Contacts of the strand formed by residues 146 - 151 (chain E) in PDB entry 1PV2
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 TYR 146 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49E HIS* 4.2 3.3 + - - -
50E LYS* 3.3 14.6 - - + +
52E LEU* 3.7 39.2 - - + +
93E GLU* 2.8 34.5 + - + -
131E LYS* 4.2 2.9 + - - -
136E VAL* 3.7 35.6 - - + +
140E LEU* 3.8 22.7 - - + -
144E SER* 3.0 8.1 + - - -
145E GLU* 1.3 86.6 - - - +
147E ALA* 1.3 61.3 + - - +
148E ALA 4.4 7.0 - - - +
173E TRP* 3.5 20.7 - + + -
179E ARG* 3.3 28.9 + - - +
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Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E HIS* 3.5 28.8 - - + +
50E LYS 2.7 12.2 + - - +
90E PHE* 4.0 13.2 - - + -
146E TYR* 1.3 74.1 - - - +
148E ALA* 1.3 61.1 + - - +
179E ARG* 3.9 9.5 - - - +
180E PHE* 3.3 27.1 + - - +
277E MET* 3.6 21.3 - - + -
281E TYR 4.4 7.2 - - - +
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Residues in contact with ALA 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E LYS 3.7 2.7 + - - +
51E ILE* 4.0 10.5 - - + -
52E LEU* 2.8 29.6 + - - +
146E TYR* 3.4 3.8 - - - +
147E ALA* 1.3 83.6 + - - +
149E ILE* 1.3 64.7 + - - +
150E PHE 4.0 0.4 - - - -
173E TRP* 5.8 0.2 - - - -
179E ARG* 4.8 2.0 - - - -
180E PHE* 3.2 25.4 - - + +
182E ILE* 3.8 20.2 - - + -
277E MET* 3.9 10.5 - - + -
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Residues in contact with ILE 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 3.3 35.2 - - + +
54E ILE* 3.8 25.1 - - + -
140E LEU* 5.8 0.7 - - + -
148E ALA* 1.3 77.3 - - - +
150E PHE* 1.3 59.9 + - - +
151E VAL* 4.3 5.5 - - + +
170E ALA* 4.1 24.0 - - + +
171E LEU* 4.2 18.8 - - + -
173E TRP* 4.5 14.8 - - + -
174E ALA* 3.6 24.5 - - + -
180E PHE 2.8 11.5 + - - +
181E VAL* 3.6 4.9 - - - +
182E ILE 2.9 25.9 + - - +
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Residues in contact with PHE 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ILE* 3.8 17.0 - - + -
52E LEU 2.5 14.7 + - - +
53E VAL* 3.4 11.9 - - + -
54E ILE* 2.8 28.8 + - - +
77E GLU 3.4 23.1 - - - -
78E THR* 3.6 21.8 - - - -
81E PRO* 3.9 15.5 - - + -
82E LEU* 3.8 22.9 - - + -
85E LEU* 6.0 2.5 - - + -
148E ALA 4.0 0.6 - - - -
149E ILE* 1.3 71.5 - - - +
151E VAL* 1.3 64.0 + - - +
152E PRO* 3.4 32.5 - - + +
182E ILE* 3.4 42.6 - - + -
184E LEU* 4.2 10.3 - - + -
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Residues in contact with VAL 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ILE* 4.0 19.3 - - + +
149E ILE* 4.3 14.6 - - + +
150E PHE* 1.3 79.1 - - - +
152E PRO* 1.3 72.0 - - - +
157E ALA* 5.0 0.2 - - + -
161E LEU* 3.9 17.5 - - + -
167E VAL* 6.1 0.4 - - + -
171E LEU* 4.9 9.2 - - + -
181E VAL* 5.8 0.4 - - + -
182E ILE 2.7 11.9 + - - +
183E SER* 2.7 36.8 + - - +
187E GLY* 3.5 23.5 - - - +
190E ALA* 3.7 20.2 - - + -
191E PHE* 5.0 4.9 - - + -
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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