Contacts of the helix formed by residues 141 - 154 (chain A) in PDB entry 1T2E
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ARG* 3.7 24.9 - - + +
110A ASP* 4.6 1.3 - - - +
113A LEU* 3.8 28.5 - - + +
140A ASN* 1.3 83.7 - - + +
142A VAL* 1.3 67.0 + - - +
143A ASP 3.3 2.2 - - - +
144A VAL* 3.0 15.9 + - + -
145A MET* 2.9 26.8 + - + +
195A HIS 5.6 3.1 - - - +
325A MET* 4.0 35.7 - - + -
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.2 30.5 - - + +
138A VAL 3.6 8.3 - - - +
139A THR 3.2 9.4 - - - +
140A ASN* 3.0 9.5 - - - +
141A PRO* 1.3 71.6 - - - +
143A ASP* 1.3 66.7 + - - +
146A VAL* 2.8 28.9 + - - +
162A GLY* 3.8 7.2 - - - -
163A LEU 3.2 30.5 - - - +
195A HIS* 3.4 28.6 + - + +
272A SER* 5.2 0.4 - - - -
336A NAI 3.4 15.7 - - - +
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Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PRO 3.3 0.8 - - - -
142A VAL* 1.3 79.5 + - - +
144A VAL* 1.3 62.3 + - + +
146A VAL* 3.4 11.8 - - - +
147A GLN* 3.8 5.9 + - - +
193A GLY 4.4 1.3 - - - -
194A ALA* 3.2 18.1 - - - +
195A HIS* 2.7 37.3 + - - +
272A SER* 2.8 35.9 + - - +
286A PHE* 3.8 12.5 - - - +
288A GLY* 4.2 5.9 + - - -
322A THR* 3.7 29.0 - - + +
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 4.6 0.7 - - + -
141A PRO* 3.0 14.1 + - + +
143A ASP* 1.3 78.1 - - + +
145A MET* 1.3 72.4 + - + +
147A GLN* 3.2 6.6 + - - +
148A LEU* 3.1 19.9 + - - +
322A THR* 3.7 29.4 - - + +
325A MET* 3.9 40.6 - - + +
326A LYS* 4.3 6.7 - - + -
329A ALA* 3.4 31.9 - - + -
330A HIS* 6.0 1.4 - - + -
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Residues in contact with MET 145 (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 LEU* 4.3 8.5 - - + -
116A ASN* 4.0 22.7 - - - +
117A ASN* 4.1 4.7 - - - -
120A MET* 3.6 33.1 - - + +
137A VAL* 4.2 3.6 - - + -
139A THR* 3.2 28.3 - - + +
140A ASN 3.6 10.3 - - - +
141A PRO* 2.9 27.4 + - + +
142A VAL 3.9 0.9 - - - +
144A VAL* 1.3 98.6 - - + +
146A VAL* 1.3 64.0 + - - +
148A LEU* 3.3 7.2 + - + +
149A LEU* 2.9 25.1 + - - +
329A ALA* 3.8 14.8 - - + -
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Residues in contact with VAL 146 (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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137A VAL* 3.8 18.4 - - + +
142A VAL 2.8 21.8 + - - +
143A ASP 3.4 11.2 - - - +
145A MET* 1.3 79.3 - - - +
147A GLN* 1.3 62.9 + - - +
149A LEU* 3.3 2.3 + - - +
150A HIS* 2.8 26.3 + - - +
160A ILE* 3.7 17.9 - - + -
161A ILE 3.6 29.4 - - - +
162A GLY* 4.2 3.8 - - - -
272A SER* 3.7 11.7 - - - +
286A PHE* 3.4 27.1 - - + -
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Residues in contact with GLN 147 (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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143A ASP 4.1 6.6 - - - +
144A VAL* 3.2 8.9 + - - +
146A VAL* 1.3 82.9 - - - +
148A LEU* 1.3 58.5 + - - +
150A HIS* 3.1 3.2 + - - +
151A GLN* 2.8 52.5 + - + +
274A LEU* 4.2 10.9 - - - +
283A ASP* 3.2 27.5 + - - +
285A ILE* 3.6 22.4 - - - +
286A PHE* 3.5 25.2 + - + -
322A THR* 5.7 0.2 - - - +
326A LYS* 3.3 26.0 - - - +
330A HIS* 6.0 0.7 - - + -
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Residues in contact with LEU 148 (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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117A ASN* 3.3 44.9 - - + +
120A MET* 3.9 10.5 - - + -
121A ILE* 4.0 15.0 - - + -
144A VAL 3.1 16.0 + - - +
145A MET* 3.7 6.5 - - - +
147A GLN* 1.3 75.4 - - - +
149A LEU* 1.3 63.6 + - - +
151A GLN* 3.3 1.8 + - - -
152A HIS* 3.0 43.5 + - + +
329A ALA* 4.3 11.4 - - + +
330A HIS* 3.3 49.1 - - + +
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Residues in contact with LEU 149 (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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96A VAL* 3.7 30.5 - - + -
120A MET* 3.1 32.0 - - + +
123A ILE* 4.2 8.1 - - + -
124A GLY* 2.9 39.3 - - - +
127A ILE* 4.3 9.2 - - + -
135A ILE* 4.5 0.9 - - + -
137A VAL* 3.8 19.3 - - + -
145A MET 2.9 17.8 + - - +
146A VAL 3.7 2.9 - - - +
148A LEU* 1.3 75.8 - - - +
150A HIS* 1.3 66.4 + - - +
153A SER* 2.8 29.8 + - - -
160A ILE* 4.4 5.4 - - + -
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Residues in contact with HIS 150 (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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146A VAL 2.8 18.6 + - - +
147A GLN* 3.3 10.9 + - - +
149A LEU* 1.3 72.7 - - - +
151A GLN* 1.3 71.6 + - + +
153A SER* 3.3 5.3 + - - -
154A GLY* 3.1 20.8 + - - -
155A VAL* 3.1 29.6 + - + -
157A LYS* 3.9 13.6 + - + -
160A ILE* 3.7 24.1 - - + +
274A LEU* 4.3 24.1 - - + +
286A PHE* 3.6 25.2 - + + -
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Residues in contact with GLN 151 (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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128A LYS* 5.8 1.6 + - - -
147A GLN* 2.8 45.1 + - + +
148A LEU* 3.8 5.4 - - - +
149A LEU 3.1 0.2 - - - -
150A HIS* 1.3 89.9 - - + +
152A HIS* 1.3 66.1 + - + +
154A GLY* 3.9 5.9 + - - -
326A LYS* 3.4 27.6 + - - +
330A HIS* 4.0 15.9 + - - +
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Residues in contact with HIS 152 (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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120A MET 4.6 0.2 - - - +
121A ILE* 3.6 63.2 + - + +
124A GLY* 3.4 15.0 - - - +
125A GLY* 3.9 3.8 + - - +
128A LYS* 4.1 12.9 + - - +
148A LEU* 3.0 40.1 + - + +
149A LEU 4.1 1.1 - - - +
151A GLN* 1.3 80.0 + - + +
153A SER* 1.3 64.3 + - - +
154A GLY 3.3 0.6 + - - -
330A HIS* 4.7 7.5 + - - -
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Residues in contact with SER 153 (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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124A GLY* 3.2 22.6 + - - -
127A ILE* 3.9 22.2 - - - -
128A LYS* 3.3 25.3 - - - +
132A PRO* 5.2 2.3 - - - +
135A ILE* 5.6 0.4 - - - -
149A LEU* 2.8 31.1 + - - +
150A HIS* 3.3 6.1 + - - -
152A HIS* 1.3 74.2 - - - +
154A GLY* 1.3 63.0 + - - +
155A VAL* 3.2 26.0 + - - +
160A ILE* 4.9 1.2 - - - +
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Residues in contact with GLY 154 (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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128A LYS* 4.7 14.6 - - - +
132A PRO* 6.3 1.3 - - - -
150A HIS 3.1 9.6 + - - -
151A GLN 3.9 4.6 + - - -
152A HIS 3.3 3.4 + - - -
153A SER* 1.3 78.8 + - - +
155A VAL* 1.3 65.4 + - - +
156A PRO* 3.7 2.9 - - - +
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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