Contacts of the strand formed by residues 148 - 155 (chain A) in PDB entry 3DF0
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 GLU 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ILE* 4.6 17.6 - - + +
144A TRP* 3.6 4.5 - - - -
145A GLN* 2.8 37.0 + - - +
146A TYR 4.3 3.1 - - - +
147A GLY* 1.3 88.6 - - - +
149A TRP* 1.3 69.4 + - - +
150A VAL* 3.8 9.3 + - + -
360A LYS* 4.3 9.6 + - - +
641A GLN* 5.1 8.1 - - - +
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Residues in contact with TRP 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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24A ALA* 3.6 17.4 - - + -
25A ILE* 2.8 27.6 + - - +
123A ARG* 3.7 57.4 - - + +
124A VAL* 4.9 2.5 - - + -
142A GLN* 4.3 15.9 - - + +
143A PHE* 3.4 28.3 - - - -
144A TRP* 3.5 37.0 - + + -
148A GLU* 1.3 75.2 - - - +
150A VAL* 1.3 60.9 + - - +
206A ASP 4.5 0.2 - - - -
207A PHE* 3.2 31.0 - - - -
208A THR* 3.7 23.5 + - - -
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 5.0 0.2 - - - -
25A ILE* 3.3 20.9 - - + +
27A TYR* 3.6 38.1 - - + -
142A GLN* 3.3 2.8 - - - -
143A PHE* 2.7 45.5 + - - +
145A GLN* 4.4 22.7 - - + -
148A GLU* 4.3 14.6 - - + +
149A TRP* 1.3 81.3 - - - +
151A GLU* 1.3 59.9 + - - +
152A VAL* 4.0 9.6 + - + +
188A ILE* 5.3 0.9 - - + -
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Residues in contact with GLU 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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24A ALA* 4.7 6.9 - - + +
25A ILE 3.0 11.4 + - - +
26A LYS* 3.9 28.8 - - + +
27A TYR* 3.0 25.5 + - - +
30A GLN 4.7 2.6 - - - +
31A ASP* 4.5 0.2 - - - +
32A TYR* 4.0 20.9 + - - +
140A HIS* 3.3 36.0 - - + -
141A PHE 3.2 11.7 - - - +
142A GLN* 3.9 20.1 - - + +
150A VAL* 1.3 72.9 - - - +
152A VAL* 1.3 64.0 + - - +
153A VAL* 4.4 6.0 + - + +
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Residues in contact with VAL 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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27A TYR* 3.7 19.7 - - + -
140A HIS* 3.3 3.1 - - - -
141A PHE* 2.8 34.4 + - - +
143A PHE* 3.5 35.0 - - + -
150A VAL* 4.0 17.3 - - + +
151A GLU* 1.3 80.1 - - - +
153A VAL* 1.3 65.8 + - - +
154A VAL* 4.3 3.0 + - + -
184A ALA* 4.3 12.7 - - + +
187A LYS* 3.6 31.0 - - + -
188A ILE* 4.6 7.2 - - + +
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Residues in contact with VAL 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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27A TYR 5.8 0.2 - - - +
30A GLN* 3.5 46.2 + - + +
31A ASP 4.6 2.9 - - - -
32A TYR* 4.2 29.6 - - + +
35A LEU* 5.6 3.6 - - + -
48A ASP* 3.5 3.6 - - - +
138A ILE* 4.2 15.7 - - + -
139A PHE 3.1 15.0 - - - +
140A HIS* 4.2 9.4 - - + -
151A GLU* 4.4 7.2 + - + +
152A VAL* 1.3 75.7 - - - +
154A VAL* 1.3 66.8 + - - +
187A LYS* 2.7 29.7 + - - +
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Residues in contact with VAL 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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48A ASP* 3.8 8.5 - - - -
51A PHE* 4.9 4.3 - - + -
138A ILE* 3.4 4.0 - - - -
139A PHE* 2.8 42.8 + - + +
141A PHE* 4.7 6.5 - - + -
152A VAL* 4.3 1.3 + - + -
153A VAL* 1.3 80.0 - - - +
155A ASP* 1.3 70.0 + - - +
180A LEU* 4.1 25.6 - - + +
183A LYS* 4.2 17.5 - - + +
184A ALA* 3.8 28.9 - - + +
187A LYS* 4.0 15.3 - - + -
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Residues in contact with ASP 155 (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 PHE 3.1 26.5 - - - +
47A GLN 4.2 0.4 - - - +
48A ASP* 3.4 32.0 + - - +
51A PHE* 4.3 4.9 - - - +
53A ALA* 4.9 2.6 - - - +
77A ARG* 4.5 0.9 - - - +
137A GLY 3.2 6.5 - - - +
138A ILE* 4.4 0.9 - - + +
154A VAL* 1.3 80.8 - - - +
156A ASP* 1.3 58.6 + - - +
157A ARG* 2.9 48.3 + - - +
180A LEU* 4.6 0.5 - - - +
183A LYS* 2.8 40.9 + - - +
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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