Contacts of the strand formed by residues 148 - 152 (chain B) in PDB entry 6CAJ
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 PHE 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLN* 3.3 24.5 - - + +
45B ALA 4.0 0.9 - - - +
46B VAL* 3.6 35.2 - - + -
135B LEU* 4.5 15.9 - - + -
138B VAL* 5.2 0.9 - - + -
144B VAL* 3.6 42.0 - - + -
146B SER 5.1 0.4 - - - +
147B ASP* 1.3 78.3 - - - +
149B LEU* 1.3 66.0 + - - +
150B LEU* 4.6 2.9 - - + -
251B ILE* 3.3 3.3 - - - +
252B CYS* 3.0 52.5 + - - +
253B SER 3.2 31.6 - - - -
254B PRO* 3.7 5.8 - - + -
256B VAL* 5.4 0.9 - - + -
257B ALA* 5.1 9.0 - - + -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.8 20.6 - - + -
44B GLN 3.1 18.5 + - - +
45B ALA* 3.4 11.6 - - + +
46B VAL 2.8 28.7 + - - +
82B PHE* 5.2 0.2 - - + -
83B LEU* 4.0 22.2 - - + -
86B THR* 4.1 21.1 - - + +
88B VAL* 3.8 8.7 - - + -
148B PHE* 1.3 75.5 - - - +
150B LEU* 1.3 62.2 + - - +
151B VAL* 3.6 2.8 + - + +
161B ILE* 4.2 16.8 - - + -
249B ILE* 4.6 13.2 - - + +
251B ILE* 3.8 32.1 - - + +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 4.0 9.2 - - + +
48B VAL* 4.5 15.0 - - + -
131B LEU* 4.7 9.2 - - + -
135B LEU* 3.8 45.5 - - + -
148B PHE* 3.8 6.6 + - + -
149B LEU* 1.3 69.8 - - - +
151B VAL* 1.3 64.6 + - - +
152B TYR* 6.1 4.9 - - + -
181B MET* 4.9 9.0 - - + -
248B HIS 3.7 2.8 - - - +
249B ILE* 3.7 4.0 - - - +
250B SER* 3.4 40.1 + - - +
251B ILE* 4.5 0.2 - - - +
252B CYS* 3.8 18.6 - - - -
256B VAL* 5.8 0.2 - - + -
260B PHE* 5.8 1.1 - - + -
269B ARG* 4.4 26.0 - - + -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL 3.2 17.5 + - - +
47B LEU* 4.4 4.5 - - - -
48B VAL* 3.1 25.7 + - - +
79B THR* 4.7 5.6 - - + -
82B PHE* 5.1 3.8 - - + -
83B LEU* 3.9 38.6 - - + -
149B LEU* 4.1 6.3 - - + +
150B LEU* 1.3 78.9 - - - +
152B TYR* 1.3 75.1 + - - +
155B VAL* 3.7 21.5 - - + -
248B HIS 3.8 9.9 - - - +
249B ILE* 4.2 17.7 - - + -
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Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 5.0 0.2 - - - -
48B VAL* 3.5 21.8 - - + -
51B SER* 5.0 13.5 - - - -
79B THR* 3.3 18.0 - - - +
131B LEU* 3.7 37.3 - - + +
150B LEU* 6.1 5.4 - - + -
151B VAL* 1.3 81.1 - - - +
153B GLY* 1.3 58.2 + - - +
154B ASP* 3.2 22.5 + - - +
155B VAL* 3.4 12.3 - - + +
248B HIS* 3.9 30.9 + + + -
268B THR* 3.7 10.6 + - - -
269B ARG* 4.3 17.2 + - - +
299B ARG* 3.5 32.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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