Contacts of the helix formed by residues 143 - 152 (chain A) in PDB entry 7NG0
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 THR 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ILE* 3.7 4.8 - - - +
142A LEU* 1.3 76.5 - - - +
144A GLN* 1.3 58.0 + - - +
145A GLU* 3.2 12.9 + - - +
146A ALA* 2.9 40.5 + - + +
147A LEU 3.0 11.1 + - - -
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Residues in contact with GLN 144 (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 ILE* 4.0 10.7 - - + +
143A THR* 1.3 71.7 - - - +
145A GLU* 1.3 55.6 + - - +
147A LEU* 3.6 3.0 - - - +
148A ALA* 3.1 26.7 + - - +
155A GLN* 4.5 9.1 - - + +
158A ILE* 3.9 15.5 - - + +
159A ALA* 3.5 33.9 - - - +
162A LEU* 3.6 27.4 - - + +
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Residues in contact with GLU 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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143A THR* 3.1 9.5 + - - +
144A GLN* 1.3 77.2 - - - +
146A ALA* 1.3 58.9 + - - +
148A ALA* 3.4 7.1 + - - +
149A GLN* 3.0 32.2 + - - +
155A GLN* 4.7 14.6 - - + +
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Residues in contact with ALA 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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142A LEU* 3.6 29.0 - - + +
143A THR* 2.9 33.2 + - + +
145A GLU* 1.3 73.9 - - - +
147A LEU* 1.3 61.8 + - - +
149A GLN* 3.5 10.9 + - - +
150A ARG* 3.2 23.9 + - - +
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Residues in contact with LEU 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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133A TYR* 3.4 37.0 - - + +
136A LEU* 3.6 31.6 - - + +
137A ILE* 3.7 24.7 - - + +
142A LEU* 4.4 10.3 - - + +
143A THR 3.0 9.9 + - - +
144A GLN 3.6 8.3 - - - +
146A ALA* 1.3 71.3 - - - +
148A ALA* 1.3 65.5 + - - +
150A ARG* 3.0 7.6 + - + +
151A LEU* 2.9 43.7 + - + +
158A ILE* 3.6 23.8 - - + -
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Residues in contact with ALA 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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144A GLN 3.1 14.5 + - - +
145A GLU 3.6 6.1 - - - +
147A LEU* 1.3 76.9 - - - +
149A GLN* 1.3 56.9 + - - +
151A LEU* 5.1 0.2 - - - -
152A GLY* 3.0 23.4 + - - -
153A LYS 3.0 30.4 + - - +
154A GLY 3.7 2.5 - - - +
155A GLN* 3.5 31.4 - - + +
158A ILE* 4.0 11.5 - - + +
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Residues in contact with GLN 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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57A LEU* 4.4 8.8 - - - +
145A GLU 3.0 18.3 + - - +
146A ALA* 3.7 10.4 - - - +
147A LEU 3.2 0.2 - - - -
148A ALA* 1.3 76.0 - - - +
150A ARG* 1.3 61.4 + - - +
152A GLY* 3.8 7.1 + - - -
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Residues in contact with ARG 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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57A LEU* 4.6 10.2 - - - +
58A THR* 4.2 14.4 + - + +
61A THR* 5.1 17.9 - - - -
140A HIS* 3.7 49.2 + - - +
142A LEU* 4.1 14.2 - - + +
146A ALA 3.2 16.6 + - - +
147A LEU* 3.0 7.7 + - + +
149A GLN* 1.3 77.5 - - - +
151A LEU* 1.3 69.3 + - + +
152A GLY 3.7 0.3 + - - -
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Residues in contact with LEU 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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54A GLU* 3.2 31.7 - - - +
57A LEU* 5.1 0.2 - - - -
58A THR* 4.9 12.0 - - + +
133A TYR* 3.4 39.3 - - + -
136A LEU* 4.1 20.0 - - + -
147A LEU* 2.9 35.8 + - + +
148A ALA 4.5 0.9 - - - +
150A ARG* 1.3 84.6 - - + +
152A GLY* 1.3 57.6 + - - +
153A LYS* 3.4 8.2 + - + +
158A ILE* 4.0 9.0 - - + -
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Residues in contact with GLY 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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50A GLU 4.5 2.4 - - - +
53A ASP* 6.0 0.5 - - - +
54A GLU* 3.2 19.5 + - - +
57A LEU* 3.7 26.4 - - - +
148A ALA 3.0 8.6 + - - -
149A GLN* 4.3 2.2 - - - -
150A ARG 3.4 3.4 + - - -
151A LEU* 1.3 78.5 - - - +
153A LYS* 1.3 58.1 + - - +
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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