Contacts of the strand formed by residues 57 - 63 (chain J) in PDB entry 4CDC
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 SER 57 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B ALA* 5.4 4.7 - - - -
335B LEU* 6.4 1.3 - - - -
338B LEU* 5.4 10.7 - - - +
49J THR* 4.6 11.4 - - - -
50J ALA 3.2 7.4 - - - -
51J TYR* 4.4 6.3 - - - -
55J GLY 4.2 1.7 + - - -
56J ASN* 1.3 76.6 - - - +
58J GLY* 1.3 59.4 + - - +
59J HIS* 6.1 0.2 - - - -
72J LEU* 3.6 7.0 - - - +
73J ASN 5.3 1.7 + - - -
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Residues in contact with GLY 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J THR* 3.6 4.9 - - - +
50J ALA* 2.6 31.6 + - - -
57J SER* 1.3 74.8 - - - +
59J HIS* 1.3 79.9 + - - -
71J VAL 3.3 13.2 - - - -
72J LEU* 3.5 7.5 - - - +
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Residues in contact with HIS 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J ASP* 3.2 37.7 - - - +
49J THR* 4.9 2.7 - - - -
50J ALA* 4.0 2.7 - - - +
58J GLY* 1.3 85.7 + - - -
60J PHE* 1.3 63.6 + - - +
70J ILE* 3.5 4.0 - - - +
71J VAL* 2.9 39.8 + - + +
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Residues in contact with PHE 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J TYR* 3.9 22.7 - + - -
11J LEU* 3.8 30.3 - - + -
12J LEU* 3.7 19.7 - - + -
44J LEU* 3.7 23.6 - - + -
45J GLN 3.1 27.4 - - - -
47J LEU 3.9 4.2 - - - +
48J ASP* 3.1 31.8 + - - +
49J THR 3.2 24.2 - - - -
59J HIS* 1.3 77.6 - - - +
61J THR* 1.3 69.3 + - - +
68J PHE* 5.9 0.4 - - + -
69J GLU 3.2 13.5 - - - +
70J ILE* 3.9 16.4 - - + -
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Residues in contact with THR 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J TYR* 6.3 0.2 - - - -
60J PHE* 1.3 85.1 - - - +
62J ILE* 1.3 78.1 + - - +
63J ILE* 4.5 4.7 - - + -
68J PHE* 3.2 4.9 - - - +
69J GLU 3.0 37.9 + - - +
280K TYR* 3.6 36.3 - - + +
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Residues in contact with ILE 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J CYS 4.0 7.6 - - - +
7J THR 3.7 24.9 - - - +
8J TYR* 3.7 33.2 - - + +
11J LEU* 3.8 23.5 - - + +
60J PHE* 4.4 2.4 - - - -
61J THR* 1.3 89.7 + - - +
63J ILE* 1.3 59.7 + - - +
64J TYR 3.7 26.4 + - - +
67J GLY 3.2 20.0 - - - +
81J PHE* 4.2 12.1 - - + -
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Residues in contact with ILE 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J THR* 4.4 5.2 - - + +
62J ILE* 1.3 74.9 - - - +
64J TYR* 1.3 66.9 + - - +
65J ASN 2.9 4.7 + - - -
66J GLN* 3.0 20.5 + - + +
67J GLY 2.8 12.8 + - - +
68J PHE* 3.4 35.0 - - - +
69J GLU* 3.6 10.1 - - + +
78J PHE* 4.0 18.8 - - + -
278K PHE* 4.4 19.3 - - + -
280K TYR* 4.0 29.8 - - + -
281K LEU* 4.1 25.4 - - + -
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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