Contacts of the strand formed by residues 149 - 152 (chain A) in PDB entry 1K86
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 VAL 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLY* 3.4 2.6 - - - -
146A GLU* 3.0 33.8 + - + +
147A GLU 3.1 26.9 - - - +
148A ASN* 1.3 80.9 - - - +
150A ILE* 1.3 61.7 + - - +
156A VAL* 3.3 38.8 - - + +
157A THR 3.0 26.7 - - - +
158A PRO* 3.8 3.8 - - + -
159A ILE* 3.9 6.6 - - - +
185A ALA* 5.2 0.3 - - - +
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A MET* 4.0 16.4 - - + -
141A LEU* 4.4 12.3 - - + +
143A SER* 4.7 9.9 - - - +
144A HIS 3.6 5.4 - - - +
149A VAL* 1.3 75.3 - - - +
151A TYR* 1.3 63.8 + - - +
156A VAL* 3.3 4.9 - - - +
157A THR* 2.8 61.9 + - - +
159A ILE* 3.9 12.6 - - + -
162A LEU* 3.5 32.1 - - + -
183A ILE* 4.2 15.5 - - + -
185A ALA* 3.8 27.4 - - + -
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Residues in contact with TYR 151 (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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75A ASN* 2.9 11.6 + - - -
78A PHE* 3.6 11.2 - + + -
82A THR* 3.9 22.3 + - - -
84A MET* 3.2 44.6 - - + -
119A MET* 4.0 4.0 - - - +
143A SER* 2.7 25.3 + - - +
144A HIS* 2.8 35.2 + - + +
145A GLY* 4.2 3.6 - - - -
146A GLU* 3.9 30.9 + - + -
150A ILE* 1.3 73.6 - - - +
152A GLY* 1.3 63.4 + - - +
155A GLY* 2.9 24.5 - - - -
156A VAL* 3.6 17.3 - - + -
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Residues in contact with GLY 152 (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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75A ASN* 4.0 0.9 - - - -
78A PHE* 3.2 13.4 - - - -
114A CYS 3.7 5.4 - - - -
116A CYS* 3.5 16.6 - - - -
119A MET* 3.3 23.3 - - - +
150A ILE 3.8 0.6 + - - -
151A TYR* 1.3 76.9 - - - +
153A LYS* 1.3 66.1 + - - +
154A ASP 3.2 2.6 + - - -
155A GLY 3.2 15.8 + - - +
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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