Contacts of the helix formed by residues 147 - 159 (chain A) in PDB entry 4CNT
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 SER 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ASN* 2.9 10.2 + - - -
146A ASP* 1.3 75.5 - - - +
148A VAL* 1.3 65.6 + - - +
149A LYS 3.1 1.8 - - - -
150A GLN* 2.9 17.5 + - - +
151A GLU* 3.0 26.2 + - - +
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Residues in contact with VAL 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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116A LEU* 3.9 28.9 - - + -
141A ILE* 4.2 5.4 - - + -
143A HIS* 3.7 37.9 - - + +
144A TRP* 4.1 11.9 - - + -
145A ASN* 3.2 40.1 + - - +
147A SER* 1.3 77.5 - - - +
149A LYS* 1.3 64.1 + - - +
151A GLU* 3.1 12.5 + - - +
152A VAL* 2.9 23.4 + - + +
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Residues in contact with LYS 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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144A TRP* 3.8 32.9 - - + -
145A ASN 3.3 10.3 + - - +
146A ASP* 3.5 25.1 - - - +
148A VAL* 1.3 82.0 - - - +
150A GLN* 1.3 60.7 + - - +
152A VAL* 3.5 5.6 + - - +
153A GLN* 3.4 19.6 + - - +
187A CYS* 4.4 19.6 - - + +
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Residues in contact with GLN 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 ASP 3.6 7.0 + - - +
147A SER* 2.9 15.4 + - - +
149A LYS* 1.3 78.4 - - - +
151A GLU* 1.3 66.6 + - + +
153A GLN* 3.2 24.1 + - - +
154A ASN* 3.0 58.7 + - - +
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Residues in contact with GLU 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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114A SER 4.7 0.9 - - - +
115A SER* 2.7 26.6 + - - -
116A LEU* 3.0 37.5 + - + +
117A THR* 2.5 30.1 + - - +
147A SER* 3.0 21.0 + - - +
148A VAL* 3.1 14.1 + - - +
150A GLN* 1.3 77.6 - - + +
152A VAL* 1.3 57.5 + - - +
154A ASN* 3.1 10.8 + - - +
155A LEU* 2.8 35.8 + - + +
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Residues in contact with VAL 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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116A LEU* 4.1 9.9 - - + -
141A ILE* 4.0 24.7 - - + -
144A TRP* 4.7 4.3 - - + -
148A VAL* 2.9 24.2 + - + +
149A LYS* 3.7 8.7 - - - +
150A GLN 3.2 0.2 - - - -
151A GLU* 1.3 77.3 - - - +
153A GLN* 1.3 65.0 + - - +
155A LEU* 3.3 9.2 + - - +
156A ILE* 3.1 31.1 + - + +
164A PHE* 3.8 21.0 - - + -
187A CYS* 4.6 4.7 - - - -
188A LEU* 4.0 21.1 - - + -
191A LEU* 4.1 9.6 - - + -
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Residues in contact with GLN 153 (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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149A LYS 3.4 10.2 + - - +
150A GLN* 3.2 31.0 + - - +
151A GLU 3.1 0.2 - - - -
152A VAL* 1.3 82.8 - - - +
154A ASN* 1.3 58.0 + - - +
156A ILE* 3.4 3.3 + - - +
157A LYS* 3.0 37.0 + - + +
191A LEU* 3.9 38.3 - - + +
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Residues in contact with ASN 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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117A THR* 5.5 5.5 + - + +
150A GLN* 3.0 45.7 + - - +
151A GLU* 3.1 11.5 + - - +
153A GLN* 1.3 77.0 - - - +
155A LEU* 1.3 60.2 + - + +
157A LYS* 4.4 10.3 - - - +
158A ASP* 2.8 44.9 + - - +
159A LYS* 3.7 4.9 + - + +
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Residues in contact with LEU 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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116A LEU* 4.2 23.8 - - + -
117A THR* 4.4 14.8 - - + +
120A TYR* 3.9 31.2 - - + -
139A VAL* 4.3 7.9 - - + -
151A GLU* 2.8 29.5 + - + +
152A VAL* 3.3 4.7 + - - +
154A ASN* 1.3 73.3 - - - +
156A ILE* 1.3 58.9 + - - +
159A LYS* 2.9 50.3 + - + +
160A GLY 3.4 5.2 + - - -
161A VAL* 3.4 12.2 + - + -
164A PHE* 3.9 27.8 - - + -
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Residues in contact with ILE 156 (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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152A VAL* 3.1 21.6 + - + +
153A GLN* 3.8 4.0 - - - +
155A LEU* 1.3 79.3 - - - +
157A LYS* 1.3 63.3 + - + +
159A LYS 4.6 0.9 + - - -
160A GLY* 4.6 4.5 + - - -
161A VAL 3.2 22.0 - - - +
162A ASN* 4.6 1.8 - - - -
164A PHE* 3.6 24.9 - - + -
191A LEU* 3.9 38.8 - - + +
193A ALA* 4.0 12.6 - - + -
471A CYS 5.4 1.0 - - - +
473A PRO* 3.8 39.8 - - + +
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Residues in contact with LYS 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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153A GLN* 3.0 25.6 + - + +
154A ASN* 3.8 11.2 - - - +
156A ILE* 1.3 80.5 - - - +
158A ASP* 1.3 81.1 + - - +
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Residues in contact with ASP 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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154A ASN* 2.8 26.2 + - + +
157A LYS* 1.3 110.7 + - - +
159A LYS* 1.3 77.2 + - + +
160A GLY 3.7 1.8 - - - -
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Residues in contact with LYS 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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117A THR* 4.4 19.3 - - + -
120A TYR* 2.5 48.1 + - + +
121A GLU* 3.9 19.1 + - - -
154A ASN* 3.9 4.9 - - + +
155A LEU* 2.9 43.4 + - + +
158A ASP* 1.3 93.8 - - + +
160A GLY* 1.3 63.3 + - - +
161A VAL* 3.2 1.4 + - + -
468A PHE* 3.5 7.3 - - - -
470A PRO* 5.4 0.4 - - - -
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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