Contacts of the strand formed by residues 153 - 160 (chain A) in PDB entry 1PQA
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 LEU 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.9 23.3 - - + +
19A GLY 5.6 4.9 - - - +
20A THR* 3.3 16.4 - - - +
21A SER* 3.8 16.8 - - - +
22A ALA 4.6 0.4 - - - -
136A ALA* 3.2 7.1 - - - +
137A GLY 2.9 36.4 + - - +
141A THR* 3.6 31.4 - - + -
149A PRO* 3.9 14.6 - - + -
151A ASN 3.9 10.8 - - - +
152A LEU* 1.4 83.6 - - - +
154A LYS* 1.4 61.3 + - - +
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Residues in contact with LYS 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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16A ILE* 3.8 4.7 - - - -
19A GLY* 3.0 2.8 - - - -
20A THR* 2.8 55.4 + - - +
21A SER 4.1 9.0 - - - -
22A ALA* 4.1 3.8 - - + -
23A SER* 4.7 4.0 + - - +
26A ASP* 2.7 34.1 + - - +
27A PHE* 4.0 29.6 - - + -
134A THR* 4.3 9.2 - - + -
135A VAL 3.2 12.8 - - - +
136A ALA* 4.1 0.2 - - + -
153A LEU* 1.4 74.9 - - - +
155A VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 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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16A ILE* 3.6 18.2 - - + -
17A VAL 3.8 3.4 - - - +
18A GLY 3.5 23.3 - - - +
19A GLY* 3.9 0.7 - - - -
133A ALA 3.9 0.2 - - - +
134A THR* 3.3 2.9 - - - -
135A VAL* 2.9 53.8 + - + +
154A LYS* 1.3 77.0 - - - +
156A THR* 1.3 67.0 + - - +
157A VAL* 4.1 5.6 + - + -
188A LYS* 3.7 31.9 - - + -
189A ASP 4.1 15.5 - - - +
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Residues in contact with THR 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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132A SER* 3.0 32.1 - - - +
133A ALA 3.1 8.7 - - - +
134A THR* 2.8 22.5 + - - +
155A VAL* 1.3 75.1 - - - +
157A VAL* 1.3 69.3 - - - +
158A PRO* 4.9 0.2 - - - +
183A VAL* 5.4 0.2 - - - +
188A LYS* 3.6 22.3 + - - +
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Residues in contact with VAL 157 (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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132A SER* 4.6 2.7 - - - -
133A ALA* 2.8 37.5 + - + +
135A VAL* 4.7 16.2 - - + -
155A VAL* 4.5 5.6 - - + -
156A THR* 1.3 82.9 - - - +
158A PRO* 1.3 68.7 - - + +
181A ALA* 4.0 20.0 - - + -
182A GLY* 4.0 14.8 - - - +
183A VAL* 4.4 3.6 - - + -
188A LYS* 3.5 41.1 - - + +
189A ASP* 4.6 2.2 - - - +
199A ILE* 4.9 2.5 - - + -
225A TYR* 5.2 2.5 - - - +
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Residues in contact with PRO 158 (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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130A GLY* 4.2 13.9 - - - +
131A SER 3.3 10.5 - - - +
132A SER* 4.6 1.3 - - - -
156A THR 4.9 0.2 - - - +
157A VAL* 1.3 85.7 - - + +
159A ILE* 1.3 68.3 + - - +
160A VAL* 5.4 1.1 - - + -
181A ALA* 3.3 3.1 - - - -
182A GLY 3.0 46.2 + - - +
183A VAL* 3.7 13.7 - - + -
402A SO4 3.5 24.0 - - - +
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Residues in contact with ILE 159 (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 PRO* 3.6 38.4 - - + +
128A VAL 3.3 20.6 - - - +
129A ALA* 3.8 4.0 - - - -
130A GLY* 2.9 23.1 + - - +
131A SER* 3.0 32.1 + - - +
133A ALA* 3.8 22.0 - - + -
158A PRO* 1.3 76.2 - - - +
160A VAL* 1.3 69.2 + - - +
161A SER* 4.1 0.4 + - - -
179A PHE* 3.6 25.4 - - + -
180A CYS 3.5 9.9 - - - +
181A ALA* 4.3 3.4 - - + -
207A ILE* 4.0 2.9 - - + -
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Residues in contact with VAL 160 (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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158A PRO* 3.9 1.1 - - + +
159A ILE* 1.3 79.5 - - - +
161A SER* 1.3 79.6 + - - +
162A ARG 3.4 1.0 + - - -
164A THR* 3.8 24.0 - - + -
165A CYS 4.3 3.4 - - - +
168A GLN* 4.8 0.9 - - - +
180A CYS* 2.9 29.0 + - + +
181A ALA 3.9 0.4 - - - -
182A GLY 3.5 35.2 - - - +
183A VAL 6.0 0.4 - - - -
184A SER 6.1 0.2 - - - +
222A SER* 3.5 26.7 - - - +
402A SO4 6.0 0.4 - - - +
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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