Contacts of the strand formed by residues 145 - 151 (chain F) in PDB entry 5DSV
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 GLY 145 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139F SER* 3.9 1.6 + - - +
140F TYR* 3.5 13.0 - - - -
141F SER 2.9 34.1 + - - +
142F VAL 3.6 6.6 + - - -
143F ASN 3.5 1.6 - - - -
144F ASP* 1.3 83.6 - - - +
146F ALA* 1.3 60.7 + - - -
147F GLN* 4.0 3.6 - - - +
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Residues in contact with ALA 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ARG* 3.1 39.9 + - + +
41F CYS 4.3 2.9 - - - +
42F LYS 4.6 5.8 + - - +
44F GLY* 3.5 42.2 - - - +
139F SER 3.6 5.4 - - - -
140F TYR* 3.5 9.1 - - + -
144F ASP 4.5 1.2 - - - +
145F GLY* 1.3 69.7 - - - -
147F GLN* 1.3 68.8 + - - +
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Residues in contact with GLN 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ARG* 4.4 5.6 - - - +
45F VAL* 3.4 7.2 - - - +
107F PRO 5.0 0.2 - - - -
108F LEU* 3.4 37.7 - - + +
109F LYS* 3.6 36.1 - - - +
138F GLY* 3.3 4.9 - - - -
139F SER* 3.0 37.6 + - - +
144F ASP* 3.8 35.5 + - - +
145F GLY 4.0 9.4 - - - +
146F ALA* 1.3 81.3 - - - +
148F LEU* 1.3 60.1 + - - +
149F TYR* 4.0 10.3 + - + -
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Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLY 3.7 23.8 - - - +
39F ILE* 3.9 2.7 - - - +
40F ARG* 4.5 6.5 - - + +
45F VAL* 3.9 13.5 - - + -
47F PHE* 3.5 38.1 - - + -
136F MET* 4.2 14.4 - - + -
137F LEU 3.4 7.6 - - - +
147F GLN* 1.3 77.0 - - - +
149F TYR* 1.3 66.7 + - - +
159F GLY* 3.5 4.5 - - - -
160F TYR* 2.9 61.5 + - + +
161F TRP 4.0 3.4 - - - +
162F GLY* 3.7 11.2 - - - -
163F CYS 4.1 2.7 - - - +
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Residues in contact with TYR 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F LEU* 3.7 22.4 - - + -
109F LYS* 3.4 47.6 - - - +
112F ALA* 3.9 18.6 - - + -
136F MET* 2.9 9.8 - - - +
137F LEU* 2.8 44.6 + - + +
147F GLN* 4.0 16.3 + - + -
148F LEU* 1.3 77.4 - - - +
150F MET* 1.3 58.6 + - - +
151F ILE* 5.1 3.4 - - + -
157F SER* 3.6 17.7 - - - +
158F TYR* 3.1 18.2 - - - -
159F GLY* 3.4 20.4 - - - -
160F TYR* 4.9 0.7 - - - +
59G GLU* 5.3 4.8 + - - -
61G GLY 5.7 0.5 + - - -
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Residues in contact with MET 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F SER* 4.4 1.8 - - - -
135F PHE 3.3 11.7 - - - +
136F MET* 4.0 20.6 - - + -
149F TYR* 1.3 76.0 - - - +
151F ILE* 1.3 77.5 + - - +
152F ASP* 4.0 19.7 - - + +
156F VAL 3.3 3.1 - - - +
157F SER* 3.7 0.2 - - - -
158F TYR* 2.8 56.0 + - + -
160F TYR* 3.9 27.6 - - + +
163F CYS* 4.5 6.1 - - - -
165F ILE* 4.1 23.6 - - + -
169F ARG* 5.7 4.3 - - - +
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Residues in contact with ILE 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ALA* 4.0 34.1 - - + +
115F VAL* 5.2 0.4 - - + -
116F ALA* 4.0 10.3 - - + +
119F VAL* 4.2 16.8 - - + -
134F SER* 3.2 5.4 - - - -
135F PHE* 2.9 76.0 + - + -
137F LEU* 4.4 5.2 - - + -
149F TYR* 5.1 0.4 - - + -
150F MET* 1.3 82.8 - - - +
152F ASP* 1.3 74.9 + - - +
155F GLY* 4.4 6.3 - - - -
156F VAL 3.3 11.4 - - - +
157F SER* 3.8 13.2 - - - +
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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