Contacts of the strand formed by residues 79 - 84 (chain A) in PDB entry 2E9J
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 THR 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA* 5.8 3.6 - - + -
46A ILE 3.1 17.9 - - - +
47A ASP* 3.7 24.2 - - + +
75A ASN* 3.5 33.5 + - - +
76A LYS 4.4 3.1 + - - -
77A ASP* 3.3 11.7 + - - +
78A GLY* 1.3 88.2 + - - +
80A TYR* 1.3 80.7 + - - +
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Residues in contact with TYR 80 (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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45A ALA* 3.6 1.9 - - - -
46A ILE* 2.8 66.0 + - + +
48A ALA* 5.7 6.5 - - + -
52A GLY 5.4 1.3 - - - -
53A GLU* 2.5 31.4 + - - -
54A GLY 5.7 0.9 - - - -
56A LEU* 4.0 17.7 - - + -
72A VAL* 6.3 2.7 - - + -
73A HIS 4.1 6.7 - - - +
74A ASP* 3.7 23.1 - - - -
75A ASN* 3.8 4.3 - - - +
76A LYS* 5.7 2.5 - - - -
78A GLY* 5.1 4.5 - - - -
79A THR* 1.3 90.7 - - - +
81A ALA* 1.3 62.2 + - - +
98A TYR* 3.6 26.4 + + - -
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Residues in contact with ALA 81 (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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43A ASP* 5.4 7.0 - - + +
44A PHE 3.5 10.8 - - - +
45A ALA* 4.8 2.2 - - + +
72A VAL* 4.2 0.7 - - - +
73A HIS* 2.9 53.2 + - + +
75A ASN* 3.6 14.4 - - - +
80A TYR* 1.3 72.8 - - - +
82A VAL* 1.3 69.9 + - - +
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Residues in contact with VAL 82 (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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42A VAL 3.9 0.2 - - - +
43A ASP* 3.0 22.2 - - - +
44A PHE* 3.2 51.6 + - + -
46A ILE* 4.2 12.1 - - + -
56A LEU* 4.5 12.1 - - + -
58A VAL* 4.0 26.9 - - + -
60A ILE* 5.6 0.4 - - + -
70A ALA* 4.6 3.4 - - + -
71A ILE 3.3 18.8 - - - +
72A VAL* 5.0 4.7 - - + -
73A HIS* 4.8 0.4 - - - +
81A ALA* 1.3 83.1 - - - +
83A THR* 1.3 68.3 + - - +
84A TYR* 5.5 1.3 - - + -
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Residues in contact with THR 83 (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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41A PRO* 4.4 15.0 - - + -
42A VAL 3.4 21.1 - - - +
43A ASP* 3.2 19.6 + - + +
69A ARG 4.4 0.2 - - - +
70A ALA* 3.7 2.6 - - - -
71A ILE* 3.0 54.8 + - + +
73A HIS* 3.7 18.9 + - - -
82A VAL* 1.3 74.8 - - - +
84A TYR* 1.3 67.3 + - - +
85A ILE* 5.0 3.8 - - + -
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Residues in contact with TYR 84 (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 GLY* 3.2 34.1 + - - -
36A VAL* 3.8 19.5 - - + +
42A VAL* 2.8 56.6 + - + +
44A PHE* 4.4 17.9 - + - -
60A ILE* 3.3 39.7 - - + -
68A LYS* 6.5 0.7 - - + -
69A ARG 4.1 8.1 - - - +
71A ILE* 6.1 0.2 - - - -
82A VAL* 5.5 1.3 - - + -
83A THR* 1.3 76.6 - - - +
85A ILE* 1.3 62.1 + - - +
86A PRO* 3.0 39.7 - - + +
92A TYR* 5.6 6.5 - + + -
94A ILE* 4.9 8.1 - - + -
110A ILE* 4.4 4.0 - - + +
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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