Contacts of the strand formed by residues 66 - 71 (chain A) in PDB entry 1EFT
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.7 40.2 - - + +
52A LYS* 5.5 7.0 - - - +
64A ASN 3.5 3.0 + - - +
65A THR* 1.3 75.3 - - - +
67A HIS* 1.3 64.1 + - - +
68A VAL* 5.0 4.2 - - + +
79A HIS 3.6 0.7 - - - +
80A VAL* 3.3 5.4 - - - +
81A ASP* 2.9 35.7 + - + +
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Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 5.9 2.3 - - - -
65A THR* 4.2 7.4 + - - -
66A ALA* 1.3 79.4 - - - +
68A VAL* 1.3 66.7 + - - +
78A SER* 5.3 3.2 - - - -
79A HIS 3.2 6.0 + - - +
80A VAL* 3.7 20.5 - - + +
98A GLN* 2.9 27.6 - - - -
226A GLU* 3.0 30.4 + - - -
273A HIS* 4.7 17.4 + - + +
285A ASN* 3.5 24.2 + - - +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.7 33.7 - - + -
32A THR* 3.9 20.6 - - + -
45A LYS* 4.4 22.9 - - + +
50A ILE* 4.4 12.6 - - + -
66A ALA* 5.0 6.5 - - + -
67A HIS* 1.3 80.9 - - - +
69A GLU* 1.3 62.3 + - - +
70A TYR* 4.3 5.4 - - + -
78A SER* 3.5 3.6 - - - -
79A HIS* 2.8 46.7 + - + +
273A HIS* 3.6 6.5 + - - -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.7 12.8 - - - -
32A THR* 4.2 8.0 - - - +
41A ASN 5.3 7.7 - - - +
42A VAL* 3.8 15.8 - - + +
43A GLU* 4.3 5.9 + - - +
68A VAL* 1.3 76.7 - - - +
70A TYR* 1.3 65.8 + - - +
71A GLU* 5.5 3.8 - - - +
76A HIS* 2.8 36.0 + - + +
77A TYR 3.4 5.4 - - - +
273A HIS* 3.3 31.4 + - + +
275A LYS* 3.2 28.5 + - - -
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.3 16.3 - - + +
28A THR 5.3 0.2 - - - -
31A LEU* 3.5 34.3 - - + +
32A THR* 4.5 4.3 - - + -
35A THR* 3.5 24.2 - - + +
42A VAL* 4.1 11.2 - - + -
68A VAL* 4.3 9.9 - - + -
69A GLU* 1.3 77.7 - - - +
71A GLU* 1.3 66.9 + - - +
76A HIS* 4.1 3.3 - - - -
77A TYR* 2.9 52.1 + + + +
79A HIS* 2.9 44.4 + + + -
103A ILE* 4.2 4.0 - - - +
203A LEU* 3.7 27.7 - - + +
206A ILE* 5.6 3.6 - - + +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 4.8 2.9 + - - -
9A LYS* 2.8 25.8 + - - +
35A THR* 3.6 20.4 - - - +
39A ASN* 3.1 31.5 + - + +
41A ASN* 4.3 16.9 + - - +
42A VAL* 4.0 11.6 - - + +
69A GLU* 5.5 3.5 - - - +
70A TYR* 1.3 80.2 - - - +
72A THR* 1.3 69.2 + - - +
75A ARG 3.3 16.2 - - - +
76A HIS* 3.9 21.8 - - - -
77A TYR* 4.1 2.9 - - - -
200A TRP* 5.7 0.2 - - - -
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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