Contacts of the strand formed by residues 60 - 65 (chain E) in PDB entry 5D7I
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 PHE 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E GLN* 4.4 16.4 - - - -
46E LEU* 4.0 42.4 - - + -
57E LYS* 2.7 46.0 + - + +
58E GLY 4.0 0.7 - - - +
59E ARG* 1.3 118.1 - - + +
61E SER* 1.3 58.6 + - - +
73E LEU* 4.5 11.2 - - + -
74E LEU 3.2 4.0 - - - +
75E LEU* 3.6 42.4 - - + -
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Residues in contact with SER 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LEU* 4.1 16.6 - - - +
55E GLU 3.4 9.0 - - - -
56E GLU* 3.3 24.1 - - - +
60E PHE* 1.3 75.6 + - - +
62E SER* 1.3 64.5 + - - +
63E PHE 4.3 0.2 - - - -
72E TYR* 5.6 0.7 - - - -
73E LEU* 3.4 5.4 - - - +
74E LEU* 2.7 57.6 + - - +
76E LYS* 3.6 12.8 + - - -
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Residues in contact with SER 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E TRP* 3.9 5.9 - - - -
47E SER* 2.5 32.8 + - - -
49E ASN* 3.0 29.9 + - - -
54E LEU* 3.5 2.4 - - - -
55E GLU* 2.8 41.2 + - - -
61E SER* 1.3 71.0 - - - +
63E PHE* 1.3 61.2 + - - +
71E SER* 5.3 0.2 - - - -
72E TYR 3.4 5.8 - - - -
73E LEU* 3.5 15.1 - - - +
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Residues in contact with PHE 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ASN* 4.3 2.3 - - - -
53E GLY* 3.2 27.4 - - - -
54E LEU* 4.2 10.5 - - + +
61E SER 4.3 0.2 - - - -
62E SER* 1.3 74.3 - - - +
64E LEU* 1.3 83.0 + - - +
65E SER* 3.8 11.9 - - - -
70E TYR* 3.8 32.3 - + - -
71E SER* 2.8 30.5 + - - -
72E TYR* 2.9 59.5 + + + +
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Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E TYR* 3.8 28.5 - - + +
29E PHE* 3.7 16.6 - - + -
32E LEU* 4.8 3.6 - - + -
49E ASN* 3.7 17.5 - - + +
50E VAL* 3.6 33.4 - - - +
51E LEU 3.5 20.9 - - - +
52E ASP* 3.4 4.5 - - - +
53E GLY 2.9 31.3 + - - -
63E PHE* 1.3 85.4 - - - +
65E SER* 1.3 69.5 + - - +
66E ARG* 4.0 5.2 - - + +
70E TYR 3.5 14.6 - - - +
71E SER* 4.2 7.0 - - - -
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Residues in contact with SER 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E TYR* 4.0 0.7 + - - -
52E ASP* 3.7 5.0 - - - -
63E PHE* 3.8 19.5 - - - -
64E LEU* 1.3 75.4 - - - +
66E ARG* 1.3 58.2 + - - +
67E SER* 3.5 9.4 + - - -
68E LYS* 3.2 34.7 + - - +
69E GLY* 2.9 23.4 + - - -
70E TYR* 2.9 23.8 + - - +
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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