Contacts of the strand formed by residues 47 - 50 (chain B) in PDB entry 4C02
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 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 4.0 22.9 - - + -
200A VAL* 3.8 27.8 - - + -
203A THR* 3.4 26.7 - - - -
23B CYS 3.4 1.4 - - - +
24B VAL* 3.4 2.9 - - - -
25B VAL* 2.8 55.4 + - + +
27B TYR* 3.6 33.0 - + + -
40B SER* 4.4 2.6 - - - -
43B ARG* 4.8 2.5 - - - +
45B LYS 3.4 1.4 + - - -
46B PRO* 1.3 71.5 - - - +
48B LYS* 1.3 75.5 + - - +
49B PHE* 3.7 23.1 - + + -
56B VAL* 4.0 15.3 - - + -
60B PHE* 4.5 2.2 - + - -
1110B EDO 3.7 12.3 - - - -
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Residues in contact with LYS 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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203A THR* 4.3 2.9 - - - +
22B THR* 3.8 16.2 - - + -
23B CYS 3.1 5.4 - - - +
24B VAL* 4.0 25.4 - - + -
46B PRO* 4.6 8.5 - - - +
47B PHE* 1.3 84.6 - - - +
49B PHE* 1.3 64.2 - - - +
108B GLU* 3.4 23.9 + - - -
1110B EDO 3.2 39.3 + - - +
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 4.9 0.7 - - - +
21B GLN 3.7 0.2 - - - +
22B THR* 4.3 4.0 - - - +
23B CYS* 2.8 54.2 + - + +
25B VAL* 4.2 11.7 - - + -
47B PHE* 3.7 27.6 - + + -
48B LYS* 1.3 75.7 - - - +
50B ARG* 1.3 68.5 + - - +
51B ILE* 4.0 20.2 - - + -
55B GLU* 3.6 24.0 - - + +
56B VAL* 3.8 23.6 - - + -
60B PHE* 3.7 24.2 - + - -
61B GLU* 4.2 10.5 - - + -
64B ALA* 4.0 18.8 - - + -
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Residues in contact with ARG 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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207A GLN* 3.6 13.5 - - - +
20B GLY* 3.6 26.0 - - - +
21B GLN 3.3 4.0 - - - +
22B THR* 3.8 17.0 - - - +
49B PHE* 1.3 78.5 - - - +
51B ILE* 1.3 65.0 + - - +
52B GLY 3.3 0.7 + - - -
53B LYS* 3.2 49.8 + - + +
54B GLN 4.6 1.7 + - - -
55B GLU* 2.6 49.7 + - - +
61B GLU* 4.4 2.3 - - - +
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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
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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