Contacts of the strand formed by residues 46 - 51 (chain B) in PDB entry 2C47
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 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ASP* 4.1 18.9 - - - +
44B PRO 4.1 17.0 - - - -
45B ASN* 1.3 80.0 + - - +
47B ARG* 1.3 68.4 + - - +
64B LYS 3.2 8.5 - - - +
65B ASN* 3.7 39.5 - - + -
66B LEU* 4.7 1.3 - - - +
72B VAL* 4.1 10.3 - - + -
74B ILE* 4.6 6.3 - - + -
106B TYR* 3.8 19.3 - + + -
107B TYR* 3.9 25.6 - + + -
111B CSD 4.4 19.8 - - - +
118B VAL* 3.6 35.9 - - + -
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Residues in contact with ARG 47 (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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256A LYS* 3.7 21.1 + - + +
257A ALA* 3.2 32.8 - - - +
258A ASP* 3.3 23.1 + - - +
266A LYS* 3.5 25.8 - - - +
46B PHE* 1.3 75.2 - - - +
48B VAL* 1.3 60.9 + - - +
63B GLY* 3.1 5.9 - - - -
64B LYS* 2.9 34.7 + - + +
66B LEU* 3.3 42.5 - - + +
74B ILE* 3.7 5.1 - - - +
111B CSD 5.4 0.4 - - - -
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Residues in contact with VAL 48 (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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256A LYS* 3.3 5.5 - - - -
257A ALA 2.8 36.6 + - - +
258A ASP 4.6 2.0 - - - +
259A THR* 3.7 19.5 - - - +
260A LEU* 3.7 28.9 - - + +
263A ARG* 3.3 7.2 - - + -
47B ARG* 1.3 73.9 - - - +
49B GLY* 1.3 62.7 + - - +
61B ARG* 3.7 32.1 - - + -
62B LEU 3.9 1.6 - - - +
74B ILE* 4.1 20.9 - - + -
76B LEU* 4.8 4.5 - - + -
111B CSD 4.8 10.7 + - + +
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Residues in contact with GLY 49 (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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255A LEU 4.1 1.8 - - - -
256A LYS* 3.8 20.7 - - - +
263A ARG* 3.6 15.5 + - - -
48B VAL* 1.3 73.8 - - - +
50B LYS* 1.3 62.2 + - - -
61B ARG* 3.0 29.8 + - - +
62B LEU 2.6 18.4 + - - -
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Residues in contact with LYS 50 (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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217A ARG* 4.2 25.2 - - - +
253A GLN* 6.2 0.2 - - - +
254A GLY* 6.0 8.5 - - - +
256A LYS* 5.1 2.3 - - - +
263A ARG* 3.8 20.2 - - - +
49B GLY* 1.3 72.8 - - - -
51B LYS* 1.3 71.8 + - - +
52B ILE* 4.2 16.8 - - + -
61B ARG* 3.1 5.3 - - - +
62B LEU* 2.8 44.4 + - + +
337B PRO* 2.6 34.7 + - - +
338B ILE 4.7 1.8 - - - -
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Residues in contact with LYS 51 (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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50B LYS* 1.3 83.5 - - - +
52B ILE* 1.3 67.8 + - - +
59B GLU* 4.3 12.6 - - + +
60B LEU 3.5 6.7 - - - +
61B ARG* 3.3 33.8 - - - +
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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