Contacts of the strand formed by residues 65 - 70 (chain X) in PDB entry 3F6E
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 ALA 65 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17X ILE* 6.0 0.4 - - - -
21X PHE* 4.1 9.2 - - + -
54X ALA* 3.5 35.0 - - + +
57X TYR* 4.3 0.4 - - + -
58X ALA* 3.9 6.3 - - + -
63X LYS* 3.3 16.9 + - - +
64X PRO* 1.3 73.0 - - - +
66X PHE* 1.3 56.5 + - - +
67X ILE* 4.1 1.7 + - - +
91X PRO 3.0 6.5 + - - -
92X LEU* 3.5 8.9 - - + +
93X ILE* 2.8 33.7 + - - +
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Residues in contact with PHE 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X LEU* 3.9 24.2 - - + -
17X ILE* 3.7 18.5 - - + +
19X THR 3.6 14.4 + - - +
20X VAL* 3.6 27.0 - - + -
21X PHE* 2.9 31.2 + - - -
31X PHE* 3.8 33.4 - + - -
65X ALA* 1.3 74.1 - - - +
67X ILE* 1.3 70.6 + - - +
68X ASN* 4.4 0.2 - - + -
93X ILE* 3.7 20.9 - - + -
95X THR* 3.6 35.0 - - + -
139X MET* 3.8 19.7 - - + -
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Residues in contact with ILE 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X PHE* 3.2 11.0 - - + +
50X VAL* 4.0 6.1 - - + -
51X VAL* 4.1 16.8 - - + -
54X ALA* 3.5 32.8 - - + -
65X ALA 4.5 1.6 - - - +
66X PHE* 1.3 81.0 - - - +
68X ASN* 1.3 64.1 + - - +
69X LEU* 3.6 31.2 - - + -
92X LEU* 3.9 34.3 - - + -
93X ILE 2.9 12.5 + - - +
94X VAL* 4.0 18.6 - - + -
95X THR* 2.9 29.8 + - - -
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Residues in contact with ASN 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X VAL* 3.9 19.7 - - + +
21X PHE 2.9 8.1 + - - -
22X GLY* 3.2 22.3 - - - -
23X ASN 3.4 8.3 + - - +
24X PRO* 5.4 1.8 - - - +
28X GLU* 3.4 36.7 - - - +
31X PHE* 3.8 16.9 - - + +
32X LEU* 3.6 23.6 - - - +
41X TYR* 5.3 2.0 + - + -
66X PHE* 4.4 0.2 - - + -
67X ILE* 1.3 75.6 - - - +
69X LEU* 1.3 64.9 + - - +
95X THR* 2.9 23.7 + - - +
96X ALA* 4.4 1.4 + - - -
97X GLY 4.7 0.7 + - - -
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Residues in contact with LEU 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X ASN 4.1 5.8 - - - +
28X GLU* 3.2 14.4 - - - +
47X GLU* 3.7 22.2 - - + -
50X VAL* 3.9 17.0 - - + -
51X VAL* 4.2 2.5 - - + -
67X ILE* 3.6 21.3 - - + -
68X ASN* 1.3 81.9 - - - +
70X HIS* 1.3 62.3 + - - +
71X SER 3.8 0.2 - - - -
74X GLY 3.8 23.1 - - - +
75X THR* 3.9 14.6 - - + +
78X ALA* 3.8 18.4 - - + -
82X LEU* 6.2 0.2 - - + -
94X VAL* 3.8 21.8 - - + -
95X THR 2.8 12.5 + - - +
96X ALA* 3.1 21.9 - - - -
97X GLY 3.3 0.7 + - - -
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Residues in contact with HIS 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X ASN 4.0 3.9 + - - +
25X GLY* 3.5 10.8 - - - +
26X SER 3.6 8.3 - - - -
27X ASN* 3.8 18.4 - - - -
28X GLU* 2.7 28.1 + - - +
47X GLU* 5.0 1.2 + - - -
69X LEU* 1.3 73.9 - - - +
71X SER* 1.3 66.6 - - - +
72X ALA 3.6 0.2 + - - -
73X ALA* 3.7 4.2 + - + -
74X GLY* 2.7 34.4 + - - -
110X LEU* 3.7 31.1 - - + +
602X 8PA 3.2 66.4 + + + +
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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