Contacts of the strand formed by residues 55 - 61 (chain B) in PDB entry 1E8O
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 LYS 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A MET 3.2 15.1 - - - +
74A VAL* 5.0 0.7 - - - -
32B LYS* 3.7 7.3 - - - +
33B TYR* 3.4 39.2 + - + +
54B ASN* 1.3 84.8 + - - +
56B CYS* 1.3 62.3 + - - +
70B VAL* 3.4 31.3 - - + +
71B VAL 3.5 9.2 - - - +
72B SER* 4.1 19.9 - - - -
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Residues in contact with CYS 56 (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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70A MET* 3.9 24.2 - - - +
73A MET* 3.3 33.2 - - + -
74A VAL* 5.7 1.1 - - + -
30B LEU* 3.2 27.8 - - - -
31B LYS 3.5 5.6 - - - +
33B TYR* 3.7 4.3 - - - +
55B LYS* 1.3 79.7 - - - +
57B LEU* 1.3 60.0 + - - +
58B LEU* 3.9 2.0 + - - +
69B THR 3.9 0.2 - - - +
70B VAL* 3.6 1.6 - - - -
71B VAL* 3.1 35.0 + - - +
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Residues in contact with LEU 57 (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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3B LEU* 4.2 16.4 - - + -
29B THR 3.9 0.6 - - - +
30B LEU* 3.6 6.8 - - - +
31B LYS* 2.7 43.2 + - + +
33B TYR* 3.8 27.9 - - + +
56B CYS* 1.3 73.7 - - - +
58B LEU* 1.3 61.4 + - - +
59B ARG* 4.3 32.1 - - + +
68B SER* 4.7 2.7 - - - -
69B THR 3.5 20.0 - - - +
70B VAL* 3.6 19.3 - - + +
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Residues in contact with LEU 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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66A HIS* 5.5 1.3 - - + -
70A MET* 3.5 18.4 - - + -
9B PHE* 3.9 17.5 - - + -
28B ILE* 4.5 13.7 - - + -
29B THR 3.5 13.7 - - - +
30B LEU* 3.6 30.7 - - + -
56B CYS* 4.9 2.9 - - - +
57B LEU* 1.3 73.9 - - - +
59B ARG* 1.3 63.2 + - - +
68B SER* 3.1 3.3 - - - -
69B THR* 2.7 50.5 + - + +
71B VAL* 5.0 2.2 - - + -
79B PHE* 3.5 33.0 - - + -
83B TYR* 4.4 13.2 - - + +
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Residues in contact with ARG 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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26A ARG* 4.0 23.2 - - - +
9B PHE* 4.7 2.2 - - - -
28B ILE* 3.2 5.9 - - - +
29B THR* 2.6 55.6 + - - +
31B LYS* 6.0 2.8 - - - +
57B LEU* 4.3 22.8 - - + +
58B LEU* 1.3 74.1 - - - +
60B ALA* 1.3 61.0 + - - +
66B LYS* 6.6 0.2 - - - -
67B ILE 3.3 5.8 - - - +
68B SER* 3.2 28.3 - - - -
1002B SO4 3.7 27.3 + - - -
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Residues in contact with ALA 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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9B PHE* 4.5 5.2 - - + -
13B LEU* 4.0 17.3 - - + -
16B LEU* 3.8 4.6 - - + +
26B VAL* 5.1 0.4 - - + -
27B TYR 2.9 13.5 - - - +
28B ILE* 4.0 17.0 - - + -
59B ARG* 1.3 77.2 - - - +
61B THR* 1.3 63.4 + - - +
66B LYS* 4.6 0.2 - - - +
67B ILE* 2.8 49.9 + - + +
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Residues in contact with THR 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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16B LEU* 3.9 9.4 - - - +
26B VAL* 3.6 2.5 - - - +
27B TYR* 2.8 49.2 + - + +
59B ARG* 6.6 0.2 - - + -
60B ALA* 1.3 76.5 - - - +
62B ASP* 1.3 64.5 + - - +
63B GLY* 3.0 19.9 + - - +
65B LYS 2.4 28.1 + - - -
66B LYS* 3.7 17.9 - - + +
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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