Contacts of the strand formed by residues 149 - 154 (chain A) in PDB entry 3APO
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 TRP 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ILE* 4.1 37.0 - - + -
134A LEU* 3.9 25.8 - - + -
142A ALA* 3.1 32.1 + - + -
143A VAL* 3.6 24.9 - - + -
145A SER* 3.8 5.9 + - - -
147A GLU* 3.1 30.7 + - - +
148A LEU* 1.3 77.4 - - - +
150A PHE* 1.3 59.4 + - - +
151A VAL* 4.1 10.5 - - + -
179A LEU* 4.8 0.2 - - - -
180A ARG* 3.4 32.2 - - + +
182A GLY* 4.4 6.3 - - - -
206A ILE* 3.3 11.0 - - - +
207A PHE* 2.8 48.7 + - + +
441A TYR* 3.6 30.5 - + + -
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Residues in contact with PHE 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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149A TRP* 1.3 72.9 - - - +
151A VAL* 1.3 60.6 + - - +
168A TRP* 3.3 25.5 - + - -
171A PHE* 3.6 17.3 - + - -
179A LEU* 4.0 10.3 - - + -
180A ARG 2.9 7.5 + - - -
181A ILE* 3.6 18.1 - - + -
182A GLY 3.1 19.4 + - - -
204A LEU* 3.9 18.4 - - + -
205A PHE 3.1 20.9 - - - -
206A ILE* 3.4 20.4 - - + -
216A TYR* 4.1 7.4 - - + -
225A LEU* 3.5 45.3 - - + -
228A PHE* 3.9 20.2 - + - -
229A ALA* 4.4 1.3 - - + -
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Residues in contact with VAL 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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134A LEU* 4.4 4.5 - - + -
139A PHE* 4.4 1.3 - - + -
143A VAL* 4.4 16.2 - - + -
149A TRP* 4.4 14.6 - - + -
150A PHE* 1.3 76.2 - - - +
152A ASN* 1.3 66.2 + - - +
153A PHE* 3.6 23.5 + - + -
168A TRP* 4.0 2.9 - - - -
182A GLY* 3.3 11.9 - - - +
184A VAL* 3.8 24.0 - - + -
203A SER 3.6 1.2 - - - +
204A LEU* 3.5 5.0 - - - -
205A PHE 2.9 31.8 + - - -
207A PHE* 3.7 30.5 - - + -
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Residues in contact with ASN 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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125A TYR* 3.0 34.8 + - - -
151A VAL* 1.3 71.6 - - - +
153A PHE* 1.3 74.4 + - - +
154A TYR* 3.6 11.7 - - - +
161A SER* 5.4 1.4 + - - +
164A LEU* 3.9 16.2 - - - +
168A TRP* 3.4 31.7 - - + +
182A GLY 2.8 10.0 + - - +
183A ALA* 3.3 4.1 - - - -
184A VAL 2.8 25.7 + - - +
202A PRO* 5.2 1.4 - - - +
203A SER 3.7 3.3 + - - +
204A LEU* 3.6 17.6 - - + +
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Residues in contact with PHE 153 (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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139A PHE* 3.9 25.6 - + - -
151A VAL* 3.6 29.2 - - + -
152A ASN* 1.3 73.4 - - - +
154A TYR* 1.3 59.4 + - - +
184A VAL* 3.5 34.1 - - + -
186A CYS* 3.9 16.6 - - - -
192A LEU* 5.0 9.6 - - + -
193A CYS* 4.0 10.1 - - + -
202A PRO* 3.4 6.0 - - - +
203A SER* 2.8 51.2 + - - +
205A PHE* 3.9 26.7 - + + -
207A PHE* 4.2 8.7 - + - -
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Residues in contact with TYR 154 (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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123A GLY* 5.9 0.9 - - - -
124A ILE* 4.2 26.7 + - + +
125A TYR* 3.9 28.3 + + + +
133A THR* 5.1 6.2 - - - +
152A ASN* 3.6 21.8 - - - +
153A PHE* 1.3 74.7 - - - +
155A SER* 1.3 84.0 + - - +
156A PRO* 4.8 0.9 - - + -
161A SER* 3.4 24.0 - - - +
183A ALA* 3.8 18.6 - - + +
184A VAL 3.1 24.8 + - - -
185A ASN* 3.2 39.6 + - + +
186A CYS* 3.3 29.1 + - - +
202A PRO* 4.7 4.5 - - - -
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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