Contacts of the helix formed by residues 149 - 160 (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 PRO 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D TYR* 3.2 50.9 - - + +
147D SER 3.0 11.4 - - - +
148D LEU* 1.3 83.3 - - + +
150D SER* 1.3 63.0 + - - +
152D LEU* 3.0 10.9 + - + +
153D LYS* 3.0 23.4 + - - +
51F C 4.7 7.9 - - - +
52F T 3.8 15.0 - - - +
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Residues in contact with SER 150 (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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148D LEU* 4.0 5.4 + - - +
149D PRO* 1.3 80.8 - - - +
151D ARG* 1.3 70.8 + - - +
153D LYS* 3.6 13.8 + - - +
154D ARG* 3.4 16.1 + - - +
52F T 2.8 61.1 + - - +
53F A 4.2 12.0 + - - -
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Residues in contact with ARG 151 (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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146D PHE* 4.6 13.7 - - + -
148D LEU* 2.8 31.1 + - + +
150D SER* 1.3 82.2 + - - +
152D LEU* 1.3 68.6 + - - +
154D ARG* 2.9 65.5 + - - +
155D HIS* 3.2 5.7 + - - +
9E G 4.0 10.9 + - - -
10E G 3.2 34.1 + - - -
11E T 3.6 20.0 + - - +
52F T 6.3 0.7 - - + -
53F A 5.6 4.6 - - - +
54F A 4.4 9.5 - - - +
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Residues in contact with LEU 152 (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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135D TYR* 3.2 20.9 - - + +
136D GLU 3.1 39.5 - - - +
137D CYS* 3.4 5.2 - - + +
138D PRO* 4.5 3.6 - - + -
146D PHE* 3.4 31.5 - - + -
148D LEU 3.4 2.2 + - - -
149D PRO* 3.0 16.1 + - + +
151D ARG* 1.3 75.5 - - - +
153D LYS* 1.3 72.1 + - + +
155D HIS* 2.7 26.5 + - - +
156D GLU* 2.9 40.0 + - - +
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Residues in contact with LYS 153 (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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149D PRO 3.0 7.2 + - - +
150D SER* 3.6 14.8 - - - +
152D LEU* 1.3 83.0 - - + +
154D ARG* 1.3 64.2 + - - +
156D GLU* 3.1 30.2 - - + +
157D LYS* 3.9 6.2 + - - +
53F A 4.5 20.3 + - - +
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Residues in contact with ARG 154 (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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150D SER 3.4 8.1 + - - +
151D ARG* 2.9 69.1 + - - +
152D LEU 2.8 0.8 + - - -
153D LYS* 1.3 78.6 - - - +
155D HIS* 1.3 64.3 + - - +
157D LYS* 3.0 42.3 + - - +
8E T 3.9 34.7 + - + +
9E G 3.5 31.9 + - - -
54F A 5.5 0.4 - - - +
55F C 3.8 19.0 - - - +
56F C 4.3 2.2 - - - +
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Residues in contact with HIS 155 (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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137D CYS* 3.7 9.4 - - + -
142D CYS* 3.1 10.2 - - - -
144D LYS* 4.0 8.4 + - + +
146D PHE* 3.6 33.7 - + + -
151D ARG 3.2 1.9 + - - +
152D LEU* 2.7 14.3 + - + +
154D ARG* 1.3 76.6 - - - +
156D GLU* 1.3 63.3 + - + +
157D LYS 2.9 1.9 + - - -
158D VAL* 2.9 29.8 + - + +
159D HIS* 2.5 19.7 + + - -
205D ZN 2.0 38.3 - - - -
8E T 3.1 38.9 + - - +
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Residues in contact with GLU 156 (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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137D CYS* 4.5 4.0 - - - -
138D PRO* 3.5 33.0 - - - +
139D HIS* 4.8 3.6 + - - -
152D LEU* 2.9 40.1 + - + +
153D LYS* 3.1 22.9 - - + +
155D HIS* 1.3 72.3 - - + +
157D LYS* 1.3 51.7 + - - +
158D VAL 2.4 20.1 + - - -
159D HIS* 3.0 35.3 + - - +
160D ALA* 4.0 2.7 - - - +
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Residues in contact with LYS 157 (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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153D LYS 4.1 4.5 - - - +
154D ARG* 3.0 34.5 - - - +
155D HIS 2.9 0.4 + - - -
156D GLU* 1.3 74.8 - - - +
158D VAL* 1.3 62.6 + - - +
160D ALA* 4.3 13.8 - - - +
7E C 3.8 24.3 + - - +
8E T 5.7 7.7 - - - +
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Residues in contact with VAL 158 (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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155D HIS* 3.1 33.9 - - + +
156D GLU 2.4 6.9 + - - -
157D LYS* 1.3 77.0 - - + +
159D HIS* 1.3 64.4 + - + +
160D ALA* 2.7 18.2 + - - +
173D VAL* 3.3 23.2 - - + +
7E C 3.4 47.5 + - - +
8E T 4.7 0.2 - - - +
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Residues in contact with HIS 159 (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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137D CYS* 3.1 10.6 - - - -
139D HIS* 3.7 46.4 - + + +
140D GLU 5.7 1.6 + - - -
142D CYS* 3.2 15.9 - - + +
155D HIS* 2.5 21.6 + + - -
156D GLU* 3.0 26.9 + - - +
158D VAL* 1.3 78.1 - - + +
160D ALA* 1.3 60.0 + - - +
163D PRO* 6.4 1.6 - - - -
173D VAL* 4.2 9.9 - - + -
205D ZN 1.9 38.1 - - - -
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Residues in contact with ALA 160 (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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156D GLU 4.0 10.3 - - - +
157D LYS* 4.3 13.6 - - - +
158D VAL 2.7 11.8 + - - +
159D HIS* 1.3 76.3 - - - +
161D GLY* 1.3 58.8 + - - +
163D PRO* 5.8 0.8 - - - +
173D VAL* 4.3 7.8 - - - +
174D GLY 4.9 2.1 - - - -
175D LYS* 4.9 5.2 + - - +
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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