Contacts of the strand formed by residues 146 - 156 (chain A) in PDB entry 4STD
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 GLY 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.8 9.3 - - - +
47A ARG 3.0 15.9 - - - -
48A ILE* 4.4 0.2 - - - -
133A HIS* 3.5 0.2 - - - -
134A TRP* 3.0 27.3 + - - -
144A PHE* 3.4 22.1 - - - -
145A ALA* 1.3 79.4 - - - +
147A LEU* 1.3 66.3 + - - +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A TRP* 3.8 21.5 - - + +
30A TYR* 4.6 2.2 - - - +
47A ARG 3.1 3.8 + - - -
48A ILE* 4.0 17.9 - - + -
49A ASP* 3.0 26.9 + - - +
50A TYR* 4.0 20.6 - - + +
66A PHE* 4.6 3.8 - - + -
131A ASN* 4.3 1.6 - - - +
132A LEU 3.2 7.0 - - - -
133A HIS* 3.5 19.5 - - + +
134A TRP* 3.5 5.7 - - - -
144A PHE* 3.7 12.1 - - + -
146A GLY* 1.3 77.0 - - - +
148A LYS* 1.3 61.5 + - - +
149A PRO* 3.8 9.4 - - + -
173A BFS 3.6 34.5 - - - +
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Residues in contact with LYS 148 (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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49A ASP* 3.2 38.9 + - + +
51A ARG* 4.1 17.9 - - - +
130A ALA 3.8 1.6 - - - +
131A ASN* 4.7 0.2 - - - -
132A LEU* 2.7 53.6 + - + +
134A TRP* 3.8 13.9 - - + -
147A LEU* 1.3 73.6 - - - +
149A PRO* 1.3 63.9 - - - +
150A ASP* 3.5 6.4 + - + +
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Residues in contact with PRO 149 (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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49A ASP 3.1 14.0 - - - +
50A TYR* 4.1 7.0 - - + -
52A SER* 2.9 23.9 - - - -
53A PHE* 3.4 27.6 - - + -
129A SER* 4.5 0.4 - - - +
131A ASN* 3.5 24.5 - - - +
147A LEU* 3.6 14.1 - - + +
148A LYS* 1.3 87.1 - - - +
150A ASP* 1.3 60.2 + - - +
151A ILE* 3.4 3.8 + - + +
173A BFS 3.6 24.9 - - + +
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Residues in contact with ASP 150 (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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52A SER* 4.0 7.4 + - - -
129A SER* 3.6 2.5 - - - -
130A ALA* 3.0 39.7 + - + +
131A ASN* 4.4 0.4 - - - +
148A LYS* 3.5 5.3 + - + +
149A PRO* 1.3 70.6 - - - +
151A ILE* 1.3 61.0 + - - +
152A ARG* 3.0 39.5 + - - +
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Residues in contact with ILE 151 (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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52A SER* 3.0 19.0 + - - +
53A PHE* 3.8 29.8 - - + -
127A ALA* 4.0 11.9 - - + -
128A HIS 4.1 3.4 - - - +
129A SER* 3.4 17.7 - - - +
149A PRO* 4.4 3.6 - - + +
150A ASP* 1.3 71.9 - - - +
152A ARG* 1.3 63.1 + - - +
153A TRP* 4.3 10.5 - - - +
158A PHE* 3.4 39.3 - - + -
173A BFS 3.6 28.0 - - + -
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Residues in contact with ARG 152 (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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128A HIS* 3.0 10.4 + - + +
129A SER* 4.6 1.8 - - - +
130A ALA* 3.4 21.3 - - - +
150A ASP* 3.0 49.7 + - - +
151A ILE* 1.3 74.0 - - - +
153A TRP* 1.3 72.0 + - + +
28B ASP* 2.6 45.2 + - - -
31B ASP* 4.0 20.8 + - + +
32B SER* 3.7 22.1 - - - -
37B ARG* 4.4 1.4 - - - +
82B ARG* 3.6 32.8 + - - +
118B MET* 5.3 1.2 - - - +
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Residues in contact with TRP 153 (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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127A ALA* 3.8 1.4 - - - -
128A HIS* 3.0 78.3 + + + +
151A ILE* 3.6 8.7 - - - +
152A ARG* 1.3 94.7 - - + +
154A GLY* 1.3 75.9 + - - +
155A GLU* 4.3 2.7 - - + -
158A PHE* 5.9 0.2 - - - -
82B ARG* 3.6 39.5 - - + +
83B THR* 2.9 43.6 + - - +
84B GLN 4.2 0.4 - - - -
109B PRO* 4.2 18.6 - - + -
110B HIS 4.9 0.2 - - - -
111B GLN* 3.8 34.8 - - + -
113B TYR* 3.9 13.5 - - - +
118B MET* 4.9 3.8 - - - -
126B HIS* 5.7 1.1 - - - -
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Residues in contact with GLY 154 (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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126A HIS 3.1 11.7 - - - -
127A ALA* 4.3 2.2 - - - -
153A TRP* 1.3 83.9 - - - +
155A GLU* 1.3 63.3 + - - -
156A PHE 4.0 6.4 + - - +
158A PHE* 4.5 13.2 - - - -
159A ASP* 6.2 0.2 - - - -
111B GLN* 3.5 17.2 + - - -
113B TYR* 3.8 3.9 + - - -
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Residues in contact with GLU 155 (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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107A ARG* 3.9 17.3 + - - -
125A GLY* 3.5 0.9 - - - -
126A HIS* 2.7 40.2 + - + +
128A HIS* 3.8 18.1 + - + -
153A TRP* 4.4 1.8 - - + -
154A GLY* 1.3 71.6 - - - -
156A PHE* 1.3 94.9 + - + +
157A ASP 3.5 0.2 + - - -
158A PHE 4.2 0.7 + - - -
107B ARG* 4.3 5.2 + - - -
109B PRO* 4.9 1.0 - - - +
111B GLN* 3.6 21.1 - - - +
124B LYS* 3.1 22.4 + - - +
126B HIS* 3.2 28.1 + - - +
156B PHE* 3.8 3.8 - - - -
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Residues in contact with PHE 156 (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 LYS* 3.4 44.2 - - + +
126A HIS* 3.6 31.4 - + - -
154A GLY 4.0 5.8 + - - +
155A GLU* 1.3 99.3 - - + +
157A ASP* 1.3 65.5 + - - +
158A PHE 3.9 1.4 + - - -
159A ASP* 5.4 1.6 - - - +
111B GLN* 4.6 4.0 + - - +
121B VAL* 6.2 1.2 - - - +
124B LYS* 3.8 18.2 - - - +
156B PHE* 4.7 5.2 - + - -
155C GLU* 3.8 6.7 - - - -
156C PHE* 4.6 9.4 - + - -
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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