Contacts of the strand formed by residues 146 - 152 (chain B) in PDB entry 3A4Y
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 ALA 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B LEU 5.4 0.2 - - - +
58B THR* 2.7 36.9 + - - +
83B THR* 4.8 1.6 - - + -
123B TYR* 3.9 5.6 - - + -
136B PHE* 3.4 41.3 - - + -
137B GLY 3.1 11.9 - - - +
139B ALA* 3.6 7.2 - - - +
144B GLY 4.5 3.1 - - - +
145B SER* 1.3 76.4 - - - +
147B PHE* 1.3 61.4 + - - +
160B SER 3.8 5.4 - - - +
161B GLY* 4.5 0.3 - - - -
162B ASP 5.0 0.7 + - - +
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Residues in contact with PHE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR* 4.8 0.4 - - - -
136B PHE* 3.4 6.9 - - - -
137B GLY* 3.0 56.4 + - - -
138B GLN 3.7 13.0 - - - -
139B ALA* 4.2 5.2 - - + -
146B ALA* 1.3 74.9 - - - +
148B VAL* 1.3 75.6 + - - +
149B VAL* 3.7 22.9 - - + -
158B VAL* 4.2 9.0 - - + -
159B TYR 3.3 8.1 - - - +
160B SER* 3.2 24.0 - - - +
163B LEU* 5.2 0.7 - - + -
175B SER* 3.4 25.1 - - - -
176B LEU 3.9 17.0 - - - -
177B PRO* 3.9 8.3 - - + -
178B PRO* 4.2 8.3 - - + -
389B TRP* 3.9 12.8 - + + -
126C TRP* 4.4 6.1 - + - -
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 4.6 12.6 - - + -
56B LEU* 4.0 14.4 - - + -
58B THR* 4.1 16.6 - - + -
134B LEU* 3.9 18.6 - - + -
135B ALA 3.8 4.7 - - - +
136B PHE* 3.7 24.9 - - + -
147B PHE* 1.3 80.8 - - - +
149B VAL* 1.3 79.4 + - - +
150B ALA* 4.5 2.0 - - + +
157B LEU* 3.7 1.1 - - + +
158B VAL* 3.2 9.0 - - - +
159B TYR* 2.6 53.4 + - + +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TRP* 4.3 12.1 - - + -
133B SER 3.7 0.2 - - - +
134B LEU* 3.2 8.0 - - - +
135B ALA 2.9 38.2 + - - +
136B PHE 5.8 0.2 - - - -
137B GLY 5.6 0.7 - - - +
147B PHE* 3.7 23.8 - - + -
148B VAL* 1.3 78.6 - - - +
150B ALA* 1.3 67.1 + - - +
151B GLN* 4.9 3.4 - - + +
156B THR* 4.7 8.7 - - + -
157B LEU 3.6 5.8 - - - +
158B VAL* 4.3 1.8 - - + -
178B PRO* 3.7 27.1 - - + -
126C TRP* 3.8 29.4 - - + +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.5 4.0 - - - +
19B LEU* 4.0 18.2 - - + -
132B LEU* 4.3 4.9 - - + -
133B SER 3.3 4.3 - - - +
134B LEU* 3.4 23.3 - - + -
148B VAL* 4.8 3.4 - - + -
149B VAL* 1.3 75.1 - - - +
151B GLN* 1.3 60.5 + - - +
152B GLY 4.3 0.6 + - - -
155B ARG 3.9 0.5 - - - +
156B THR* 3.5 3.5 - - - +
157B LEU* 2.9 50.7 + - + +
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Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TRP* 5.1 9.6 - - + -
131B ALA 4.3 0.3 - - - +
132B LEU* 3.8 4.0 - - - +
133B SER* 2.8 44.3 + - - +
149B VAL* 4.2 5.8 - - + -
150B ALA* 1.3 74.5 - - - +
152B GLY* 1.3 78.6 + - - +
153B GLU 4.2 0.2 - - - +
154B GLY* 3.7 10.9 - - - +
155B ARG 3.3 25.1 + - - +
156B THR* 3.9 10.5 - - + +
151C GLN* 4.7 7.4 - - + +
154C GLY 5.5 0.6 + - - -
156C THR* 3.7 25.6 + - + +
178C PRO* 5.6 1.7 - - + +
179C LEU* 3.4 24.8 - - - +
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Residues in contact with GLY 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.5 17.4 - - - +
131B ALA 3.8 14.1 - - - -
132B LEU* 4.4 1.1 - - - -
151B GLN* 1.3 84.9 - - - +
153B GLU* 1.3 78.2 + - - +
154B GLY 3.2 2.0 - - - -
155B ARG* 2.9 20.4 + - - +
179C LEU* 6.0 1.6 - - - -
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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