Contacts of the helix formed by residues 142 - 147 (chain A) in PDB entry 3NDR
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 ASN 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A SER* 1.3 71.6 + - - +
143A THR* 1.3 70.9 + - - +
144A PHE 3.0 5.6 - - - -
145A PHE* 3.0 22.5 + - + +
146A ALA* 3.2 12.3 + - - +
148A THR* 5.5 0.4 + - - -
183A THR* 3.8 3.6 - - - -
184A PRO 2.9 15.2 + - - +
185A GLY* 3.2 24.9 - - - -
186A LEU 4.6 0.8 - - - +
240A ASN* 3.3 24.2 - - - +
242A ASP* 2.9 21.6 - - - +
245A MSE 3.9 21.0 - - - +
246A VAL* 4.3 5.2 - - + +
251A NAD 5.2 0.4 - - - -
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Residues in contact with THR 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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141A SER* 3.0 23.2 + - - +
142A ASN* 1.3 85.0 - - - +
144A PHE* 1.3 59.3 + - - +
146A ALA* 3.6 0.9 - - - -
147A GLY* 2.8 30.1 + - - -
148A THR* 3.5 37.1 + - + +
151A MSE 4.1 17.7 - - + -
154A TYR* 3.7 11.8 - - + -
155A VAL* 3.5 22.0 - - - +
158A LYS* 4.9 0.9 - - - +
251A NAD 5.6 2.0 - - + -
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER 3.6 13.6 + - - +
142A ASN 3.0 0.2 - - - -
143A THR* 1.3 84.3 + - - +
145A PHE* 1.3 79.6 + + - +
147A GLY 4.4 0.5 + - - -
155A VAL* 3.8 10.3 - - + +
158A LYS* 4.9 4.0 - - + -
159A GLY* 3.4 35.2 - - - +
162A ILE* 3.5 26.2 - - + -
166A ARG* 6.3 0.9 - - - -
144D PHE* 3.7 29.6 - + - -
159D GLY 4.1 2.9 - - - -
162D ILE* 4.4 7.6 - - + -
163D GLY* 3.7 27.4 - - - -
166D ARG* 3.2 46.4 + - - +
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Residues in contact with PHE 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 SER 4.8 0.7 - - - -
142A ASN* 3.0 16.4 + - - +
144A PHE* 1.3 101.4 - + - +
146A ALA* 1.3 58.0 + - - +
147A GLY 3.6 0.4 - - - -
162A ILE* 5.0 2.5 - - + -
166A ARG* 6.0 1.8 - - - -
183A THR* 3.4 35.9 - - + -
238A THR* 4.4 6.5 - - + -
240A ASN* 4.0 6.7 - - + -
246A VAL* 3.9 32.9 - - + +
247A ARG 6.1 0.2 - - - -
248A HIS* 3.5 43.5 - + + -
247B ARG* 3.5 28.2 + - - +
166D ARG* 3.8 11.2 - - - +
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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 ASN 3.2 14.5 + - - +
143A THR* 4.1 0.4 - - - +
145A PHE* 1.3 80.7 - - - +
147A GLY* 1.3 62.4 + - - +
148A THR* 3.5 17.7 + - - +
245A MSE 5.4 9.2 - - + -
246A VAL* 4.4 14.8 - - + -
245B MSE 5.6 1.4 - - - +
247B ARG* 3.8 21.3 + - - +
170D THR* 4.5 0.2 - - - +
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Residues in contact with GLY 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 THR 2.8 10.7 + - - -
144A PHE 4.3 1.0 + - - -
145A PHE 3.6 1.6 - - - -
146A ALA* 1.3 79.2 - - - +
148A THR* 1.3 68.6 + - - +
149A PRO* 3.4 0.7 - - - +
155A VAL* 4.8 0.7 - - - -
247B ARG* 3.9 3.3 - - - +
166D ARG* 3.8 29.2 - - - -
167D ALA* 3.6 8.9 - - - -
170D THR* 2.7 25.5 + - - +
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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