Contacts of the strand formed by residues 145 - 152 (chain E) in PDB entry 1XFB
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 PHE 145 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ILE* 3.6 28.9 - - + -
30E ILE* 4.4 7.4 - - + -
76E GLY* 4.3 5.4 - - - -
77E VAL 3.7 22.7 - - - -
78E ILE* 3.6 20.2 - - + -
104E VAL* 3.6 21.8 - - + -
105E VAL 3.2 19.7 - - - -
106E GLY* 2.9 43.1 - - - -
107E ILE* 3.2 8.3 + - - +
144E ASP* 1.3 82.0 - - - +
146E ALA* 1.3 62.1 + - - +
183E ILE* 3.7 5.3 - - - +
184E VAL* 2.9 22.0 - - + +
186E ILE* 3.6 35.4 - - + -
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Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ILE* 5.8 0.2 - - - -
107E ILE* 3.2 17.7 - - + +
109E VAL* 3.9 17.5 - - + -
135E CYS* 5.7 0.4 - - - -
145E PHE* 1.3 78.8 - - - +
147E LYS* 1.3 61.5 + - - +
174E TYR* 3.2 10.8 - - + +
178E CYS* 4.1 10.5 - - - -
183E ILE* 3.7 15.0 - - + +
184E VAL 2.8 7.5 + - - -
186E ILE* 2.8 31.5 + - - +
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Residues in contact with LYS 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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32E ALA* 5.1 0.6 - - - +
34E ASP* 3.2 33.6 + - - +
78E ILE* 4.0 28.9 - - + -
107E ILE 3.0 5.1 + - - -
108E LYS* 3.4 12.0 - - + +
109E VAL* 3.0 27.4 + - - +
110E ASP* 3.9 1.9 + - - +
146E ALA* 1.3 76.8 - - - +
148E TRP* 1.3 64.4 + - - +
149E ARG* 4.2 16.9 - - - +
174E TYR* 3.3 3.6 - - - -
186E ILE* 4.0 9.0 - - + +
188E GLU* 2.8 31.2 + - + +
230E LYS* 3.0 31.4 - - + +
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Residues in contact with TRP 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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109E VAL* 4.0 3.4 - - + -
110E ASP* 3.6 22.7 - - + -
125E THR* 3.3 35.4 - - + -
126E GLN 3.5 0.7 - - - -
127E GLY* 3.4 28.7 - - - -
128E LEU* 3.4 38.1 - - + -
131E LEU* 4.4 5.2 - - + -
147E LYS* 1.3 76.1 - - - +
149E ARG* 1.3 64.0 + - - +
150E CYS* 3.6 12.2 - - - -
170E VAL* 3.3 25.5 - - + +
171E LEU* 3.6 18.2 - - + +
174E TYR* 3.3 50.3 + + + -
186E ILE 3.7 1.8 + - - -
188E GLU* 3.3 24.9 + - - +
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Residues in contact with ARG 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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108E LYS* 5.7 2.9 - - - +
110E ASP* 3.2 17.1 + - - +
112E GLY 5.7 0.2 - - - -
113E VAL* 5.6 2.1 - - - +
125E THR* 2.8 21.3 + - - +
147E LYS* 4.2 11.9 - - - +
148E TRP* 1.3 76.0 - - - +
150E CYS* 1.3 69.3 + - - +
151E VAL* 3.4 31.4 + - + +
188E GLU* 3.3 33.2 - - + +
190E GLU* 2.4 43.0 + - - +
192E LEU* 4.3 7.5 - - - +
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Residues in contact with CYS 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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125E THR* 3.3 10.3 - - - -
148E TRP* 3.6 23.3 - - - -
149E ARG* 1.3 78.9 - - - +
151E VAL* 1.3 66.3 + - - +
152E LEU* 5.6 2.0 - - + -
167E ASN* 3.3 36.3 - - + +
170E VAL* 4.6 2.7 - - - -
171E LEU* 3.6 25.8 - - + -
188E GLU 3.0 13.2 + - - +
189E PRO* 4.5 6.5 - - + -
190E GLU* 3.2 21.3 + - - +
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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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113E VAL* 4.7 13.1 - - + +
123E THR* 3.5 30.7 + - - +
124E THR 5.9 0.2 - - - -
125E THR* 4.5 1.4 + - - -
149E ARG* 3.4 39.3 - - + +
150E CYS* 1.3 82.9 - - - +
152E LEU* 1.3 72.8 + - - +
153E LYS* 5.9 0.2 - - + -
167E ASN* 4.2 2.9 + - - +
190E GLU 3.4 3.8 - - - +
192E LEU* 3.5 40.2 - - + -
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Residues in contact with LEU 152 (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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122E GLU* 5.5 0.9 - - - +
123E THR 5.2 0.2 - - - +
150E CYS* 5.6 1.6 - - + -
151E VAL* 1.3 80.8 - - - +
153E LYS* 1.3 61.5 + - - +
159E PRO* 5.0 9.2 - - + -
163E ALA* 3.8 19.1 - - + +
164E ILE* 4.6 13.9 - - + -
167E ASN* 3.5 35.0 - - + +
189E PRO* 5.6 5.8 - - + -
190E GLU 2.8 12.4 + - - +
191E ILE* 4.2 13.7 - - + -
192E LEU* 2.9 31.6 + - - +
209E VAL* 3.3 45.8 - - + -
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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