Contacts of the strand formed by residues 45 - 51 (chain A) in PDB entry 5X6E
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 ILE 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 5.0 0.2 - - - -
44A GLY* 1.3 82.6 - - - +
46A THR* 1.3 64.9 + - - +
62A TYR* 4.8 2.5 - - + -
63A TYR 3.2 6.1 - - - +
64A LYS* 3.7 27.6 - - + -
65A GLY 4.9 0.2 - - - +
87A VAL* 3.2 21.1 - - - +
88A ILE* 3.3 33.5 + - + -
89A SER* 3.2 19.3 + - - +
92A ALA* 4.2 0.9 - - - +
154A TYR* 3.5 35.4 - - + +
166A LEU* 5.4 8.3 - - + -
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 5.3 3.1 - - - -
41A LEU* 3.6 17.5 - - + -
44A GLY 4.3 0.4 + - - -
45A ILE* 1.3 74.5 - - - +
47A LYS* 1.3 61.1 + - - +
62A TYR* 3.4 7.3 - - - +
63A TYR* 2.8 59.6 + - + +
69A ILE* 5.0 0.4 - - + -
85A LEU* 3.3 24.8 - - + +
86A GLU 2.3 32.7 + - - -
87A VAL* 4.0 8.8 - - - +
88A ILE* 3.2 13.4 - - - +
92A ALA* 5.9 0.9 - - - -
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Residues in contact with LYS 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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46A THR* 1.3 77.9 + - - +
48A LEU* 1.3 63.1 + - - +
49A THR* 3.7 21.0 + - + +
57A ILE* 5.1 4.8 - - - +
59A ASN* 3.5 28.5 + - - +
61A GLN 3.8 5.2 - - - +
62A TYR* 4.1 12.6 - - + -
63A TYR* 5.2 0.2 - - - -
84A ASN 3.4 0.2 - - - +
85A LEU* 3.3 10.3 - - - +
86A GLU* 2.5 62.8 + - + +
88A ILE* 3.5 18.2 - - + -
173A GLU* 2.8 35.8 + - - +
176A TYR* 5.1 5.3 - - - -
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Residues in contact with LEU 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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29A PHE* 4.6 7.9 - - + -
47A LYS* 1.3 73.4 - - - +
49A THR* 1.3 61.0 + - - +
59A ASN* 3.6 4.5 - - - -
60A LEU* 2.9 45.4 + - + +
61A GLN* 2.9 26.0 + - + +
63A TYR* 3.3 32.8 - - + +
69A ILE* 5.3 4.0 - - + -
83A TYR* 3.8 23.3 - - + -
84A ASN 3.2 18.8 - - - +
85A LEU* 4.4 10.1 - - + +
128B LEU* 4.2 23.8 - - + -
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Residues in contact with THR 49 (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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27A LEU* 5.5 0.3 - - - +
47A LYS* 3.7 37.5 - - + +
48A LEU* 1.3 78.5 - - - +
50A SER* 1.3 62.0 + - - +
51A ILE* 4.9 8.3 - - - +
57A ILE* 5.6 6.7 - - + -
58A MET 3.4 8.3 - - - -
59A ASN* 4.4 4.5 - - - +
60A LEU* 4.9 1.3 - - - -
83A TYR* 3.7 11.2 - - - +
84A ASN* 2.9 57.1 + - - +
86A GLU* 4.4 15.7 + - + +
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Residues in contact with SER 50 (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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31A GLN* 4.5 2.9 - - - -
49A THR* 1.3 76.3 - - - +
51A ILE* 1.3 62.9 + - - +
52A SER* 4.8 1.6 + - - -
56A THR 3.2 10.6 - - - +
57A ILE* 3.2 1.7 - - - -
58A MET* 3.1 24.8 + - - +
60A LEU* 4.6 2.7 - - - -
82A TYR 5.1 0.7 - - - -
83A TYR* 4.2 11.9 - - - -
132B ASN* 3.2 27.1 + - - -
220B LYS* 3.2 30.4 - - - +
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Residues in contact with ILE 51 (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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31A GLN* 3.1 31.8 + - - +
32A TRP* 4.9 12.0 - - + -
49A THR* 4.9 6.1 - - - +
50A SER* 1.3 82.7 + - - +
52A SER* 1.3 68.9 + - - +
55A GLY* 3.2 26.0 - - - +
56A THR 3.1 2.5 - - - -
57A ILE* 3.9 20.2 - - + -
84A ASN* 4.2 18.6 - - - +
220B LYS* 5.3 2.6 - - - +
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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