Contacts of the strand formed by residues 64 - 70 (chain E) in PDB entry 6AHU
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 ILE 64 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E LEU* 4.1 21.3 - - + -
11E CYS 3.5 10.3 - - - +
12E GLU* 4.5 15.9 - - + -
57E TYR* 3.6 19.3 - - + +
58E LEU* 3.6 26.2 - - - +
59E ASN* 3.8 5.8 + - - +
62E THR* 3.8 22.6 - - + +
63E GLY* 1.3 87.5 - - - +
65E VAL* 1.3 63.3 + - - +
100E THR* 5.9 4.0 - - + -
114E LEU* 3.8 33.4 - - + -
117E TYR* 5.0 13.5 - - + -
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Residues in contact with VAL 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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9E LEU 3.5 2.1 - - - +
10E LEU* 3.4 6.6 - - - +
11E CYS* 2.9 45.7 + - + +
13E LEU* 5.2 7.6 - - + -
24E LEU* 6.1 0.9 - - + -
29E LEU* 3.8 29.8 - - + -
57E TYR 4.0 2.7 - - - +
58E LEU* 3.8 17.0 - - + -
63E GLY* 5.1 3.4 - - - +
64E ILE* 1.3 79.3 - - - +
66E LEU* 1.3 62.3 + - - +
67E LEU* 3.9 23.1 - - + -
97E PHE* 3.6 25.4 - - + -
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Residues in contact with LEU 66 (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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8E TYR* 3.8 39.7 - - + -
9E LEU 3.7 13.7 - - - +
10E LEU* 3.8 20.4 - - + -
29E LEU* 5.6 0.3 - - - +
55E VAL* 4.2 2.4 - - - +
56E ARG* 3.9 30.0 + - + -
57E TYR* 3.2 43.6 + - + +
65E VAL* 1.3 74.0 - - - +
67E LEU* 1.3 70.9 + - - +
107E ILE* 4.3 14.6 - - + -
110E CYS* 4.1 6.7 - - - -
111E GLN* 4.9 10.3 - - - +
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Residues in contact with LEU 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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7E ARG 3.7 0.9 - - - +
8E TYR* 3.6 28.6 - - - -
9E LEU* 3.4 37.5 + - + +
11E CYS* 5.0 1.8 - - - -
29E LEU* 4.4 5.4 - - + -
33E VAL* 4.4 17.5 - - + -
53E PHE* 3.6 36.8 - - + -
54E ALA 4.0 2.2 - - - +
55E VAL* 3.8 18.2 - - + -
65E VAL* 3.9 22.0 - - + -
66E LEU* 1.3 84.3 - - - +
68E ARG* 1.3 64.1 + - - +
77E VAL* 4.6 7.4 - - + -
81E LEU* 4.9 8.1 - - + -
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Residues in contact with ARG 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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273A C 5.7 2.0 - - - -
6E HIS* 3.3 36.3 + - - +
7E ARG 4.0 3.6 - - - -
8E TYR* 3.6 31.6 + - + -
52E GLY* 3.3 21.8 + - - +
53E PHE* 3.2 29.2 - - - +
54E ALA* 3.3 39.1 + - - +
56E ARG* 3.7 30.5 - - + +
67E LEU* 1.3 75.5 - - - +
69E CYS* 1.3 64.0 + - - +
70E ARG* 5.8 0.4 - - - +
77E VAL* 5.3 0.5 - - - +
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Residues in contact with CYS 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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6E HIS* 3.6 8.9 + - - +
7E ARG* 2.9 52.9 + - - -
9E LEU* 4.0 23.6 - - + -
49E CYS* 5.9 1.6 - - + -
52E GLY 4.4 6.0 + - - -
53E PHE* 5.3 0.7 - - - +
68E ARG* 1.3 76.2 - - - +
70E ARG* 1.3 63.2 + - - +
73E PHE 4.1 13.0 - - - +
74E TYR* 3.7 19.3 - - - -
77E VAL* 4.4 13.7 - - + -
102E HIS* 4.6 0.4 - - - -
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Residues in contact with ARG 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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4E PHE* 3.4 37.5 - - - +
5E LYS 4.1 7.0 - - - -
6E HIS* 3.3 29.8 - - - -
7E ARG* 3.3 16.6 - - - +
48E ALA 5.2 2.2 - - - +
51E ILE* 3.1 51.0 + - + +
52E GLY* 3.5 16.0 - - - -
68E ARG* 5.8 0.6 - - - +
69E CYS* 1.3 79.3 - - - +
71E LYS* 1.3 65.5 + - - +
72E GLU* 3.3 15.0 - - - +
73E PHE* 4.0 19.3 - - + +
74E TYR* 3.5 13.5 + - - +
175J ASN* 5.2 1.6 + - - -
178J GLN* 4.5 14.3 + - - +
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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