Contacts of the strand formed by residues 66 - 72 (chain E) in PDB entry 5X11
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 GLU 66 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58E THR* 4.1 17.9 - - + -
59E THR 3.7 4.9 - - - +
60E ILE* 4.5 3.8 - - + +
64E LYS 3.3 6.0 + - - +
65E LEU* 1.3 83.3 - - - +
67E LYS* 1.3 61.9 + - - +
68E LYS* 6.1 0.2 - - - -
7M A 4.3 1.6 - - - +
8M T 4.1 15.3 - - - +
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Residues in contact with LYS 67 (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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18E SER* 4.1 14.8 - - - -
21E ASP* 5.4 2.6 + - - +
57E ARG 3.8 0.3 - - - +
58E THR* 3.3 3.8 - - - +
59E THR* 2.8 64.2 + - + +
61E GLN* 5.1 12.1 - - + +
66E GLU* 1.3 77.0 - - - +
68E LYS* 1.3 65.7 + - - +
69E MET* 3.8 18.6 + - - +
7M A 3.3 61.5 + - - +
8M T 3.8 5.8 - - - +
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Residues in contact with LYS 68 (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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18E SER* 3.2 23.8 - - - -
56E PHE* 3.6 40.4 - - + -
57E ARG 3.9 3.1 - - - -
58E THR* 4.2 9.9 - - + +
67E LYS* 1.3 73.7 - - - +
69E MET* 1.3 61.8 + - - +
70E TYR* 3.7 27.0 - - + +
8M T 3.1 17.9 + - - +
9M G 3.9 22.2 - - - +
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Residues in contact with MET 69 (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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16E GLU* 3.7 57.0 - - + +
17E LEU* 3.5 5.2 - - - +
18E SER* 3.8 16.4 - - - +
21E ASP* 4.9 4.9 - - - +
55E THR 3.8 0.2 - - - +
56E PHE* 3.1 4.0 - - - -
57E ARG* 2.9 44.8 + - + +
59E THR* 4.1 22.0 - - + -
67E LYS* 3.8 24.0 - - - +
68E LYS* 1.3 71.7 - - - +
70E TYR* 1.3 62.1 + - - +
71E THR* 4.9 1.7 + - - -
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Residues in contact with TYR 70 (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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12E LEU* 3.4 23.6 - - + +
16E GLU* 3.1 24.6 - - - -
17E LEU 2.7 27.0 + - - +
18E SER 4.6 2.7 - - - -
19E GLY 4.6 3.1 - - - -
22E ILE* 5.3 0.4 - - + -
42E TYR* 5.5 1.6 + + - -
45E LEU* 3.6 46.1 - - + +
46E LYS* 4.8 1.4 + - - -
49E THR* 3.7 19.9 + - - -
54E ILE* 3.5 22.9 - - + -
55E THR 3.2 8.7 - - - +
56E PHE* 3.6 24.0 - + + -
68E LYS* 3.7 37.1 - - + +
69E MET* 1.3 74.0 - - - +
71E THR* 1.3 61.6 + - - +
8M T 5.8 0.4 - - - -
9M G 4.8 4.5 + - - -
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Residues in contact with THR 71 (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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12E LEU* 5.0 3.8 - - - +
15E GLY* 5.6 4.0 - - - -
16E GLU* 4.1 20.0 + - - +
54E ILE* 3.3 6.9 - - - +
55E THR* 2.7 43.8 + - + +
69E MET 4.9 1.6 + - - -
70E TYR* 1.3 75.1 + - - +
72E LEU* 1.3 75.5 + - + +
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Residues in contact with LEU 72 (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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9E LEU* 3.4 54.3 - - + +
12E LEU* 3.7 28.2 + - + +
13E ARG* 3.9 11.7 - - - +
53E PHE 3.6 4.0 - - - +
54E ILE* 3.8 7.9 - - + -
55E THR* 4.7 2.4 - - - +
71E THR* 1.3 91.3 - - + +
73E THR* 1.3 69.8 + - - +
76E GLY* 4.5 4.7 - - - -
77E LYS* 3.9 36.5 - - + +
80E LEU* 4.7 5.8 - - + -
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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