Contacts of the strand formed by residues 53 - 59 (chain A) in PDB entry 1PS9
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.1 28.0 - - + -
20A VAL 3.6 3.7 + - - +
21A LEU* 3.2 20.3 - - + +
22A MET 2.8 23.0 + - - -
51A VAL* 3.4 1.3 - - - +
52A ALA* 1.3 82.8 - - + +
54A ILE* 1.3 80.3 + - - +
55A VAL* 4.8 1.1 - - + -
96A LYS* 3.8 20.0 - - + -
97A ILE 4.1 1.3 - - - +
98A ALA* 4.0 16.6 - - + +
156A ASP* 5.0 1.8 - - + -
210A ILE* 4.7 17.7 - - + -
212A ILE* 3.9 26.7 - - + -
244A ILE* 4.7 7.9 - - + -
306A MET* 5.2 0.4 - - + -
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Residues in contact with ILE 54 (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 MET* 3.8 16.6 - - + -
43A TYR* 3.8 59.9 - - + +
46A ARG* 4.3 6.7 - - + -
47A ALA* 4.3 18.8 - - + +
51A VAL* 3.5 21.8 - - + +
53A LEU* 1.3 77.7 - - - +
55A VAL* 1.3 72.5 + - - +
90A VAL* 4.7 4.9 - - + -
96A LYS 3.1 17.5 + - - +
97A ILE* 4.0 9.0 - - + -
98A ALA 2.8 26.3 + - - -
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Residues in contact with VAL 55 (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 LEU* 4.0 34.1 - - + -
22A MET* 3.0 14.1 + - - +
23A GLY 3.7 2.6 - - - +
24A SER* 3.3 19.5 - - - +
25A MET 4.2 0.7 + - - -
43A TYR* 4.5 2.1 + - - -
53A LEU* 4.8 2.0 - - + -
54A ILE* 1.3 84.2 - - - +
56A SER* 1.3 76.1 + - - +
98A ALA* 3.5 9.4 - - + +
100A GLN* 4.0 5.6 - - + +
159A GLU* 3.1 41.7 - - + +
212A ILE* 4.0 15.5 - - + -
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Residues in contact with SER 56 (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 SER* 2.8 17.7 + - - -
25A MET 4.2 1.1 - - - -
43A TYR* 3.4 23.3 - - - -
54A ILE* 4.1 1.4 - - - +
55A VAL* 1.3 77.2 - - - +
57A GLY* 1.3 73.7 + - - +
59A ILE* 3.9 10.7 - - - +
97A ILE* 4.6 6.7 - - - +
98A ALA 3.0 15.7 + - - -
99A LEU* 3.6 5.4 - - - -
100A GLN* 3.3 19.9 + - - +
155A TYR* 4.8 9.0 - - - -
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Residues in contact with GLY 57 (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 SER* 3.5 2.2 - - - -
25A MET 3.2 31.1 + - - -
26A HIS* 3.6 5.6 - - - -
30A GLU* 4.5 6.7 + - - -
43A TYR* 3.5 9.7 + - - -
56A SER* 1.3 90.7 + - - +
58A GLY* 1.3 67.8 + - - +
59A ILE* 3.4 7.7 + - - +
100A GLN 4.0 1.9 - - - +
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Residues in contact with GLY 58 (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 SER* 3.5 0.2 + - - -
26A HIS* 3.1 25.8 + - - -
30A GLU* 5.1 0.2 - - - +
57A GLY* 1.3 71.8 - - - -
59A ILE* 1.3 62.2 + - - +
72A ALA* 4.4 1.2 - - - +
100A GLN* 3.1 26.0 + - - -
102A LEU* 3.8 15.3 - - - -
702A FMN 2.7 19.8 + - - -
704A MDE 4.8 1.9 - - - -
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Residues in contact with ILE 59 (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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30A GLU* 5.4 7.0 - - + -
56A SER* 3.9 10.8 - - - +
57A GLY 3.4 7.4 - - - +
58A GLY* 1.3 79.8 - - - +
60A ALA* 1.3 65.9 + - - +
72A ALA* 3.8 11.2 - - + -
73A MET* 3.6 35.9 - - - +
74A LEU* 3.7 10.8 - - + +
83A HIS* 3.9 17.9 - - + +
99A LEU* 3.6 34.8 - - + -
100A GLN 3.1 10.5 + - - +
101A ILE* 3.5 7.1 - - - +
102A LEU 2.8 27.5 + - - +
146A CYS* 4.7 1.7 - - - -
155A TYR* 4.9 1.1 - - - +
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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