Contacts of the strand formed by residues 58 - 63 (chain E) in PDB entry 6CP3
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 THR 58 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E THR* 4.9 8.1 - - + +
22E ASP* 4.9 4.0 - - + -
23E VAL 3.6 15.5 - - - +
24E HIS* 3.3 18.6 - - + -
30E LEU* 4.2 2.5 - - - +
53E HIS* 3.9 1.7 - - - +
54E LEU* 3.1 39.2 + - + -
55E GLY 2.8 18.5 + - - +
56E GLU* 3.0 20.4 + - - +
57E ASN* 1.3 70.1 - - - +
59E VAL* 1.3 72.2 + - - +
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Residues in contact with VAL 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ASP* 3.4 4.3 - - - +
23E VAL* 2.9 56.8 + - + +
25E PHE* 4.8 11.0 - - + -
30E LEU* 4.1 19.3 - - + -
31E PRO* 4.7 3.6 - - + +
37E LEU* 4.8 1.8 - - + -
50E VAL* 3.8 32.1 - - + -
52E GLN 3.5 4.9 - - - +
53E HIS* 3.5 25.4 - - + +
54E LEU* 5.2 1.1 - - - -
58E THR* 1.3 81.9 - - - +
60E ARG* 1.3 61.8 + - - +
61E THR* 4.4 2.5 - - + -
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Residues in contact with ARG 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ILE* 5.4 7.2 - - - +
20E ILE* 3.7 24.0 - - + +
21E VAL 3.6 3.6 - - - -
22E ASP* 3.1 27.0 + - - +
50E VAL* 4.8 0.2 - - - -
51E ALA* 3.1 7.3 + - - +
52E GLN* 2.8 61.6 + - + +
54E LEU* 3.6 35.1 - - + +
59E VAL* 1.3 74.6 - - - +
61E THR* 1.3 64.1 + - - +
271E LEU 5.7 0.8 + - - -
272E LEU* 4.1 30.2 + - + +
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Residues in contact with THR 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE* 3.4 9.0 - - - +
21E VAL* 2.9 51.4 + - - +
23E VAL* 4.7 2.5 - - + -
37E LEU* 4.6 5.6 - - + -
48E LEU* 3.5 26.8 - - + +
49E GLU 3.3 15.5 - - - -
50E VAL* 3.7 30.1 - - + +
51E ALA* 4.2 1.1 - - - +
59E VAL* 4.4 7.2 - - + -
60E ARG* 1.3 76.6 - - - +
62E ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ALA* 3.5 5.4 - - + +
20E ILE* 3.8 19.7 - - + -
48E LEU* 3.7 4.2 - - - +
49E GLU* 3.4 34.2 + - + +
51E ALA* 4.8 7.2 - - + -
61E THR* 1.3 80.5 - - - +
63E ALA* 1.3 64.8 + - - +
64E MET* 4.4 2.2 - - - +
227E GLY* 3.7 27.1 - - - +
231E ARG* 3.6 28.9 - - - +
268E VAL* 3.8 26.5 - - + -
271E LEU* 6.4 0.2 - - + -
272E LEU* 3.8 17.9 - - + -
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Residues in contact with ALA 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ALA* 2.7 26.8 + - - +
46E LEU* 5.7 0.2 - - + -
48E LEU* 3.8 11.0 - - + +
62E ILE* 1.3 78.4 - - - +
64E MET* 1.3 72.0 + - - +
65E ASP 3.5 17.7 - - - +
67E THR* 3.7 19.1 - - + -
225E PRO* 3.8 13.0 - - + -
227E GLY* 3.4 16.7 + - - -
228E ALA 3.8 0.3 + - - -
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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