Contacts of the strand formed by residues 166 - 173 (chain A) in PDB entry 2ORY
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 ALA 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLU 5.2 0.4 - - - -
83A GLY* 3.2 21.5 - - - +
85A TYR* 4.3 2.7 - - + -
160A ILE* 3.4 35.9 - - + -
164A GLY 4.0 1.0 + - - -
165A LYS* 1.3 79.8 - - - +
167A LYS* 1.3 63.6 + - - +
198A ASN 3.3 7.7 + - - +
199A ILE* 3.2 7.7 - - + +
200A ASP* 2.9 27.2 + - - +
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Residues in contact with LYS 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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5A LYS* 4.6 17.3 - - - +
83A GLY 2.6 14.6 + - - +
84A GLU* 3.5 35.9 - - + +
85A TYR* 2.8 27.4 + - - -
166A ALA* 1.3 76.1 - - - +
168A ILE* 1.3 69.9 + - - +
169A CYS* 5.5 0.9 - - + +
200A ASP* 3.6 15.3 - - + +
202A SER* 5.9 1.8 - - - +
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Residues in contact with ILE 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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85A TYR* 3.3 20.9 - - + +
87A ILE* 3.8 30.3 - - + -
156A LEU* 3.7 35.7 - - + -
160A ILE* 4.1 8.3 - - + -
167A LYS* 1.3 82.9 - - - +
169A CYS* 1.3 64.7 + - - +
170A VAL* 4.1 9.2 - - + -
187A LEU* 5.1 4.0 - - + -
199A ILE* 3.0 33.4 - - + +
200A ASP 2.9 11.0 + - - +
201A ILE* 3.4 5.1 - - + +
202A SER* 3.0 26.5 + - - +
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Residues in contact with CYS 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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5A LYS* 3.9 24.0 - - - +
9A MET* 3.2 42.5 - - + +
84A GLU* 6.1 0.4 - - - +
85A TYR 3.0 10.3 + - - +
86A VAL* 3.4 6.3 - - + -
87A ILE 2.9 23.7 + - - +
167A LYS* 5.5 1.3 - - + +
168A ILE* 1.3 73.2 - - - +
170A VAL* 1.3 62.3 + - - +
202A SER* 3.2 21.1 - - - +
204A ILE* 4.2 17.7 - - - -
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Residues in contact with VAL 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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87A ILE* 3.3 25.4 - - + +
89A ILE* 4.1 2.5 - - + -
168A ILE* 4.1 16.4 - - + -
169A CYS* 1.3 74.8 - - - +
171A THR* 1.3 60.9 + - - +
180A SER* 3.5 35.2 - - - +
183A LEU* 4.1 17.0 - - + -
184A ALA* 3.8 25.1 - - + -
187A LEU* 4.6 3.6 - - + -
201A ILE* 4.6 4.3 - - + -
202A SER 2.8 12.2 + - - +
203A THR* 2.6 32.6 + - - -
204A ILE 3.2 2.3 + - - -
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Residues in contact with THR 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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9A MET* 3.2 48.4 + - + +
12A PHE* 4.2 3.6 - - + -
13A SER* 3.0 16.5 + - - +
86A VAL* 4.2 7.9 - - + -
87A ILE 2.9 13.2 + - - +
88A ALA* 3.3 13.2 - - + -
89A ILE 3.0 22.9 + - - -
169A CYS 3.9 0.4 + - - -
170A VAL* 1.3 73.2 - - - +
172A GLY* 1.3 62.2 + - - +
180A SER* 3.5 11.3 - - - -
204A ILE 2.6 24.0 + - - -
206A PHE* 3.6 1.2 - - - -
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Residues in contact with GLY 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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13A SER* 3.1 14.5 + - - -
89A ILE 3.4 12.8 - - - -
171A THR* 1.3 81.5 + - - +
173A HIS* 1.3 58.0 + - - -
176A GLY 3.4 18.2 - - - -
177A GLY* 3.3 5.5 - - - -
180A SER* 3.6 3.0 + - - -
204A ILE 3.9 0.4 + - - -
205A PRO* 3.6 0.2 - - - +
206A PHE* 2.9 26.0 + - - -
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Residues in contact with HIS 173 (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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13A SER* 3.8 17.2 + - - +
14A TYR* 3.3 27.7 + + + -
17A TYR* 2.9 46.3 + + + +
89A ILE 4.0 4.2 + - - +
91A GLY 5.0 1.4 + - - -
94A PRO* 4.3 6.1 - - + -
172A GLY* 1.3 72.2 - - - -
174A SER* 1.3 71.1 + - - +
176A GLY* 2.9 16.6 + - - -
177A GLY 3.5 1.3 - - - -
206A PHE* 3.5 14.6 - - + -
207A ALA* 3.8 17.4 - - + +
312A HIS* 2.8 52.9 + + - -
313A VAL* 4.6 2.9 - - + -
316A TYR* 4.0 4.4 - + - -
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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