Contacts of the strand formed by residues 66 - 71 (chain B) in PDB entry 1SAX
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 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B SER* 3.6 15.5 - - - -
62B LYS* 4.3 2.5 - - - -
63B ASP 2.9 30.5 + - - +
64B ASN* 3.2 14.3 + - - +
65B LYS* 1.3 80.6 - - + +
67B PHE* 1.3 72.4 + - - +
68B GLN* 3.2 23.5 + - - +
3D A 4.3 27.6 - - - +
4D A 3.6 5.6 - - - +
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Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B SER* 3.3 21.1 - - - -
27B ALA 4.1 0.7 + - - -
60B ARG* 3.2 63.0 - - + +
61B LYS* 3.5 7.6 - - - -
62B LYS* 3.9 39.0 - - + -
65B LYS 4.1 0.4 + - - -
66B ILE* 1.3 74.8 - - - +
68B GLN* 1.3 60.2 + - - +
69B TYR* 3.7 25.5 - - + +
4D A 2.8 44.2 + - - +
5D A 3.7 10.3 - - - -
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.5 44.1 - - + +
25B ALA* 3.6 10.0 + - - +
26B SER* 3.3 20.4 + - - -
29B ASN* 4.3 5.0 - - - +
59B ASP 3.7 0.2 - - - +
60B ARG* 3.0 25.5 - - - +
61B LYS 2.8 13.4 + - - +
63B ASP* 3.7 28.2 - - + +
64B ASN* 5.2 1.4 - - - +
66B ILE* 3.2 38.2 + - - +
67B PHE* 1.3 74.7 + - - +
69B TYR* 1.3 60.4 + - - +
70B TYR* 4.2 2.4 - - - -
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Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 4.2 24.4 - - + +
23B LYS 4.0 0.5 - - - +
24B TYR* 3.4 6.1 + - - -
25B ALA* 2.8 40.4 + - - +
27B ALA* 4.1 17.0 - - + -
30B ILE* 4.5 3.4 - - + -
49B ILE* 3.7 27.1 - - + +
50B THR* 6.1 0.3 - - - -
53B TYR* 4.5 10.8 - + - -
58B ILE* 3.8 21.8 - - + -
59B ASP 3.3 13.5 - - - -
60B ARG* 3.2 45.0 + - + -
67B PHE* 3.7 26.1 - - + +
68B GLN* 1.3 73.4 - - - +
70B TYR* 1.3 61.3 + - - +
4D A 5.0 5.0 + - - +
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.9 8.5 - - - -
23B LYS 3.3 20.2 - - - +
24B TYR* 4.0 25.4 - + + -
58B ILE* 3.2 5.8 - - - +
59B ASP* 3.0 69.7 + - + +
60B ARG* 3.7 12.6 - - - -
61B LYS* 3.5 31.7 + - + +
68B GLN 4.2 1.3 - - - -
69B TYR* 1.3 77.0 - - - +
71B SER* 1.3 70.6 + - - +
72B LEU* 4.2 12.7 - - + +
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 4.2 3.7 - - - +
19B ILE* 3.7 12.7 - - - +
20B TRP* 3.1 28.6 + - - -
23B LYS 4.6 1.8 + - - -
57B PHE 3.8 5.8 + - - -
58B ILE* 4.4 1.6 - - - -
70B TYR* 1.3 85.7 - - - +
72B LEU* 1.3 61.5 + - - +
73B VAL* 2.5 36.5 + - - +
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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