Contacts of the strand formed by residues 145 - 150 (chain H) in PDB entry 2VUU
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 SER 145 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H HIS* 4.5 2.5 - - - -
108H TYR* 2.9 19.3 - - - +
138H VAL* 3.4 18.4 - - - +
139H ARG* 4.8 4.3 + - - +
143H LEU 2.6 15.9 + - - -
144H PRO* 1.3 72.8 - - - +
146H THR* 1.3 65.2 + - - +
147H PHE* 3.4 23.7 - - - -
212H ASN* 3.1 9.9 + - - +
213H GLY* 2.6 34.5 + - - -
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Residues in contact with THR 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H HIS* 3.1 25.0 + - - -
108H TYR 3.3 3.5 + - - +
109H ILE* 3.2 12.4 - - + +
110H TYR 3.1 23.0 + - - -
145H SER* 1.3 73.1 + - - +
147H PHE* 1.3 69.7 + - - +
148H VAL* 4.9 3.8 - - + -
203H ILE* 4.3 7.0 - - + -
211H TRP* 2.6 29.2 + - + +
214H HIS 3.5 14.1 - - - +
216H ILE* 3.7 30.3 - - + -
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Residues in contact with PHE 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H TYR* 3.3 35.9 - + + +
112H SER* 4.3 1.1 - - - -
135H GLU* 3.4 45.3 - - + +
138H VAL* 3.3 37.7 - - + -
139H ARG* 3.5 44.6 - - + -
145H SER* 3.4 16.8 - - - -
146H THR* 1.3 74.6 - - - +
148H VAL* 1.3 62.7 + - - +
149H TYR* 3.5 10.6 - - + -
213H GLY* 5.1 1.3 - - - -
214H HIS 2.8 14.7 + - - +
215H ARG* 3.2 4.8 - - + -
216H ILE 2.8 24.2 + - - -
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Residues in contact with VAL 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H PHE* 4.1 9.9 - - + -
109H ILE* 3.7 22.2 - - + -
110H TYR 3.2 2.6 + - - -
111H SER* 3.5 22.7 + - - +
112H SER 2.9 27.4 + - - +
146H THR* 4.2 1.5 + - + -
147H PHE* 1.3 74.8 - - - +
149H TYR* 1.3 61.6 + - - +
150H ALA 3.9 0.4 - - - -
200H LEU* 4.2 4.0 - - + -
203H ILE* 3.9 28.7 - - + -
216H ILE* 3.2 16.6 - - + -
218H LEU* 3.8 29.6 - - + -
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Residues in contact with TYR 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H SER* 3.5 17.8 + - - -
113H MET* 3.9 19.3 - - - -
114H PRO* 3.9 20.0 - - + -
132H PHE* 4.1 7.0 - + - -
135H GLU* 2.6 29.4 + - - -
147H PHE* 3.5 17.7 - - + -
148H VAL* 1.3 76.0 - - - +
150H ALA* 1.3 62.0 + - - +
151H GLY 3.7 0.2 + - - -
215H ARG* 3.3 33.3 + - + -
216H ILE 2.7 15.0 + - - +
217H ALA* 3.4 6.0 - - - -
218H LEU* 2.5 28.6 + - - -
277H PHE* 3.6 21.5 - + + -
279H LEU* 3.8 17.4 - - + +
282H PHE* 3.9 16.2 - + + -
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Residues in contact with ALA 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H GLN* 4.3 15.5 - - - +
111H SER* 4.9 2.9 + - - +
112H SER 4.4 3.8 + - - -
113H MET* 4.0 2.4 - - - +
148H VAL 3.9 3.8 + - - -
149H TYR* 1.3 71.8 - - - +
151H GLY* 1.3 65.4 + - - +
153H TYR* 4.3 5.6 - - + -
190H LEU* 3.6 17.3 - - + -
218H LEU* 3.9 12.1 - - + +
276H TYR* 3.5 4.9 - - - -
277H PHE* 3.3 12.7 - - - -
1353H NAP 3.4 32.5 - - + -
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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