Contacts of the strand formed by residues 119 - 126 (chain A) in PDB entry 2DOS
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 HIS 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER* 6.0 1.0 - - - -
13A LEU 5.5 1.4 + - - +
72A SER* 3.8 11.0 - - - -
116A TYR* 2.6 73.5 + + + +
118A GLU* 1.3 77.1 - - - +
120A TRP* 1.3 99.2 + - - +
121A PHE* 3.5 27.1 - + + -
134A ASN* 3.0 17.7 + - + -
136A LEU* 4.0 25.3 - - + +
137A LEU* 5.5 3.1 - - + -
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Residues in contact with TRP 120 (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 LEU* 3.2 52.5 - - + +
18A CYS* 5.2 10.3 - - - -
72A SER* 5.0 4.8 + - - -
75A PHE* 6.1 2.5 - - + -
76A SER* 5.0 3.1 - - - -
77A ILE* 3.2 45.1 - - + -
80A ILE* 3.8 37.5 - - + -
113A ILE* 4.2 25.8 - - + -
114A CYS 3.7 6.3 - - - -
115A ASN* 3.1 26.7 - - + +
119A HIS* 1.3 98.3 + - - +
121A PHE* 1.3 61.0 + - - +
122A THR* 5.5 1.8 - - - +
134A ASN* 2.7 30.6 - - - +
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Residues in contact with PHE 121 (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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113A ILE* 3.5 8.8 - - - +
114A CYS* 2.8 56.5 + - + +
119A HIS* 3.5 25.4 - + + +
120A TRP* 1.3 75.3 - - - +
122A THR* 1.3 77.0 + - - +
123A VAL* 4.1 2.7 - - + -
132A ASN* 3.7 32.5 - - + -
133A LEU* 3.8 16.6 - - - -
134A ASN* 4.3 5.8 - - + -
137A LEU* 4.2 14.1 - - + -
141A GLU* 3.6 21.5 - - - -
151A PHE* 5.7 9.4 - + - -
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Residues in contact with THR 122 (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 LEU* 6.1 0.5 - - - +
18A CYS* 3.1 45.9 - - - +
21A ASN* 5.4 3.6 - - + -
22A LEU* 4.5 15.3 - - + +
113A ILE* 3.7 18.6 - - + +
120A TRP* 5.5 2.4 - - - +
121A PHE* 1.3 74.4 - - - +
123A VAL* 1.3 68.4 + - - +
124A ARG* 5.8 1.8 - - + -
131A PHE* 4.0 3.8 - - + +
132A ASN* 3.5 2.1 - - - -
133A LEU* 2.9 50.6 + - + +
134A ASN* 4.7 6.3 + - - +
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Residues in contact with VAL 123 (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 LEU* 5.5 0.2 - - - +
111A SER* 3.8 4.7 + - - -
112A PHE* 2.6 59.7 + - + +
114A CYS* 5.7 5.2 - - + +
121A PHE* 4.1 8.7 + - + -
122A THR* 1.3 79.7 - - - +
124A ARG* 1.3 64.8 + - - +
130A TRP* 3.2 29.6 - - + -
131A PHE 3.5 2.2 - - - +
132A ASN* 3.0 41.7 - - + +
148A LEU* 4.3 7.6 - - + -
151A PHE* 4.9 10.3 - - + -
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Residues in contact with ARG 124 (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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21A ASN 5.4 0.7 - - - +
22A LEU* 3.5 35.6 + - + +
24A GLN* 3.5 26.9 - - + +
110A ARG* 3.6 15.9 + - - +
111A SER* 4.1 4.7 - - - -
122A THR* 4.4 2.2 + - + -
123A VAL* 1.3 75.4 - - - +
125A LYS* 1.3 90.5 + - - +
126A LEU* 4.9 1.6 - - + -
130A TRP* 3.1 9.4 - - - -
131A PHE* 2.7 56.9 + - + +
169A LEU* 3.2 47.8 - - - +
171A ASP* 3.6 20.2 + - - +
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Residues in contact with LYS 125 (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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24A GLN* 4.2 1.2 + - - -
107A ILE 3.0 23.3 + - - +
108A ASN* 4.5 7.4 + - - +
109A GLU 3.1 19.1 - - - +
110A ARG* 3.0 39.7 + - + +
124A ARG* 1.3 96.7 + - - +
126A LEU* 1.3 65.7 + - - +
127A GLY 3.8 25.2 + - - +
128A LYS* 5.1 7.2 - - - +
129A GLN 4.9 0.4 - - - +
130A TRP* 3.3 24.9 - - + +
145A ASP* 6.3 1.3 - - - -
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Residues in contact with LEU 126 (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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3A SER* 6.2 2.7 - - - -
4A ILE* 4.6 24.7 - - + -
24A GLN* 3.9 28.9 - - - +
124A ARG* 3.8 2.2 + - + -
125A LYS* 1.3 73.7 - - - +
127A GLY* 1.3 60.8 + - - +
128A LYS 2.9 7.6 + - - -
129A GLN* 2.6 49.2 + - + +
131A PHE* 3.8 37.5 - - + -
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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