Contacts of the strand formed by residues 159 - 165 (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 ASN 159 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154E ILE* 3.8 1.4 - - - -
155E ASN* 3.0 29.7 + - + +
157E ASN* 2.9 27.8 + - - +
158E GLY* 1.3 83.8 - - - +
160E MET* 1.3 60.0 - - - +
161E ARG* 4.1 1.0 + - + +
193E ASP* 3.9 29.7 + - - +
194E ILE 3.2 15.7 - - - +
195E LYS* 3.9 9.5 - - - +
196E ARG* 3.9 5.4 - - - +
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Residues in contact with MET 160 (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* 3.7 28.5 - - + -
152E PHE* 4.3 7.4 - - + -
153E GLU 3.3 12.1 - - - +
154E ILE* 4.6 3.1 - - + +
159E ASN* 1.3 75.1 - - - +
161E ARG* 1.3 66.1 + - - +
162E ILE* 5.7 0.2 - - + -
180E MET* 4.2 2.0 - - + +
193E ASP* 3.5 3.3 - - - -
194E ILE* 2.7 40.4 + - + +
196E ARG* 4.0 18.3 - - + +
200E ASN* 4.3 0.7 - - + +
201E ILE* 3.9 22.9 - - + -
204E VAL* 3.7 43.7 - - + -
205E ILE* 3.9 21.1 - - + -
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Residues in contact with ARG 161 (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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152E PHE* 3.5 3.1 - - - +
153E GLU* 2.7 68.4 + - + +
155E ASN* 5.3 13.6 - - + +
157E ASN* 5.1 9.7 - - - +
159E ASN* 5.2 2.0 - - + +
160E MET* 1.3 78.8 - - - +
162E ILE* 1.3 75.8 + - - +
163E PHE* 4.7 1.4 - - - +
180E MET* 4.9 0.7 - - - -
183E LYS* 4.9 5.4 - - - +
191E TYR* 2.8 46.0 - - - -
192E LEU 3.1 11.9 - - - +
193E ASP* 2.9 28.8 + - - +
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Residues in contact with ILE 162 (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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149E ILE* 3.9 31.2 - - + -
151E ASN 3.5 2.9 - - - -
152E PHE* 4.1 21.8 - - + -
160E MET* 5.7 0.9 - - + -
161E ARG* 1.3 81.6 - - - +
163E PHE* 1.3 65.7 + - - +
167E MET* 4.7 4.3 - - - -
175E PHE* 3.3 42.8 - - + -
180E MET* 4.3 8.1 - - + -
190E VAL 3.6 1.2 - - - +
191E TYR* 3.5 4.3 - - - -
192E LEU* 2.8 49.2 + - + +
204E VAL* 3.7 18.4 - - + -
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Residues in contact with PHE 163 (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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199D GLU* 5.7 3.4 - - + -
149E ILE* 3.8 1.0 - - - +
150E ARG* 2.8 68.5 + - - +
151E ASN* 3.0 37.3 + - - +
153E GLU* 3.6 21.3 - - - +
161E ARG* 4.1 2.0 - - + +
162E ILE* 1.3 73.9 - - - +
164E GLY* 1.3 62.5 + - - +
189E ASN* 3.9 20.9 - - + -
190E VAL 3.5 4.7 - - - -
191E TYR* 3.5 44.2 - + + +
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Residues in contact with GLY 164 (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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148E GLY 3.0 15.0 - - - -
149E ILE* 4.1 2.0 - - - -
150E ARG* 4.1 5.8 - - - -
162E ILE* 4.0 1.6 - - - +
163E PHE* 1.3 80.1 - - - +
165E TYR* 1.3 62.0 + - - +
167E MET* 4.2 10.3 - - - -
189E ASN* 3.4 8.1 + - - -
190E VAL* 2.8 34.9 + - - +
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Residues in contact with TYR 165 (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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203D ALA* 6.6 0.2 - - - -
206D THR* 3.7 27.3 - - + +
207D VAL* 6.2 0.2 - - - +
210D GLU* 4.3 11.4 + - - -
145E ARG* 3.4 26.8 - - - +
148E GLY* 2.8 23.8 + - - +
150E ARG* 3.7 23.6 - - - +
164E GLY* 1.3 75.8 - - - +
166E LYS* 1.3 120.0 + - + +
167E MET* 3.1 4.3 + - - +
187E ASN 3.6 10.5 - - - -
188E GLY 3.8 4.0 - - - -
189E ASN* 3.3 19.3 - - - -
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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