Contacts of the strand formed by residues 146 - 151 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D HIS* 4.3 2.8 - - - +
50D LYS* 3.2 21.3 - - + +
52D LEU* 3.7 40.5 - - + +
93D GLU* 2.6 33.2 + - + -
131D LYS* 4.3 4.0 + - - -
136D VAL* 3.7 29.8 - - + +
140D LEU* 3.8 21.8 - - + -
144D SER* 3.0 11.4 + - - -
145D GLU* 1.3 82.8 - - - +
147D ALA* 1.3 61.9 + - - +
148D ALA 4.4 6.7 - - - +
173D TRP* 3.5 17.0 - + + -
179D ARG* 3.0 30.0 + - - +
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D HIS* 3.7 13.9 - - + +
50D LYS 2.8 10.0 + - - +
90D PHE* 4.3 7.4 - - + -
146D TYR* 1.3 73.4 - - - +
148D ALA* 1.3 61.2 + - - +
179D ARG* 3.8 5.9 - - - +
180D PHE* 3.0 30.1 + - - +
277D MET* 3.5 21.1 - - + -
281D TYR* 3.5 33.4 + - + +
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LYS 3.7 3.2 + - - +
51D ILE* 3.8 11.1 - - + -
52D LEU* 3.0 27.5 + - - +
146D TYR* 3.3 5.2 - - - +
147D ALA* 1.3 83.1 - - - +
149D ILE* 1.3 65.8 + - - +
150D PHE 4.0 0.4 - - - -
173D TRP* 5.9 0.2 - - - -
179D ARG* 4.7 2.7 - - - -
180D PHE* 3.2 24.7 - - + +
182D ILE* 3.8 20.0 - - + -
277D MET* 3.9 11.7 - - + -
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Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 3.4 21.5 - - + +
54D ILE* 3.7 24.0 - - + -
140D LEU* 6.1 0.2 - - + -
148D ALA* 1.3 77.7 - - - +
150D PHE* 1.3 61.3 + - - +
151D VAL* 4.1 6.5 + - + -
170D ALA* 3.3 45.5 - - + +
171D LEU* 4.1 15.5 - - + +
173D TRP* 4.5 12.1 - - + -
174D ALA* 4.0 17.3 - - + -
180D PHE 2.8 11.9 + - - +
181D VAL* 3.5 7.2 - - + +
182D ILE 3.0 25.2 + - - +
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Residues in contact with PHE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE* 3.7 20.2 - - + -
52D LEU 2.7 10.3 + - - +
53D VAL* 3.4 11.0 - - + -
54D ILE* 3.0 25.5 + - - +
77D GLU 3.5 22.4 - - - -
78D THR* 3.8 25.8 - - - -
81D PRO* 4.2 13.9 - - + -
82D LEU* 3.9 21.8 - - + -
85D LEU* 6.0 2.2 - - + -
148D ALA 4.0 0.8 - - - -
149D ILE* 1.3 75.0 - - - +
151D VAL* 1.3 68.0 + - - +
152D PRO* 3.6 27.6 - - + +
182D ILE* 3.3 38.6 - - + -
184D LEU* 4.1 13.0 - - + -
269D LEU* 4.9 0.4 - - + -
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 4.0 17.7 - - + +
149D ILE* 4.2 17.0 - - + +
150D PHE* 1.3 81.0 - - - +
152D PRO* 1.3 67.1 - - - +
153D GLY 3.7 0.3 + - - -
161D LEU* 3.9 24.0 - - + -
171D LEU* 5.1 7.0 - - + -
181D VAL* 5.9 1.1 - - + -
182D ILE 2.8 11.5 + - - +
183D SER* 2.7 38.0 + - - +
187D GLY* 3.6 27.4 - - - +
190D ALA* 4.0 11.2 - - + -
191D PHE* 5.3 4.7 - - + -
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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