Contacts of the strand formed by residues 159 - 165 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ASN* 2.9 31.7 + - - +
157A ASN* 2.8 32.4 + - - +
158A GLY* 1.3 78.3 - - - +
160A MET* 1.3 66.5 + - - +
161A ARG 4.0 0.2 - - - -
193A ASP* 4.3 24.1 + - - +
194A ILE 3.3 11.2 - - - +
195A LYS* 2.7 41.3 + - - +
196A ARG* 3.4 7.8 - - - -
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Residues in contact with MET 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A MET* 3.2 29.8 - - + -
152A PHE* 4.2 6.3 - - + -
153A GLU 3.1 13.0 - - - +
154A ILE* 4.2 4.0 - - + -
159A ASN* 1.3 74.2 - - - +
161A ARG* 1.3 66.7 + - - +
162A ILE* 5.4 0.2 - - + -
180A MET* 4.3 2.2 - - + +
192A LEU 3.9 0.2 - - - +
193A ASP* 3.5 3.3 - - - -
194A ILE* 2.8 40.5 + - + +
196A ARG* 3.7 16.2 - - + +
201A ILE* 3.9 25.8 - - + -
204A VAL* 3.8 43.3 - - + -
205A ILE* 3.8 20.9 - - + -
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PHE* 3.5 4.2 - - - +
153A GLU* 2.7 61.8 + - - +
155A ASN* 3.7 18.9 - - - +
157A ASN* 6.3 1.1 - - - -
159A ASN 4.0 0.4 + - - -
160A MET* 1.3 77.7 - - - +
162A ILE* 1.3 78.3 + - - +
163A PHE* 4.1 1.3 - - - -
180A MET* 5.0 0.2 - - - -
191A TYR* 3.4 44.1 - - - +
192A LEU 3.1 8.5 - - - +
193A ASP* 2.8 42.7 + - - +
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Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 4.1 29.8 - - + -
151A ASN 3.6 3.6 - - - -
152A PHE* 3.9 25.6 - - + -
160A MET* 5.4 0.9 - - + -
161A ARG* 1.3 79.1 - - - +
163A PHE* 1.3 64.3 + - - +
167A MET* 4.5 4.0 - - - -
175A PHE* 3.5 39.0 - - + -
180A MET* 4.2 10.3 - - + +
190A VAL 3.6 3.8 - - - +
191A TYR* 3.7 0.3 - - - -
192A LEU* 2.8 51.7 + - + +
204A VAL* 3.6 17.9 - - + -
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Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 3.8 1.4 - - - +
150A ARG* 2.8 52.3 + - + +
151A ASN* 3.0 43.9 + - - +
153A GLU* 3.7 9.0 - - - +
161A ARG* 4.8 3.8 - - + -
162A ILE* 1.3 74.4 - - - +
164A GLY* 1.3 66.0 + - - +
189A ASN* 3.8 28.0 - - - -
190A VAL 3.6 3.6 - - - -
191A TYR* 3.4 44.2 - + - +
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Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLY 3.1 14.8 - - - -
149A ILE* 4.1 2.2 - - - -
150A ARG* 4.0 4.5 - - - -
162A ILE* 4.0 2.0 - - - +
163A PHE* 1.3 80.5 - - - +
165A TYR* 1.3 61.0 + - - +
167A MET* 4.1 11.6 - - - -
189A ASN* 3.4 7.6 + - - -
190A VAL* 2.8 35.0 + - - +
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLY* 2.8 24.6 + - - +
150A ARG* 4.0 35.2 - - - +
164A GLY* 1.3 74.8 - - - +
166A LYS* 1.3 103.6 + - + +
167A MET* 3.2 3.8 + - - +
187A ASN 3.5 21.2 + - - -
188A GLY 3.8 5.6 - - - -
189A ASN* 3.3 22.4 - - - +
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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