Contacts of the strand formed by residues 41 - 48 (chain A) in PDB entry 1XO8
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 TYR 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.3 23.1 - - + -
30A ASP 3.3 8.7 - - - +
31A LEU* 3.6 18.6 - - + -
40A GLU* 1.3 73.9 - - - +
42A LEU* 1.3 52.4 + - - +
43A ALA* 3.3 26.9 - - + -
62A PHE* 3.4 21.0 - - - -
64A PHE* 2.7 42.3 - + + -
71A ILE* 4.7 4.3 - - + -
92A ILE* 4.1 7.5 - - + +
93A PRO 2.7 21.1 - - - +
94A VAL* 2.7 21.7 - - - +
95A VAL* 2.8 52.4 - - + +
96A VAL* 4.1 6.1 - - + -
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Residues in contact with LEU 42 (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 ASP* 2.6 42.2 + - + +
32A LYS* 3.4 27.5 - - + +
41A TYR* 1.3 71.4 - - - +
43A ALA* 1.3 65.1 + - - +
44A LYS* 3.6 6.4 + - + +
91A ASP* 3.7 23.6 - - + +
92A ILE 3.6 9.4 - - - +
93A PRO* 3.3 17.0 - - + +
94A VAL* 3.5 10.6 - - + +
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Residues in contact with ALA 43 (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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28A ASP 3.7 4.0 - - - +
29A VAL* 4.0 13.0 - - + +
41A TYR* 3.3 29.9 + - + +
42A LEU* 1.3 76.2 - - - +
44A LYS* 1.3 62.3 + - - +
45A VAL* 3.5 3.9 + - + -
64A PHE* 4.7 3.8 - - + -
91A ASP* 3.6 3.1 - - - -
92A ILE* 2.9 52.8 + - + +
118A LEU* 5.8 2.7 - - + -
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Residues in contact with LYS 44 (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 VAL* 4.6 0.5 - - - -
27A THR* 2.9 30.9 + - + +
28A ASP* 2.8 45.1 + - + +
42A LEU* 3.6 7.1 + - + +
43A ALA* 1.3 70.9 - - - +
45A VAL* 1.3 64.2 + - - +
46A SER* 5.3 0.2 - - - +
89A ALA* 4.4 15.4 - - + +
90A LEU 3.5 11.9 + - - +
91A ASP* 2.7 34.1 + - - -
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Residues in contact with VAL 45 (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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25A SER* 3.0 40.2 - - - +
26A VAL* 5.3 0.2 - - - -
27A THR* 3.4 1.8 - - - +
43A ALA* 4.1 3.1 - - + +
44A LYS* 1.3 77.2 - - - +
46A SER* 1.3 62.3 + - - +
47A VAL* 3.5 19.5 - - + -
60A ILE* 4.6 3.4 - - + -
89A ALA* 3.2 6.4 - - - +
90A LEU* 2.6 57.7 + - + +
92A ILE* 3.4 35.2 - - + -
118A LEU* 5.9 3.6 - - + -
120A ILE* 5.9 1.1 - - + -
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Residues in contact with SER 46 (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 GLY* 3.2 4.2 - - - -
25A SER* 2.9 18.8 + - - -
26A VAL 3.2 24.9 + - - +
27A THR* 3.2 17.7 + - - +
44A LYS* 5.3 0.2 - - - +
45A VAL* 1.3 76.6 + - - +
47A VAL* 1.3 62.4 + - - +
48A THR* 3.5 1.4 + - - -
87A MET* 3.4 32.0 - - - +
88A THR 3.0 7.6 + - - -
89A ALA* 4.1 8.1 - - - +
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Residues in contact with VAL 47 (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 GLY 2.8 13.0 - - - +
25A SER* 3.1 17.3 - - - +
45A VAL* 3.5 17.5 - - + -
46A SER* 1.3 70.7 - - - +
48A THR* 1.3 64.3 + - - +
49A ASN* 4.7 0.9 - - - +
55A ILE* 5.3 0.7 - - + -
58A CYS* 4.9 6.3 - - + -
60A ILE* 5.4 1.8 - - + -
80A GLY* 5.8 0.7 - - - +
82A LEU* 3.7 16.0 - - + +
86A ASP 3.6 2.3 - - - +
87A MET* 3.3 0.3 - - - -
88A THR* 2.7 47.3 + - + +
90A LEU* 3.8 25.4 - - + -
124A ILE* 4.4 22.7 - - + -
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Residues in contact with THR 48 (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 PRO 5.0 3.1 - - - +
23A GLU* 2.9 34.0 - - + +
24A GLY* 2.8 29.6 + - - +
46A SER 4.0 0.2 + - - -
47A VAL* 1.3 74.8 - - - +
49A ASN* 1.3 61.8 + - - +
50A PRO* 3.9 0.9 - - - +
85A LYS 5.2 0.9 - - - -
86A ASP* 3.1 24.2 - - - +
87A MET* 3.2 32.6 - - + +
124A ILE* 4.8 2.3 - - - +
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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