASN* 1.3 85.2 - - - +
122D LEU* 1.3 63.9 + - - +
124D VAL* 3.4 10.2 + - - +
125D HIS 3.3 14.7 + - - -
135D TYR* 4.7 12.5 + - - -
51F C 5.1 8.3 + - - -
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Residues in contact with LEU 122 (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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105D TYR* 4.3 13.5 - - + -
106D VAL* 3.4 17.3 - - - +
107D CYS* 3.4 39.7 - - + +
116D PHE* 3.6 18.3 - - + -
118D LYS 3.5 5.7 + - - +
119D HIS* 2.8 25.8 + - + +
121D GLN* 1.3 76.6 - - - +
123D LYS* 1.3 67.7 + - + +
124D VAL 3.0 0.9 + - - -
125D HIS* 3.1 4.5 + - + +
126D GLN* 3.0 49.3 + - + +
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Residues in contact with LYS 123 (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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119D HIS* 3.0 36.1 + - + +
120D ASN* 2.9 14.5 + - + +
122D LEU* 1.3 82.1 - - + +
124D VAL* 1.3 67.4 + - + +
126D GLN* 3.2 29.8 - - - +
127D PHE* 3.5 25.8 - - + -
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Residues in contact with VAL 124 (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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120D ASN* 3.0 17.2 + - + +
121D GLN* 3.5 12.6 - - - +
123D LYS* 1.3 72.8 - - + +
125D HIS* 1.3 73.8 + - - +
127D PHE* 2.5 26.0 + - - +
128D SER 3.8 0.2 + - - -
134D PRO* 4.1 27.6 - - + -
135D TYR* 4.1 34.3 - - + +
51F C 6.0 1.6 - - - +
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Residues in contact with HIS 125 (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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107D CYS* 3.6 13.4 - - + +
112D CYS* 2.8 16.3 - - - -
114D LYS* 4.0 11.8 - - + +
116D PHE* 3.3 43.7 - + + -
121D GLN 3.3 2.0 + - - -
122D LEU 3.1 3.8 + - - +
124D VAL* 1.3 80.5 - - - +
126D GLN* 1.3 52.0 + - - +
128D SER* 2.3 64.8 + - - -
129D HIS* 2.8 10.3 - + - -
204D ZN 1.9 34.5 - - - -
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Residues in contact with GLN 126 (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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106D VAL 5.4 0.4 + - - -
107D CYS* 4.8 14.8 - - + +
108D HIS 5.5 1.4 - - - +
109D PHE* 6.1 1.0 - - - +
122D LEU* 3.0 43.1 + - + +
123D LYS* 3.2 27.3 - - - +
124D VAL 2.9 1.4 + - - -
125D HIS* 1.3 78.1 - - - +
127D PHE* 1.3 55.5 + - + +
129D HIS* 2.7 44.3 + - - +
130D THR* 3.5 5.4 - - - +
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Residues in contact with PHE 127 (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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123D LYS* 3.5 29.6 - - + -
124D VAL* 2.5 19.7 + - - +
126D GLN* 1.3 75.5 - - + +
128D SER* 1.3 54.3 + - - +
129D HIS 2.9 0.7 - - - -
130D THR* 2.6 41.6 + - + -
132D GLN* 3.8 21.7 - - + +
133D LEU 3.0 30.3 - - - -
134D PRO* 3.2 29.8 - - + -
145D ARG* 4.1 14.4 - - - -
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Residues in contact with SER 128 (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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124D VAL 3.8 0.2 + - - -
125D HIS* 2.3 54.0 + - - -
127D PHE* 1.3 68.5 - - - +
129D HIS* 1.3 76.0 + - - +
130D THR 3.1 5.9 + - - +
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Residues in contact with HIS 129 (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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107D CYS* 3.5 6.3 - - - -
109D PHE* 2.8 40.3 - + + -
112D CYS* 3.1 25.7 - - + +
125D HIS* 2.8 8.2 - + - -
126D GLN* 2.7 22.1 + - - +
128D SER* 1.3 100.7 - - - +
130D THR* 1.3 63.3 + - - +
204D ZN 1.9 37.6 - - - -
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Residues in contact with THR 130 (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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126D GLN 3.5 4.0 - - - +
127D PHE* 2.6 45.2 + - + +
128D SER 3.1 4.6 - - - +
129D HIS* 1.3 84.4 - - + +
131D GLN* 1.3 77.8 + - - +
132D GLN* 2.9 35.3 + - + +
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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