Contacts of the strand formed by residues 141 - 149 (chain A) in PDB entry 3N2N
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TYR* 3.9 7.8 - - - -
42A GLY* 3.3 20.4 - - - -
44A ASP* 4.2 16.2 + - - +
79A ARG* 5.7 2.5 - - - +
134A GLU* 5.8 8.3 - - + +
135A ASN* 4.9 7.3 + - - -
139A TYR* 3.2 30.4 + - + +
140A ARG* 1.3 77.8 - - - +
142A ALA* 1.3 59.2 + - - +
143A SER* 3.3 23.8 + - - -
172A GLY 5.3 2.3 - - - +
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Residues in contact with ALA 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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40A TYR* 3.6 24.6 - - + -
42A GLY 2.9 9.2 + - - +
43A PHE* 3.4 10.5 - - + -
44A ASP 2.8 29.8 + - - +
141A THR* 1.3 71.2 - - - +
143A SER* 1.3 58.7 + - - +
144A VAL* 3.8 7.2 - - + -
174A ILE* 5.8 6.3 - - + -
215A ILE* 3.7 31.4 - - + -
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.5 13.1 + - - +
46A TYR* 4.4 14.1 + - - -
131A ILE* 4.4 15.5 - - - +
134A GLU* 6.1 0.7 - - - +
135A ASN* 5.2 1.6 + - - -
141A THR* 3.3 24.1 + - - -
142A ALA* 1.3 68.3 - - - +
144A VAL* 1.3 62.1 + - - +
172A GLY 4.1 8.2 + - - +
173A ALA* 3.2 19.6 - - - +
174A ILE* 2.9 28.6 + - - +
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Residues in contact with VAL 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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43A PHE* 3.8 22.2 - - + -
44A ASP 2.9 8.5 + - - +
45A LEU* 3.4 24.7 - - + +
46A TYR* 2.8 27.1 + - - -
142A ALA* 4.3 7.6 - - + -
143A SER* 1.3 78.3 - - - +
145A ILE* 1.3 66.6 + - - +
146A ILE* 4.1 2.5 - - + -
174A ILE* 3.4 15.9 - - + +
176A TYR* 3.6 34.3 - - + -
208A LEU* 5.5 1.8 - - + -
211A ILE* 5.9 0.9 - - + -
212A ILE* 6.4 0.4 - - + -
215A ILE* 4.1 15.7 - - + -
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Residues in contact with ILE 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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46A TYR* 3.3 26.2 - - + +
48A ILE* 3.6 22.9 - - + -
124A PHE* 4.0 19.5 - - + -
127A ALA* 3.9 17.3 - - + -
131A ILE* 4.1 2.7 - - + -
143A SER 4.2 0.2 + - - -
144A VAL* 1.3 74.0 - - - +
146A ILE* 1.3 65.5 + - - +
147A ALA 4.2 1.6 - - - +
168A SER* 3.8 32.8 - - - +
173A ALA* 4.0 14.1 - - + -
174A ILE 2.8 13.9 + - - +
175A VAL* 4.1 10.5 - - + -
176A TYR* 2.7 36.4 + - - +
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Residues in contact with ILE 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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45A LEU* 3.6 28.9 - - + -
46A TYR 2.9 9.3 + - - +
47A PHE* 3.4 25.8 - - + -
48A ILE 2.8 24.5 + - - +
65A PHE* 4.4 3.1 - - + -
69A LEU* 4.2 10.1 - - + -
144A VAL* 4.1 2.7 + - + -
145A ILE* 1.3 77.0 - - - +
147A ALA* 1.3 60.8 + - - +
148A LEU* 3.6 25.0 + - + +
176A TYR* 3.5 5.8 - - + +
178A VAL* 3.9 20.9 - - + -
208A LEU* 3.9 35.4 - - + -
212A ILE* 4.7 2.7 - - + -
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Residues in contact with ALA 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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48A ILE* 3.2 16.2 - - + +
120A MET* 4.7 12.6 - - - -
124A PHE* 4.2 28.0 - - + -
145A ILE* 4.0 1.7 - - + -
146A ILE* 1.3 71.6 - - - +
148A LEU* 1.3 58.8 + - - +
149A THR* 3.9 3.3 + - + +
175A VAL* 5.3 0.2 - - + -
176A TYR 2.9 15.9 + - - +
177A ALA* 3.4 9.0 - - + +
178A VAL 2.8 31.4 + - - +
191A ILE* 5.3 1.8 - - + -
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Residues in contact with LEU 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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47A PHE* 4.6 3.6 - - + -
48A ILE 2.9 8.3 + - - +
49A LEU* 3.8 28.3 - - + -
50A ASP* 2.9 30.6 + - - +
62A ILE* 3.9 28.9 - - + +
65A PHE* 4.1 31.2 - - + -
66A VAL* 4.8 0.2 - - + -
85A PHE* 4.4 0.7 - - - -
146A ILE* 3.6 29.2 - - + +
147A ALA* 1.3 70.7 - - - +
149A THR* 1.3 61.6 + - - +
178A VAL* 3.4 34.1 - - + +
180A VAL* 4.8 2.2 - - + -
201A VAL* 4.4 9.0 - - + -
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Residues in contact with THR 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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50A ASP* 2.7 27.3 + - - -
85A PHE* 4.3 1.1 - - - -
120A MET* 4.0 25.6 - - + -
147A ALA* 4.6 8.3 - - + +
148A LEU* 1.3 76.9 - - - +
150A ASP* 1.3 64.1 + - - +
151A GLY* 3.0 17.3 + - - +
153A LEU* 4.2 8.3 - - - +
177A ALA* 5.6 1.3 - - + -
178A VAL 3.2 4.2 + - - -
179A GLY* 3.3 9.4 - - - -
180A VAL* 3.0 27.9 + - - +
188A LEU* 3.8 25.0 - - + +
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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