Contacts of the strand formed by residues 149 - 155 (chain E) in PDB entry 1KAF
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 ILE 149 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126E PHE* 5.5 3.4 - - + -
142E LEU* 3.5 21.8 - - + +
145E ARG* 3.4 8.9 - - - -
146E THR* 2.8 38.4 + - + +
147E ASN 4.2 0.2 - - - +
148E GLY* 1.3 77.4 - - - +
150E ARG* 1.3 61.6 + - - +
151E ASN 3.9 11.4 - - - +
152E PHE* 4.0 20.6 - - + -
162E ILE* 3.9 20.9 - - + -
163E PHE 3.9 2.9 - - - -
164E GLY* 4.1 1.6 - - - -
167E MET* 3.6 28.5 - - + -
175E PHE* 4.1 20.9 - - + -
208E ALA* 4.7 2.5 - - + -
211E LEU* 4.2 11.9 - - + -
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Residues in contact with ARG 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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202D GLU* 2.5 32.9 + - - +
141E ILE* 4.3 2.0 - - + +
142E LEU* 3.0 29.9 + - - +
145E ARG* 3.5 40.3 - - - +
148E GLY 4.2 5.2 - - - +
149E ILE* 1.3 75.7 - - - +
151E ASN* 1.3 75.3 + - - +
163E PHE* 2.8 56.2 + - + +
164E GLY* 4.4 1.7 - - - -
165E TYR* 3.7 21.4 - - - +
189E ASN* 3.2 24.5 + - - +
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Residues in contact with ASN 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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139E LEU* 4.7 11.2 - - + +
140E ALA 3.3 14.8 - - - +
141E ILE* 3.6 28.2 - - - +
149E ILE* 3.9 6.2 - - - +
150E ARG* 1.3 98.6 - - - +
152E PHE* 1.3 65.7 + - - +
153E GLU* 3.4 23.9 + - + +
162E ILE* 3.5 3.6 - - - -
163E PHE* 3.0 53.8 + - + +
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Residues in contact with PHE 152 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117E MET* 3.6 18.0 - - - +
121E LEU* 3.9 31.6 - - + -
126E PHE* 4.2 11.4 - + - -
140E ALA* 2.9 33.0 + - + +
142E LEU* 4.0 25.4 - - + -
149E ILE* 4.0 23.1 - - + -
151E ASN* 1.3 76.5 - - - +
153E GLU* 1.3 60.6 + - - +
160E MET* 4.3 7.0 - - + -
161E ARG 3.5 3.6 - - - -
162E ILE* 4.1 25.4 - - + -
204E VAL* 4.6 1.3 - - + -
205E ILE* 3.5 26.2 - - + -
208E ALA* 3.8 27.1 - - + -
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Residues in contact with GLU 153 (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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117E MET* 4.4 1.7 - - - +
137E ASN* 3.2 17.9 + - - +
138E TYR 3.2 9.9 - - - +
139E LEU* 3.1 28.8 - - + +
151E ASN* 3.4 25.3 + - + -
152E PHE* 1.3 78.6 - - - +
154E ILE* 1.3 64.5 + - - +
155E ASN* 4.0 2.1 + - + +
160E MET* 3.3 10.9 - - - +
161E ARG* 2.7 68.2 + - + +
163E PHE* 3.6 18.4 - - - +
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Residues in contact with ILE 154 (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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111E GLU* 3.4 25.6 - - - +
113E ASP* 3.8 9.9 - - + +
114E LYS* 3.5 46.2 - - + +
117E MET* 3.8 26.2 - - + -
137E ASN* 3.6 3.5 - - - -
138E TYR* 3.1 37.4 + - + +
153E GLU* 1.3 77.9 - - - +
155E ASN* 1.3 64.3 + - - +
156E ASN* 4.8 1.6 - - - +
159E ASN 3.8 3.4 - - - +
160E MET* 4.8 5.4 - - + -
196E ARG* 4.4 15.5 - - + -
201E ILE* 4.2 9.4 - - + -
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Residues in contact with ASN 155 (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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111E GLU* 5.1 3.1 - - - +
136E SER* 3.4 16.6 + - - +
137E ASN* 3.5 23.5 + - - +
153E GLU* 4.0 3.3 + - + +
154E ILE* 1.3 80.3 - - - +
156E ASN* 1.3 66.2 + - - +
157E ASN* 2.7 55.5 + - - +
158E GLY* 3.2 11.4 + - - -
159E ASN* 3.0 15.0 + - + +
161E ARG* 5.3 13.8 - - + +
196E ARG* 5.3 2.4 + - - -
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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