Contacts of the strand formed by residues 59 - 63 (chain C) in PDB entry 3T0E
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 ALA 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C VAL* 4.3 13.0 - - + -
47C ILE* 4.7 2.0 - - + -
55C ASN* 4.0 0.5 - - - +
56C ASN* 2.6 39.8 + - - +
57C ARG 2.8 9.2 + - - +
58C MET* 1.3 79.9 - - + +
60C SER* 1.3 64.1 + - - +
72C LEU* 3.9 20.2 - - + -
73C ILE 3.6 13.9 - - - +
74C LEU* 4.1 7.0 - - + +
75C HIS* 4.6 11.6 + - - +
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Residues in contact with SER 60 (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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47C ILE* 4.0 3.4 - - - -
54C VAL 3.4 1.1 + - - -
55C ASN* 2.9 40.0 + - - +
59C ALA* 1.3 74.9 - - - +
61C LEU* 1.3 66.7 + - - +
72C LEU* 3.4 13.2 - - - +
73C ILE* 3.1 47.1 + - - +
75C HIS* 3.7 19.9 + - - -
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Residues in contact with LEU 61 (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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32C ILE* 4.5 6.3 - - + +
34C TRP* 3.8 26.7 - - + +
47C ILE* 3.7 14.8 - - + +
48C HIS* 3.6 41.5 - - - +
49C GLY* 3.6 7.6 - - - +
53C ASN* 2.8 23.7 + - - +
54C VAL* 2.7 32.0 + - + +
60C SER* 1.3 81.3 + - - +
62C ALA* 1.3 66.2 + - - +
63C ILE* 4.0 9.1 + - + -
70C SER* 4.5 5.6 - - - -
71C THR 3.7 16.6 - - - +
72C LEU* 4.5 2.7 - - - +
73C ILE* 4.8 2.5 - - - -
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Residues in contact with ALA 62 (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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53C ASN* 3.2 7.2 - - - +
61C LEU* 1.3 74.8 - - - +
63C ILE* 1.3 62.3 + - - +
64C ALA 4.0 0.3 + - - -
70C SER* 3.0 5.7 - - - -
71C THR* 2.6 57.5 + - + +
73C ILE* 4.3 14.1 - - + -
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Residues in contact with ILE 63 (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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32C ILE* 4.0 25.8 - - + -
49C GLY* 3.1 31.2 - - - +
50C LEU 3.4 14.8 - - - +
51C THR* 3.7 13.2 - - - +
52C SER 3.3 32.4 - - - +
53C ASN* 3.2 11.6 + - - +
61C LEU* 4.0 10.7 + - + -
62C ALA* 1.3 73.9 - - - +
64C ALA* 1.3 76.1 + - - +
67C ARG* 4.4 9.2 - - + +
69C SER 3.8 2.0 - - - +
70C SER* 4.2 5.4 - - - -
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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