Contacts of the strand formed by residues 69 - 76 (chain A) in PDB entry 2EQB
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 VAL 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A SER* 3.0 30.7 - - - +
21A MET* 4.3 24.7 - - + -
61A THR* 3.6 2.9 - - - +
62A VAL* 2.6 52.8 + - + +
67A LYS* 2.8 48.4 + - + +
68A LYS* 1.3 74.4 - - - +
70A LYS* 1.3 62.9 + - - +
71A LEU* 4.0 11.6 + - + +
177A ALA* 5.6 0.4 - - + -
181A GLN* 4.9 7.6 - - + +
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Residues in contact with LYS 70 (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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17A GLY* 3.1 35.3 - - - +
18A SER 3.8 11.7 + - - +
19A SER 2.8 8.1 + - - +
20A ILE* 3.6 28.8 - - + +
21A MET* 3.1 25.8 + - - +
59A ILE* 4.3 22.8 - - + +
60A LYS 4.1 4.0 - - - -
61A THR* 3.6 19.3 - - - +
68A LYS* 3.6 12.3 - - + +
69A VAL* 1.3 74.7 - - - +
71A LEU* 1.3 64.2 + - - +
72A GLN* 3.9 3.3 + - + +
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Residues in contact with LEU 71 (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 MET* 3.6 30.1 - - + +
23A ILE* 4.7 7.9 - - + -
40A PHE* 3.8 31.6 - - + -
58A LYS 3.5 0.9 - - - +
59A ILE* 3.0 9.0 - - - +
60A LYS* 3.0 41.1 + - + +
62A VAL* 4.4 11.4 - - + -
69A VAL* 4.5 15.5 - - + +
70A LYS* 1.3 78.8 - - - +
72A GLN* 1.3 60.2 + - - +
73A LEU* 3.3 18.1 - - + +
173A PHE* 4.3 18.6 - - + +
177A ALA* 5.2 6.1 - - + -
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Residues in contact with GLN 72 (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 ILE* 3.1 38.2 - - + +
21A MET 3.1 8.6 + - - +
22A LYS* 3.8 20.8 - - + +
23A ILE 2.8 28.3 + - - +
57A PHE* 3.7 25.5 - - + -
58A LYS 3.5 4.5 - - - -
59A ILE* 4.1 20.7 - - + +
70A LYS* 4.6 3.6 - - + +
71A LEU* 1.3 77.5 - - - +
73A LEU* 1.3 64.0 + - - +
74A TRP* 5.3 6.3 + - + +
102B GLU* 6.1 0.7 - - - +
106B ALA* 5.2 4.7 - - - +
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Residues in contact with LEU 73 (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 ILE* 3.1 24.0 - - + +
24A LEU* 5.4 0.4 - - - -
25A LEU* 5.9 1.8 - - + -
37A LEU* 3.2 34.1 - - + +
40A PHE* 4.0 24.9 - - + -
41A VAL* 4.6 7.9 - - + -
56A ASP 3.7 0.7 - - - +
57A PHE* 3.4 6.4 - - - -
58A LYS* 2.8 42.5 + - + +
60A LYS* 5.3 1.6 - - + -
71A LEU* 3.3 33.4 - - + +
72A GLN* 1.3 94.7 - - - +
74A TRP* 1.3 66.0 + - - +
173A PHE* 4.2 7.4 - - + -
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Residues in contact with TRP 74 (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 LYS* 5.9 3.5 - - + +
23A ILE 3.2 15.3 + - - -
24A LEU* 3.7 14.2 - - + +
25A LEU* 3.2 28.6 + - - +
37A LEU* 4.8 1.0 - - - +
55A ILE* 3.6 21.3 - - + -
56A ASP 3.6 2.7 - - - -
57A PHE* 3.5 41.6 - + + -
72A GLN* 5.3 5.0 + - - +
73A LEU* 1.3 77.1 - - - +
75A ASP* 1.3 61.2 + - - +
76A THR* 4.2 0.9 - - + -
89A TYR* 3.2 55.6 - + + -
102B GLU* 3.2 35.2 + - + +
105B THR* 3.3 23.1 - - - -
106B ALA* 3.7 23.8 - - + -
109B PHE* 3.8 7.2 - + - -
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Residues in contact with ASP 75 (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 LEU* 5.0 3.8 - - + -
33A LYS* 4.1 19.6 + - - +
34A SER* 3.1 28.3 + - - -
37A LEU* 3.3 31.1 - - + +
50A ILE* 3.1 32.1 - - - +
55A ILE* 3.5 1.8 - - - +
56A ASP* 3.0 30.1 + - + +
58A LYS* 5.8 2.9 + - + +
74A TRP* 1.3 73.1 - - - +
76A THR* 1.3 71.1 + - - +
201A PO4 4.6 1.4 + - - -
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Residues in contact with THR 76 (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* 4.4 20.6 - - + -
25A LEU 4.5 5.9 + - - +
27A GLY 5.4 1.0 - - - +
33A LYS* 4.5 14.2 + - - -
50A ILE* 3.6 5.2 - - - -
54A GLY 3.5 6.5 + - - -
55A ILE* 5.0 2.0 - - - -
74A TRP* 4.9 0.4 - - + -
75A ASP* 1.3 88.1 + - - +
77A ALA* 1.3 56.6 + - - +
78A GLY* 2.5 26.0 + - - -
86A THR* 3.7 33.7 - - + +
89A TYR* 4.8 8.7 - - + -
90A TYR* 6.5 0.9 - - + -
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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