Contacts of the strand formed by residues 166 - 172 (chain A) in PDB entry 2A73
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ARG* 3.8 31.4 - - + -
127A ILE 3.9 2.0 - - - -
128A PHE* 4.1 22.0 - - + -
163A GLN* 3.2 33.1 + - + +
164A LEU 4.5 2.7 - - - +
165A GLY* 1.3 78.4 - - - +
167A LEU* 1.3 70.7 + - - +
168A PRO* 3.8 10.5 - - + +
570A ARG* 4.4 17.7 - - + +
572A VAL* 3.8 23.6 - - + -
753B VAL* 5.7 0.4 - - + -
785B VAL 6.0 0.4 - - - +
787B MET* 4.3 12.8 - - + -
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Residues in contact with LEU 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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125A TYR 4.0 0.3 - - - +
126A ARG* 3.5 3.9 - - - -
127A ILE* 3.1 39.9 + - + +
129A THR* 3.9 13.0 - - + -
141A VAL* 3.5 31.0 - - + -
143A VAL* 5.8 0.4 - - + -
158A LEU* 3.7 29.8 - - + -
159A SER 3.4 23.3 - - - +
160A SER* 3.8 22.0 - - - -
163A GLN* 4.4 5.8 - - - +
166A VAL* 1.3 84.5 - - - +
168A PRO* 1.3 68.6 - - + +
169A LEU* 3.6 10.4 + - + +
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Residues in contact with PRO 168 (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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125A TYR 4.2 3.4 - - - +
126A ARG* 4.4 14.1 - - + +
158A LEU* 5.4 5.7 - - + +
163A GLN* 5.0 9.6 - - + +
166A VAL* 3.8 15.0 - - + +
167A LEU* 1.3 87.5 - - + +
169A LEU* 1.3 68.1 + - - +
751B TRP* 4.8 13.7 - - + +
753B VAL* 5.3 11.2 - - + -
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Residues in contact with LEU 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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124A LEU* 4.0 4.0 - - - +
125A TYR* 3.0 66.5 + - + +
127A ILE* 4.3 9.2 - - + -
143A VAL* 4.2 26.2 - - + -
154A LYS* 4.7 2.9 - - - +
156A ASP* 3.6 28.3 - - + +
158A LEU* 5.1 15.7 - - + -
167A LEU* 4.2 8.7 - - + +
168A PRO* 1.3 79.9 - - - +
170A SER* 1.3 62.5 + - - +
751B TRP* 4.1 7.0 - - - -
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Residues in contact with SER 170 (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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122A THR* 3.4 17.0 - - - +
123A VAL 3.5 7.9 - - - -
124A LEU* 4.5 10.3 - - - +
125A TYR* 3.8 2.2 - - - -
154A LYS* 2.8 23.4 + - - -
169A LEU* 1.3 78.6 - - - +
171A TRP* 1.3 63.2 + - - +
172A ASP* 3.8 6.9 + - - -
751B TRP* 6.0 0.7 - - - -
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Residues in contact with TRP 171 (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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122A THR* 3.3 1.3 - - - -
123A VAL* 2.7 57.9 + - + +
125A TYR* 4.1 4.5 - - + -
145A ILE* 3.9 27.6 - - + -
153A VAL* 3.7 27.3 + - + +
154A LYS* 3.8 23.5 - - + +
170A SER* 1.3 77.7 + - - +
172A ASP* 1.3 76.8 + - - +
173A ILE* 3.7 29.5 + - + -
174A PRO* 4.2 8.9 - - + +
182A TRP* 3.4 30.5 - + - -
200A PHE* 3.9 24.7 - + - -
202A VAL* 5.8 0.2 - - + -
1032B THR* 4.2 15.5 + - + +
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Residues in contact with ASP 172 (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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120A GLY 5.1 3.8 - - - +
121A SER 3.6 5.6 - - - +
122A THR* 3.0 25.5 + - - +
170A SER* 3.8 6.8 + - - -
171A TRP* 1.3 87.2 + - - +
173A ILE* 1.3 64.9 + - - +
174A PRO* 3.2 10.9 - - - +
1029B LYS* 5.9 2.3 - - - -
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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