Contacts of the helix formed by residues 140 - 146 (chain A) in PDB entry 1NUA
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 6.3 1.3 - - + -
114A GLY* 3.7 17.9 - - - +
115A GLY 4.4 1.8 + - - +
139A THR* 1.3 86.8 - - + +
141A LEU* 1.3 59.4 + - - +
142A LEU* 4.3 5.0 - - - +
143A ALA* 2.9 27.6 + - - +
144A MET* 2.9 32.6 + - - +
183A LEU* 4.0 20.4 - - + -
187A GLU* 4.3 17.9 - - + +
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Residues in contact with LEU 141 (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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140A THR* 1.3 72.8 - - - +
142A LEU* 1.3 62.9 + - - +
144A MET* 3.0 14.0 + - + +
145A VAL* 3.2 18.7 + - + +
180A LEU* 3.9 23.7 - - + +
183A LEU* 3.3 16.1 - - + +
187A GLU 4.5 1.5 + - - +
188A PHE* 3.3 37.2 - - + +
191A GLY* 3.6 10.5 - - - +
192A MET* 3.4 32.1 - - + +
195A VAL* 4.6 2.2 - - + -
243A ILE* 3.9 35.4 - - + -
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Residues in contact with LEU 142 (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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115A GLY* 6.1 4.5 - - - +
140A THR* 3.3 6.4 - - - +
141A LEU* 1.3 77.9 - - - +
143A ALA* 1.3 58.0 + - - +
145A VAL* 4.6 1.8 - - - -
146A ASP* 3.1 31.3 + - + +
147A SER* 3.2 14.0 + - - +
187A GLU* 5.1 5.1 + - - +
190A ASN* 4.4 21.3 - - - +
191A GLY* 3.9 16.8 - - - -
194A GLU* 3.2 41.1 - - + +
287A HIS* 4.4 21.1 - - + -
288A GLY 5.5 0.7 - - - +
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Residues in contact with ALA 143 (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 GLY* 3.9 17.7 - - - -
115A GLY 4.0 2.2 - - - +
138A PRO* 3.5 16.4 - - + -
140A THR* 2.9 23.5 + - - +
141A LEU 3.1 0.8 - - - -
142A LEU* 1.3 77.0 - - - +
144A MET* 1.3 58.6 + - - +
145A VAL 3.6 0.2 + - - -
147A SER* 3.2 21.5 + - - +
148A SER* 2.7 38.5 + - - +
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Residues in contact with MET 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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138A PRO* 3.5 35.9 - - + +
139A THR 3.9 6.3 - - - +
140A THR 2.9 12.6 + - - +
141A LEU* 3.0 11.8 + - + +
143A ALA* 1.3 79.3 - - - +
145A VAL* 1.3 64.9 + - + +
148A SER* 3.5 0.7 + - - -
149A ILE* 3.5 14.9 - - - +
175A ILE* 3.4 41.3 - - + +
176A ASP 3.3 24.9 - - - +
177A LEU* 4.4 5.8 - - - -
179A PHE* 3.6 16.8 - - + -
180A LEU* 3.7 36.6 - - + -
243A ILE* 5.1 0.9 - - + -
247A ALA* 4.1 1.7 - - - +
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Residues in contact with VAL 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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141A LEU* 3.5 19.1 - - + +
142A LEU* 4.1 3.4 - - - +
144A MET* 1.3 78.4 - - - +
146A ASP* 1.3 66.2 + - + +
149A ILE* 4.2 3.4 - - - -
191A GLY 4.5 1.8 - - - +
194A GLU* 4.5 10.5 - - + -
195A VAL* 4.0 19.5 - - + -
243A ILE* 3.4 45.1 - - + +
246A SER* 3.9 17.7 + - - +
247A ALA* 3.8 15.8 + - + +
250A LYS* 3.5 24.1 - - - +
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Residues in contact with ASP 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* 3.1 23.2 + - + +
144A MET 3.6 0.8 - - - -
145A VAL* 1.3 84.1 - - + +
147A SER* 1.3 69.0 + - - +
148A SER 3.6 1.6 - - - -
149A ILE* 2.9 11.8 + - - +
194A GLU* 3.8 15.0 - - + +
197A LYS* 4.3 11.5 + - - -
250A LYS* 2.8 48.1 + - - +
267A LEU* 5.7 0.7 - - - +
600A ZN 3.5 21.3 - - - -
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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