Contacts of the strand formed by residues 160 - 166 (chain A) in PDB entry 2R17
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PHE* 3.8 11.2 - - + -
110A ILE* 4.4 9.0 - - + -
128A PHE* 4.4 0.9 - - + -
153A MSE 3.7 29.4 - - + -
154A ASP 3.5 3.6 - - - +
155A ILE* 3.6 22.9 - - + -
159A THR* 1.3 75.2 - - - +
161A VAL* 1.3 68.1 + - - +
162A THR* 4.2 14.1 - - + -
178A GLU* 3.3 3.6 - - - +
179A TYR* 2.5 75.0 + - + +
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Residues in contact with VAL 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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153A MSE 3.3 1.0 - - - -
154A ASP* 2.8 41.7 + - + +
159A THR* 5.2 8.5 - - + -
160A VAL* 1.3 79.7 - - - +
162A THR* 1.3 62.2 + - - +
163A TYR* 3.6 26.8 + - + +
176A ARG* 3.4 55.2 - - + +
177A ILE 3.4 4.7 - - - +
178A GLU* 4.4 6.5 - - + -
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Residues in contact with THR 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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119A PHE* 5.7 1.7 - - - -
121A ALA* 4.5 2.8 - - - +
128A PHE* 3.6 19.3 - - + -
130A ILE* 3.8 12.1 - - - +
151A VAL* 4.2 15.3 - - - +
152A LEU 4.0 3.1 - - - -
153A MSE 3.3 39.7 - - + +
160A VAL* 4.2 7.0 - - + -
161A VAL* 1.3 74.1 - - - +
163A TYR* 1.3 63.7 + - - +
164A VAL* 3.8 1.2 + - - +
175A GLU 3.7 2.9 - - - +
177A ILE* 2.8 45.8 + - - +
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Residues in contact with TYR 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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2A LEU* 6.1 2.2 - - + -
151A VAL* 3.2 7.9 - - - -
152A LEU* 2.9 49.3 + - + +
153A MSE 5.3 0.2 - - - -
154A ASP* 4.5 16.4 - - + +
161A VAL* 3.6 26.7 - - + +
162A THR* 1.3 72.0 - - - +
164A VAL* 1.3 60.8 + - - +
165A TYR* 3.7 23.0 + + + -
174A VAL* 4.8 9.6 - - + -
175A GLU 3.6 4.7 - - - +
176A ARG* 3.8 39.4 + - + -
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Residues in contact with VAL 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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119A PHE* 3.3 58.3 - - + -
149A SER* 5.2 1.1 - - - -
150A PHE 4.5 0.4 - - - +
151A VAL* 3.5 6.3 - - + -
162A THR* 3.8 3.4 + - - +
163A TYR* 1.3 73.5 - - - +
165A TYR* 1.3 63.0 + - - +
166A GLN* 3.8 20.9 + - + +
174A VAL* 3.5 9.4 - - - +
175A GLU* 3.1 54.2 + - + +
177A ILE* 5.4 2.5 - - + -
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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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22A PHE* 3.4 4.9 - - + -
25A LEU* 3.9 20.2 - - + -
149A SER* 2.8 32.1 - - - -
150A PHE* 2.9 43.7 + + + +
152A LEU* 3.1 36.9 - - + +
163A TYR* 4.0 18.4 - - + +
164A VAL* 1.3 71.6 - - - +
166A GLN* 1.3 60.9 + - - +
172A VAL* 3.7 19.1 - - + -
173A LYS 4.1 0.7 - - - -
174A VAL* 3.6 26.4 - - + +
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Residues in contact with GLN 166 (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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22A PHE* 4.0 2.5 - - - -
119A PHE* 4.6 19.1 - - + +
147A ILE* 4.2 26.2 + - + +
148A PRO 3.5 4.3 - - - +
149A SER* 4.2 8.9 + - - -
164A VAL* 3.8 22.8 + - + +
165A TYR* 1.3 74.5 - - - +
167A LEU* 1.3 59.9 + - - +
168A ILE* 3.6 26.0 - - + +
172A VAL* 3.2 19.6 - - - +
173A LYS* 3.3 24.2 + - + +
175A GLU* 5.3 6.6 - - - +
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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