Contacts of the strand formed by residues 166 - 169 (chain A) in PDB entry 2I69
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 ARG 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A PHE* 5.5 1.1 - - + -
46A MET* 3.3 42.9 + - - +
47A ASN* 4.4 5.7 - - - +
138A GLU* 2.5 56.9 + - - +
139A VAL 3.5 3.4 - - - -
140A ALA* 4.1 16.8 - - + -
155A TYR* 3.5 27.3 + - + +
165A GLY* 1.3 70.8 - - - -
167A PHE* 1.3 61.0 + - - +
178A LEU* 4.9 2.3 - - - +
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Residues in contact with PHE 167 (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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138A GLU* 3.7 5.7 - - - +
139A VAL* 2.7 66.9 + - + +
141A ILE* 3.6 36.1 - - + -
165A GLY 4.3 4.7 - - - -
166A ARG* 1.3 76.8 - - - +
168A SER* 1.3 64.0 + - - +
169A ILE* 3.8 19.5 - - + -
176A TYR* 3.4 55.9 - + + -
178A LEU* 4.7 8.1 - - + -
188A VAL* 4.0 19.7 - - + -
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Residues in contact with SER 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 3.5 31.5 + - - -
137A TYR 3.2 12.8 - - - -
138A GLU* 4.2 7.2 - - - +
167A PHE* 1.3 78.5 - - - +
169A ILE* 1.3 74.7 + - - +
170A THR* 4.5 3.5 - - - +
173A ALA 4.5 2.4 - - - +
176A TYR* 4.8 2.9 - - - +
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Residues in contact with ILE 169 (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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136A LYS* 3.6 0.5 - - - -
137A TYR* 2.7 41.1 + - + +
139A VAL* 4.6 6.1 - - + -
167A PHE* 3.8 22.0 - - + -
168A SER* 1.3 81.5 - - - +
170A THR* 1.3 67.7 + - - +
173A ALA 3.7 4.9 - - - +
174A PRO* 3.3 38.4 - - + +
175A SER* 3.7 14.4 - - - +
176A TYR* 4.0 4.0 - - + +
188A VAL* 4.6 3.8 - - + -
190A CYS* 4.0 15.7 - - + -
192A PRO* 4.4 9.0 - - + -
286A LEU* 3.9 25.8 - - + -
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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