Contacts of the strand formed by residues 57 - 63 (chain B) in PDB entry 3ER0
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 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B CYS* 3.2 37.7 - - - +
24B SER* 3.8 7.6 - - - -
44B MET* 3.7 22.2 - - + -
45B SER 3.5 4.3 - - - +
46B THR* 3.8 18.2 - - + -
56B LYS* 1.3 70.0 - - - +
58B HIS* 1.3 61.2 + - - +
59B LEU* 3.6 27.2 - - + +
72B ASP 3.5 3.5 - - - +
73B LEU* 3.6 1.2 - - - -
74B SER 2.9 30.1 + - - -
76B SER* 3.6 20.8 - - - +
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Residues in contact with HIS 58 (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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43B ASP* 4.8 1.5 + - - -
44B MET* 3.2 5.5 - - - -
45B SER* 3.0 47.7 + - - -
47B SER* 6.1 1.6 - - - +
56B LYS 3.5 4.2 + - - +
57B VAL* 1.3 70.7 - - - +
59B LEU* 1.3 61.2 + - - +
60B VAL* 3.3 26.7 + - + +
71B GLU* 3.3 30.5 + - + +
72B ASP 3.2 19.5 - - - -
73B LEU* 4.0 25.4 - - + +
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Residues in contact with LEU 59 (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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23B CYS* 3.8 16.4 - - - +
26B LEU* 4.9 7.9 - - + -
32B VAL* 4.7 17.3 - - + -
34B ILE* 5.2 1.5 - - + +
41B ILE* 3.9 28.0 - - + -
43B ASP 3.6 4.7 - - - +
44B MET* 4.1 12.6 - - + -
57B VAL* 3.6 36.3 - - + +
58B HIS* 1.3 72.3 - - - +
60B VAL* 1.3 61.7 + - - +
61B ALA* 3.9 3.3 + - + +
70B LEU 3.8 0.5 - - - +
71B GLU* 3.2 5.7 - - - +
72B ASP* 2.8 68.2 + - + +
80B MET* 4.9 2.9 - - + -
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Residues in contact with VAL 60 (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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41B ILE* 4.1 0.6 - - - -
42B VAL* 2.8 21.7 + - + -
43B ASP* 2.6 64.0 + - + +
58B HIS* 3.3 34.3 - - + +
59B LEU* 1.3 70.3 - - - +
61B ALA* 1.3 55.7 + - - +
69B LYS* 3.8 31.9 - - + -
70B LEU 3.6 3.4 - - - +
71B GLU* 4.4 11.7 - - + +
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Residues in contact with ALA 61 (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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32B VAL* 4.3 4.9 - - + -
34B ILE* 5.2 3.8 - - + -
39B CYS* 3.7 16.3 - - + -
40B LYS 3.1 20.2 - - - +
41B ILE* 3.8 17.3 - - + -
42B VAL* 3.9 1.1 - - - +
59B LEU* 4.9 3.4 - - + +
60B VAL* 1.3 78.3 - - - +
62B ILE* 1.3 58.4 + - - +
69B LYS* 4.7 0.7 - - - -
70B LEU* 2.6 51.0 + - - +
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Residues in contact with ILE 62 (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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39B CYS* 3.6 1.3 - - - -
40B LYS* 2.6 43.2 + - + +
42B VAL* 3.2 32.0 - - + +
61B ALA* 1.3 73.2 - - - +
63B ASP* 1.3 67.8 + - - +
64B ILE* 5.6 0.2 - - - -
67B GLY* 3.1 28.3 - - - +
69B LYS* 4.3 18.8 - - + +
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Residues in contact with ASP 63 (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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37B ARG* 3.3 26.2 + - + -
38B PRO 3.3 14.1 - - - +
39B CYS* 3.4 15.8 - - - -
61B ALA 3.9 0.6 + - - -
62B ILE* 1.3 76.3 - - - +
64B ILE* 1.3 57.9 + - - +
65B PHE* 2.5 22.3 + - - +
66B THR* 2.2 35.3 + - - -
67B GLY* 3.0 29.3 + - - +
68B LYS* 4.0 9.5 + - - +
70B LEU* 4.9 2.5 - - + +
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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