Contacts of the helix formed by residues 146 - 159 (chain A) in PDB entry 4TQ1
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 GLN 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLU 3.8 2.0 + - - +
145A MET* 1.3 77.8 - - - +
147A LYS* 1.3 66.1 + - - +
148A LYS* 3.2 32.1 - - + +
149A ASP* 2.9 27.8 + - - +
150A HIS* 3.5 4.4 + - - -
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Residues in contact with LYS 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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145A MET 3.9 0.8 + - - -
146A GLN* 1.3 73.4 - - - +
148A LYS* 1.3 61.2 + - - +
150A HIS* 3.0 31.2 + - + +
151A LYS* 3.2 13.1 + - - +
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Residues in contact with LYS 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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146A GLN* 4.2 26.1 - - + +
147A LYS* 1.3 78.4 - - - +
149A ASP* 1.3 76.7 + - - +
151A LYS* 3.3 11.1 + - + +
152A GLN* 2.9 29.1 + - - +
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Residues in contact with ASP 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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145A MET* 3.9 23.3 - - + +
146A GLN* 2.9 20.8 + - - +
148A LYS* 1.3 99.7 + - - +
150A HIS* 1.3 66.5 + - - +
152A GLN* 3.2 9.7 + - - +
153A LEU* 3.1 28.0 + - - +
168A ILE* 3.8 32.3 - - + +
171A LYS* 4.7 12.0 + - - +
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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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122A GLU* 5.7 0.7 - - - -
126A MET* 3.7 25.2 - - + +
130A LYS* 4.3 17.8 + - - -
142A ILE* 2.8 45.0 + - + +
143A ASN* 5.5 2.7 - - - -
145A MET* 4.0 29.7 - - + +
146A GLN 4.3 2.2 - - - -
147A LYS* 3.0 23.3 + - + +
149A ASP* 1.3 77.2 - - - +
151A LYS* 1.3 62.4 + - + +
153A LEU* 3.2 11.8 + - + +
154A TRP* 3.2 20.4 + - - +
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Residues in contact with LYS 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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119A ASP* 5.7 0.2 + - - -
122A GLU* 2.8 39.6 + - - +
147A LYS 3.2 10.0 + - - +
148A LYS* 3.5 13.9 - - + +
149A ASP 3.2 0.2 - - - -
150A HIS* 1.3 81.3 - - + +
152A GLN* 1.3 56.7 + - - +
154A TRP* 3.3 12.5 + - + +
155A MET* 2.8 44.1 + - + +
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Residues in contact with GLN 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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148A LYS* 2.9 17.9 + - - +
149A ASP* 3.2 9.3 + - - +
151A LYS* 1.3 72.8 - - - +
153A LEU* 1.3 60.9 + - - +
155A MET* 3.8 4.9 - - - -
156A GLY* 2.8 27.2 + - - -
164A GLN* 2.9 50.6 + - + +
167A ALA* 3.9 13.3 - - - +
168A ILE* 3.6 26.5 - - + +
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Residues in contact with LEU 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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125A PHE* 4.3 2.9 - - + -
126A MET* 4.8 1.8 - - + -
129A MET* 4.0 29.8 - - + -
142A ILE* 4.6 6.7 - - + -
145A MET* 4.4 7.4 - - - -
149A ASP 3.1 19.9 + - - +
150A HIS* 3.2 14.8 + - - +
152A GLN* 1.3 76.9 - - - +
154A TRP* 1.3 61.9 + - - +
157A LEU* 3.2 18.9 + - - +
165A PHE* 3.2 41.7 - - + +
168A ILE* 3.6 17.9 - - + -
169A ASN* 3.7 33.2 - - + +
172A LEU* 4.4 8.3 - - + -
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Residues in contact with TRP 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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47A LEU* 3.5 33.2 - - + -
118A LYS* 3.8 18.1 - - + +
121A ILE* 3.6 21.5 - - + -
122A GLU* 3.5 59.7 + - + +
125A PHE* 3.9 22.4 - + + -
126A MET* 4.8 5.4 - - - -
150A HIS 3.2 9.8 + - - +
151A LYS* 3.3 11.6 + - - +
153A LEU* 1.3 81.2 - - - +
155A MET* 1.3 74.6 + - + +
157A LEU* 3.2 25.6 + - + +
158A GLN* 2.8 45.7 + - - +
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Residues in contact with MET 155 (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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151A LYS* 2.8 35.4 + - + +
152A GLN* 4.1 1.1 - - - +
154A TRP* 1.3 86.3 - - + +
156A GLY* 1.3 59.3 + - - +
158A GLN* 3.2 30.1 - - - +
159A ASN* 2.8 64.6 + - - +
164A GLN* 3.8 20.2 - - - +
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Residues in contact with GLY 156 (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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12A TRP* 3.5 8.7 - - - -
152A GLN 2.8 18.5 + - - -
153A LEU 3.7 2.0 - - - -
154A TRP 3.2 0.4 - - - -
155A MET* 1.3 75.9 - - - +
157A LEU* 1.3 60.1 + - - +
160A ASP 3.1 2.3 + - - -
161A ARG 2.8 40.1 + - - -
164A GLN* 3.6 17.0 + - - -
165A PHE* 4.2 5.4 - - - -
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Residues in contact with LEU 157 (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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12A TRP* 3.9 13.3 - - + -
42A VAL* 4.0 23.8 - - + +
43A SER* 3.9 21.9 + - - +
44A TYR* 3.8 27.4 - - + -
47A LEU* 4.0 6.3 - - + -
125A PHE* 3.9 23.1 - - + -
153A LEU 3.2 11.5 + - - +
154A TRP* 3.2 26.8 + - + +
156A GLY* 1.3 74.8 - - - +
158A GLN* 1.3 66.0 + - - +
160A ASP* 3.1 13.0 + - - +
165A PHE* 4.8 1.1 - - + -
261A PRO* 4.1 16.6 - - + -
604B VAL* 6.0 0.7 - - - +
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Residues in contact with GLN 158 (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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47A LEU* 4.1 24.3 - - + +
48A VAL* 6.0 0.5 - - - +
118A LYS* 3.6 34.7 - - - +
154A TRP* 2.8 42.6 + - + +
155A MET* 3.2 34.4 - - - +
157A LEU* 1.3 74.1 - - - +
159A ASN* 1.3 68.5 + - - +
160A ASP 3.6 0.5 + - - -
604B VAL* 3.9 17.8 - - - +
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Residues in contact with ASN 159 (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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155A MET* 2.8 47.6 + - - +
158A GLN* 1.3 88.2 - - - +
160A ASP* 1.3 72.2 + - - +
161A ARG* 3.3 19.8 + - + +
164A GLN* 4.8 3.8 + - - +
604B VAL* 4.3 7.9 - - - +
605B GLU 5.0 4.4 - - - +
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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