Contacts of the strand formed by residues 79 - 84 (chain B) in PDB entry 2A3Z
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 ARG 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A MET* 4.4 3.0 - - - +
60A SER 4.8 2.6 + - - -
61A LYS* 6.0 1.0 - - - +
37B ILE 4.1 0.7 - - - +
38B GLN* 4.2 1.4 - - - -
39B GLU 4.0 7.1 + - - -
40B VAL* 3.0 44.1 + - + +
42B ASP 2.9 29.2 + - - -
43B SER 3.1 19.6 + - - -
44B HIS* 4.6 0.6 - - - +
45B LEU* 3.6 39.9 - - - +
67B VAL* 4.1 5.2 - - + -
68B SER* 3.0 37.8 + - - +
69B GLU* 3.7 13.9 + - - +
70B PRO* 3.8 27.5 - - + +
78B GLU* 1.3 76.3 - - - +
80B TYR* 1.3 68.6 + - - +
1275B FMT 3.3 13.2 + - - +
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 5.3 0.3 - - - +
36B LEU* 4.2 8.5 - - + -
37B ILE 3.8 2.2 - - - -
38B GLN* 4.1 17.5 - - + -
66B VAL 4.5 0.4 - - - -
67B VAL* 3.3 6.4 - - - +
68B SER* 2.9 33.9 + - - +
71B LEU* 3.8 17.5 - - + -
78B GLU* 5.8 0.7 - - - -
79B ARG* 1.3 78.0 - - - +
81B LEU* 1.3 59.6 + - - +
82B PHE* 4.3 3.1 - - + -
111B ARG* 2.7 34.6 + - + +
112B GLU 3.4 21.1 - - - -
113B PRO* 4.0 1.1 - - + -
114B ALA* 3.7 36.1 - - + -
132B ALA* 4.0 16.2 - - + -
133B LEU* 3.6 7.5 - - - -
134B HIS* 2.9 44.0 + - + -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.8 2.9 - - + -
35B VAL 3.7 0.7 - - - +
36B LEU* 3.4 2.5 - - - +
37B ILE* 2.6 67.4 + - + +
40B VAL* 3.9 14.1 - - + -
48B VAL* 3.9 35.2 - - + -
51B LEU* 4.6 7.9 - - + -
65B TYR* 4.1 5.6 - - + -
66B VAL 3.4 12.1 - - - +
67B VAL* 3.8 18.6 - - + -
80B TYR* 1.3 73.6 - - - +
82B PHE* 1.3 69.1 + - - +
83B LEU* 3.9 22.7 - - + -
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 5.9 0.2 - - + -
34B ILE* 4.2 20.2 - - + -
35B VAL 3.4 4.5 - - - -
36B LEU* 4.1 21.3 - - + -
65B TYR* 3.2 8.0 - - - +
66B VAL* 2.7 54.7 + - + +
80B TYR* 4.9 1.8 - - + -
81B LEU* 1.3 78.2 - - - +
83B LEU* 1.3 62.7 + - - +
84B PHE* 5.1 2.7 - - + -
114B ALA* 4.1 22.7 - - + -
116B VAL* 3.6 29.8 - - + -
118B PHE* 4.4 9.9 - + + -
130B ILE* 3.9 36.1 - - + -
132B ALA* 3.9 22.4 - - + -
166B MET* 4.6 1.6 - - + -
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 3.9 8.5 - - + -
33B ASP 4.0 0.2 - - - +
34B ILE* 3.4 2.9 - - - +
35B VAL* 2.9 39.9 + - + +
37B ILE* 3.9 15.9 - - + -
51B LEU* 3.8 22.2 - - + -
52B LEU* 3.8 31.6 - - + -
55B LEU* 3.8 21.8 - - + -
63B TYR* 3.8 16.0 - - + -
64B HIS 3.4 3.1 - - - +
65B TYR* 3.9 10.3 - - + -
81B LEU* 3.9 17.5 - - + -
82B PHE* 1.3 80.7 - - - +
84B PHE* 1.3 61.2 + - - +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLY* 5.9 1.3 - - - -
33B ASP 3.0 12.8 - - - +
34B ILE* 4.3 8.3 - - + -
63B TYR* 3.3 7.2 - - - -
64B HIS* 2.8 72.3 + + + -
65B TYR* 4.0 13.9 - - - -
66B VAL* 4.1 6.5 - - + -
82B PHE* 4.8 2.2 - - + -
83B LEU* 1.3 75.3 - - - +
85B ARG* 1.3 58.8 + - - +
86B PRO* 3.3 13.2 - - + +
89B VAL* 3.7 40.8 - - + -
90B SER* 4.5 1.1 - - - -
91B VAL* 3.5 39.3 - - + -
118B PHE* 4.3 8.3 - + + -
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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