Contacts of the strand formed by residues 60 - 64 (chain B) in PDB entry 4BLB
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 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.4 5.2 - - + -
9B VAL 3.2 2.6 + - - -
10B ILE* 3.5 18.5 - - + -
11B TRP 3.1 23.4 + - - -
48B PHE* 5.9 0.2 - - - -
58B PRO* 3.3 10.3 - - - +
59B ASP* 1.3 88.0 - - + +
61B ILE* 1.3 63.5 + - - +
62B PHE* 3.7 24.2 - - + -
265B ALA* 3.9 15.5 - - + -
266B GLY 3.2 11.9 - - - +
267B ILE* 4.7 0.7 - - + -
277B ALA* 3.6 31.4 - - + -
280B PHE* 4.0 17.0 - - + -
281B LEU* 3.8 24.2 - - + -
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Residues in contact with ILE 61 (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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11B TRP* 3.6 7.4 - - + +
44B LEU* 3.5 30.7 - - + -
45B GLU* 5.0 0.2 - - - -
48B PHE* 3.4 59.9 - - + -
58B PRO* 5.0 0.7 - - + -
60B ILE* 1.3 73.9 - - - +
62B PHE* 1.3 68.2 + - - +
63B TRP* 4.9 2.7 - - + +
68B PHE* 3.5 18.6 - - + -
71B TYR* 3.9 16.8 - - + +
77B LEU* 4.4 4.3 - - + -
265B ALA* 3.5 0.9 - - - -
266B GLY* 2.8 47.1 + - - +
268B ASN 5.5 0.7 - - - +
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Residues in contact with PHE 62 (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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10B ILE* 3.3 35.7 - - + -
11B TRP 2.6 18.9 + - - +
12B ILE* 3.7 35.3 - - + -
13B ASN 4.5 0.9 + - - -
21B LEU* 3.9 13.0 - - + -
44B LEU* 3.9 7.3 - - - +
60B ILE* 3.7 13.0 - - + -
61B ILE* 1.3 76.1 - - - +
63B TRP* 1.3 76.5 + - - +
109B ILE* 4.0 16.8 - - + -
263B LEU* 4.4 11.7 - - + -
264B SER 3.2 7.2 - - - -
265B ALA* 3.7 19.7 - - + -
280B PHE* 5.2 0.7 - + - -
281B LEU* 4.0 4.0 - - + -
285B LEU* 3.4 33.4 - - + -
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Residues in contact with TRP 63 (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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13B ASN* 3.7 41.3 - - + -
44B LEU* 3.8 20.9 - - + -
45B GLU* 3.2 47.1 - - + +
61B ILE* 5.0 7.0 - - + -
62B PHE* 1.3 84.6 - - - +
64B ALA* 1.3 89.9 + - + +
66B ASP* 4.0 5.4 + - - -
67B ARG* 3.5 27.2 - - + +
68B PHE* 3.1 17.2 - - + -
71B TYR* 5.5 0.9 - - + +
263B LEU* 3.9 10.0 - - - +
264B SER 2.7 34.1 + - - +
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Residues in contact with ALA 64 (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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63B TRP* 1.3 97.0 - - + +
65B HIS* 1.3 66.8 + - - +
66B ASP* 3.0 18.1 + - - +
67B ARG 3.5 1.4 + - - -
68B PHE* 3.2 8.8 - - - -
112B GLU* 4.8 9.0 - - - +
261B GLY* 4.6 7.0 - - - -
262B VAL 3.5 11.4 - - - +
263B LEU* 4.3 3.7 - - - +
331B MET* 4.2 15.5 - - + -
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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