Contacts of the strand formed by residues 139 - 149 (chain A) in PDB entry 1POZ
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 PHE 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASP* 5.9 0.4 - - - -
54A LYS* 6.3 3.4 - - - -
138A ALA* 1.3 84.5 - - - +
140A ASP* 1.3 59.4 + - - +
159A GLY* 3.3 2.3 - - - -
160A GLU* 2.6 80.3 + - + +
161A TYR* 3.4 25.6 - - + -
163A THR* 3.6 22.4 - - + -
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Residues in contact with ASP 140 (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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139A PHE* 1.3 82.0 - - - +
141A GLY* 1.3 63.0 + - - +
158A LYS 5.4 3.4 - - - +
159A GLY* 4.5 3.1 - - - -
160A GLU* 2.8 17.8 - - - +
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Residues in contact with GLY 141 (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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140A ASP* 1.3 83.1 + - - +
142A PRO* 1.3 68.2 - - - +
143A ILE 2.9 2.0 + - - -
158A LYS* 3.4 5.4 - - - +
159A GLY* 2.4 40.0 + - - +
160A GLU* 3.1 9.0 - - - -
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Residues in contact with PRO 142 (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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20A ALA* 2.8 31.5 + - + +
141A GLY* 1.3 80.5 - - - +
143A ILE* 1.3 61.4 + - + +
144A THR* 3.3 1.4 + - - -
158A LYS* 3.5 31.5 + - + +
160A GLU* 4.2 7.6 - - + +
169A TYR* 6.0 0.9 - - - +
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Residues in contact with ILE 143 (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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20A ALA* 3.7 22.7 - - + -
22A ILE* 3.5 28.0 - - + -
141A GLY 2.9 0.2 + - - -
142A PRO* 1.3 76.2 - - + +
144A THR* 1.3 61.5 + - - +
145A ILE* 2.8 11.3 + - + -
158A LYS* 3.2 2.9 - - - -
159A GLY 2.8 43.4 + - - +
160A GLU* 3.4 31.2 - - + -
161A TYR* 3.6 21.8 - - + +
162A ARG 4.1 0.4 - - - +
163A THR* 3.6 29.4 - - - +
164A ASN 4.6 2.2 - - - +
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Residues in contact with THR 144 (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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20A ALA 3.0 18.6 + - - -
21A GLN* 3.2 21.4 - - + +
22A ILE 2.6 34.6 + - - +
142A PRO 3.3 2.5 + - - -
143A ILE* 1.3 67.7 - - - +
145A ILE* 1.3 52.3 + - - +
146A THR* 3.1 19.9 + - - +
156A VAL* 3.8 14.8 - - + -
157A GLN 3.4 4.7 - - - +
158A LYS* 4.6 11.7 + - + -
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Residues in contact with ILE 145 (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 LEU* 3.1 31.0 - - + -
135A LEU* 3.6 14.1 - - + -
138A ALA* 5.1 5.2 - - + -
143A ILE* 2.8 14.1 + - + +
144A THR* 1.3 66.9 - - - +
146A THR* 1.3 54.3 + - - +
147A ILE* 3.3 11.9 - - + +
157A GLN* 2.6 55.8 + - - +
159A GLY* 3.5 11.9 - - - +
160A GLU 3.5 27.4 - - - +
161A TYR* 3.3 32.1 - - + +
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Residues in contact with THR 146 (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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22A ILE 4.2 7.4 - - - -
23A ASP* 5.1 5.2 - - - +
24A LEU* 2.7 39.9 + - - +
144A THR* 3.1 12.2 + - - +
145A ILE* 1.3 68.8 - - - +
147A ILE* 1.3 58.2 + - - +
148A VAL* 3.5 17.3 + - + -
154A ARG* 5.3 4.3 - - + -
155A TYR 3.1 18.8 - - - +
156A VAL* 2.9 28.8 - - + +
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Residues in contact with ILE 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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24A LEU* 3.3 31.2 - - + -
26A ILE* 3.3 31.6 - - + -
34A PHE* 4.6 6.3 - - + -
52A LEU* 4.5 2.7 - - + -
132A VAL* 4.7 4.7 - - + -
133A THR* 3.2 22.7 - - - +
135A LEU* 4.2 7.0 - - + -
145A ILE* 3.3 22.9 - - + +
146A THR* 1.3 69.8 - - - +
148A VAL* 1.3 62.4 + - - +
149A ASN 3.6 1.4 + - - -
154A ARG* 3.5 1.2 - - - -
155A TYR* 2.7 67.1 + - + +
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Residues in contact with VAL 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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23A ASP* 5.5 6.7 - - + +
24A LEU 3.0 25.5 + - - +
25A ASN* 3.2 20.6 + - - +
26A ILE 2.7 32.0 + - - +
146A THR* 4.1 17.5 - - + +
147A ILE* 1.3 71.9 - - - +
149A ASN* 1.3 61.9 + - - +
150A ARG 3.0 9.7 + - - +
153A THR 4.0 6.5 - - - +
154A ARG* 4.2 13.7 - - + +
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Residues in contact with ASN 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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26A ILE* 3.0 32.3 + - - +
27A THR 4.4 9.6 + - - +
28A CYS* 4.6 0.8 - - - +
129A CYS* 3.6 17.3 - - - +
147A ILE 3.6 2.4 + - - -
148A VAL* 1.3 66.9 - - - +
150A ARG* 1.3 54.1 - - - +
151A ASP* 2.2 24.1 + - - -
152A GLY* 2.7 16.1 + - - +
153A THR* 2.6 51.5 + - + +
155A TYR* 2.5 34.3 + - + -
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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