Contacts of the strand formed by residues 178 - 184 (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 THR 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A GLY 3.2 4.6 + - - -
135A ARG* 3.5 41.1 - - - +
136A VAL* 2.7 31.5 + - - +
176A ASN 5.1 0.7 - - - +
177A ILE* 1.3 80.9 - - - +
179A ALA* 1.3 56.6 + - - +
180A ASN* 4.5 5.4 + - - -
231A ALA 4.9 1.4 + - - +
232A ARG 4.1 9.0 - - - +
234A ILE 3.7 23.3 + - - +
235A THR* 3.4 7.0 - - - -
210C MSE 3.6 28.7 - - + -
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Residues in contact with ALA 179 (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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136A VAL* 3.4 11.7 - - + -
165A THR* 3.5 15.6 - - + +
168A LEU* 4.0 24.5 - - + -
169A ALA* 3.7 23.6 - - - +
172A LEU* 5.4 2.2 - - + -
177A ILE 4.1 0.8 + - - +
178A THR* 1.3 73.9 - - - +
180A ASN* 1.3 60.7 + - - +
235A THR* 3.1 7.5 + - - -
236A GLY* 2.9 25.6 + - - -
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Residues in contact with ASN 180 (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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136A VAL* 2.8 12.9 + - - +
137A ILE* 3.4 5.7 - - + +
138A SER* 3.0 22.8 + - - -
165A THR* 3.7 9.9 + - - +
178A THR* 4.5 7.1 + - - -
179A ALA* 1.3 72.7 - - - +
181A ALA* 1.3 64.4 + - - +
226A LEU* 4.3 28.7 + - + +
231A ALA 4.9 1.6 + - - -
234A ILE* 2.7 40.9 + - - +
235A THR* 3.2 3.0 - - - +
236A GLY 3.0 9.5 + - - -
237A GLN 2.9 34.3 + - - +
239A LEU* 6.2 1.1 - - + -
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Residues in contact with ALA 181 (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 SER* 3.1 15.5 - - - +
140A ALA* 4.8 4.3 - - + -
161A VAL* 5.1 1.3 - - + -
162A ILE* 4.8 11.2 - - + -
165A THR* 3.8 19.3 - - + +
180A ASN* 1.3 78.3 - - - +
182A VAL* 1.3 68.3 + - - +
226A LEU* 4.6 0.9 - - - +
237A GLN 3.0 5.1 + - - +
238A THR* 3.1 22.6 - - + +
239A LEU* 2.8 24.8 + - - +
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Residues in contact with VAL 182 (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* 4.1 11.4 - - + -
138A SER 3.0 7.1 + - - +
139A ILE* 3.6 10.2 - - + -
140A ALA* 2.6 32.6 + - - -
181A ALA* 1.3 79.4 - - - +
183A THR* 1.3 67.2 - - - +
184A PRO* 3.2 11.0 - - + +
219A ILE* 4.8 11.0 - - + -
222A VAL* 5.1 6.1 - - + -
223A VAL* 4.6 11.7 - - + -
226A LEU* 3.5 27.6 - - + -
239A LEU* 3.1 14.4 - - + +
241A VAL* 3.8 23.1 - - + -
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Residues in contact with THR 183 (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 ALA* 3.9 7.9 - - + -
141A SER 3.1 33.0 - - - +
142A ASN* 3.6 2.0 - - - -
145A PHE* 3.4 13.9 - - + -
162A ILE* 4.3 4.9 - - + -
182A VAL* 1.3 73.9 - - - +
184A PRO* 1.3 64.5 - - - +
238A THR* 3.4 21.3 - - + +
239A LEU 2.7 10.2 + - - -
240A ASN* 2.5 43.2 + - - +
241A VAL 2.9 20.6 + - - +
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Residues in contact with PRO 184 (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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19A ILE* 4.8 1.3 - - + -
139A ILE* 3.9 13.9 - - + -
140A ALA 3.7 5.4 - - - +
141A SER* 3.7 11.2 - - - -
142A ASN* 2.9 21.4 + - - -
182A VAL* 3.2 14.6 - - + +
183A THR* 1.3 86.1 - - - +
185A GLY* 1.3 68.1 + - - +
187A ILE* 4.2 2.7 - - + -
219A ILE* 3.6 33.2 - - + -
241A VAL* 3.5 8.1 - - + +
251A NAD 3.2 30.5 - - + +
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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