Contacts of the strand formed by residues 41 - 47 (chain C) in PDB entry 3DOY
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 LYS 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C GLU* 3.9 25.5 + - + -
36C LEU* 3.7 0.7 - - - -
37C GLN* 3.0 62.8 + - + +
40C GLN* 1.3 84.0 - - + +
42C ILE* 1.3 64.0 + - - +
43C VAL* 5.0 10.6 - - + +
81C LEU* 3.6 10.0 - - - +
123C LEU 3.1 13.5 - - - +
124C GLU* 4.1 7.9 - - + -
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Residues in contact with ILE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 3.9 30.1 - - + -
35C GLU 3.3 12.6 - - - +
36C LEU* 3.6 21.8 - - + -
41C LYS* 1.3 75.6 - - - +
43C VAL* 1.3 72.1 + - - +
44C ALA* 4.6 1.1 - - + -
77C SER* 3.4 40.6 - - - +
80C PHE* 4.0 10.3 - - + -
81C LEU* 4.0 11.9 - - + +
121C TYR 3.6 2.3 - - - +
123C LEU* 2.8 50.4 + - + +
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 3.8 1.4 - - - +
34C THR* 2.9 36.2 + - - +
35C GLU* 2.9 50.7 + - + +
41C LYS* 5.0 12.8 - - + -
42C ILE* 1.3 78.4 - - - +
44C ALA* 1.3 65.1 + - - +
120C GLU* 3.9 14.8 - - - +
121C TYR 3.3 5.2 - - - +
122C HIS* 3.6 40.2 - - + +
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 4.0 9.9 - - + -
32C ARG 3.3 16.8 - - - +
33C ILE* 3.6 21.5 - - + -
34C THR* 4.1 4.0 - - - +
42C ILE* 4.1 4.9 - - + +
43C VAL* 1.3 76.1 - - - +
45C TYR* 1.3 64.2 + - - +
77C SER* 4.1 14.4 - - - +
120C GLU* 3.3 7.4 - - - +
121C TYR* 2.7 34.1 + - + -
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Residues in contact with TYR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.9 0.5 - - - -
31C ASP* 2.9 21.4 + - - -
32C ARG* 3.0 58.0 + - + +
34C THR* 3.7 22.7 - - + -
44C ALA* 1.3 81.7 - - - +
46C LYS* 1.3 65.5 + - - +
47C ASN* 3.7 14.8 - - - -
118C ARG* 3.1 51.6 + - + +
119C LEU 3.1 15.5 - - - +
120C GLU* 3.8 11.2 - - + -
121C TYR* 4.0 7.4 - - - -
116E GLY* 2.8 35.6 + - - -
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU 4.8 0.2 - - - -
29C LEU* 3.4 59.5 - - + +
30C VAL* 4.3 0.2 - - - -
31C ASP* 3.3 14.8 - - - +
45C TYR* 1.3 78.7 - - - +
47C ASN* 1.3 82.7 + - - +
48C ILE* 3.9 12.1 - - + +
52C GLU* 2.8 29.7 + - - -
65C PHE* 4.0 11.7 - - + -
119C LEU* 2.9 33.0 + - + +
121C TYR* 3.6 14.6 - - + +
49E THR* 3.0 14.3 + - - +
51E ASN* 3.8 5.5 - - - +
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Residues in contact with ASN 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP* 2.8 8.2 + - - +
45C TYR* 3.7 15.3 - - - -
46C LYS* 1.3 97.7 + - - +
48C ILE* 1.3 61.3 + - - +
49C THR 4.0 0.4 - - - -
117C ASP 4.0 1.6 - - - -
118C ARG* 3.9 14.4 - - - +
47E ASN* 3.5 26.0 + - + +
48E ILE 3.0 18.3 + - - +
49E THR* 3.3 6.8 - - - -
116E GLY* 2.9 26.2 + - - +
117E ASP 2.9 28.1 + - - -
118E ARG* 4.8 1.6 - - - +
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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