Contacts of the strand formed by residues 59 - 65 (chain C) in PDB entry 5DG4
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 ASN 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C THR 3.5 4.5 - - - -
54C THR* 3.6 25.3 - - + +
55C SER 4.5 4.2 - - - +
57C PHE 5.1 2.0 + - - -
58C ARG* 1.3 84.1 - - - +
60C LEU* 1.3 61.2 + - - +
61C ASP* 4.1 13.2 - - - +
76C SER* 3.9 16.7 + - - -
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Residues in contact with LEU 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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40C LYS* 5.8 2.0 - - - +
51C THR 3.9 0.9 - - - +
52C LYS* 3.4 3.3 - - - -
53C THR* 2.7 56.7 + - + +
58C ARG* 5.1 8.5 - - - +
59C ASN* 1.3 75.2 - - - +
61C ASP* 1.3 71.2 + - - +
62C VAL* 4.0 21.2 + - + +
72C GLU* 5.7 3.6 - - - +
75C LYS* 4.7 5.4 - - + +
76C SER* 3.8 25.1 - - - +
77C LEU* 5.6 10.3 - - + -
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Residues in contact with ASP 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C THR 3.6 5.6 - - - +
52C LYS* 3.7 26.2 - - + +
53C THR 4.9 0.2 + - - -
59C ASN* 4.1 12.5 + - - +
60C LEU* 1.3 88.4 + - - +
62C VAL* 1.3 61.5 + - - +
63C ASP* 5.1 2.9 - - - +
75C LYS* 5.3 11.4 + - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C THR* 2.8 60.6 + - - +
53C THR* 5.9 0.9 - - - +
60C LEU* 4.3 24.7 - - + +
61C ASP* 1.3 76.5 - - - +
63C ASP* 1.3 69.6 + - - +
64C PHE* 3.9 23.5 - - + -
70C PHE* 4.5 8.3 - - + -
72C GLU* 4.0 21.5 - - + +
106C TRP* 6.1 2.9 - - + -
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Residues in contact with ASP 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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49C PHE 3.3 9.2 - - - +
50C LYS* 3.2 35.5 - - + +
51C THR 3.5 4.9 + - - +
52C LYS* 6.1 0.3 - - - +
61C ASP* 5.1 2.6 - - - +
62C VAL* 1.3 85.5 + - - +
64C PHE* 1.3 67.0 + - - +
70C PHE* 4.2 10.9 - - - -
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Residues in contact with PHE 64 (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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48C ASN* 3.7 1.7 - - - +
49C PHE* 2.8 75.9 + + + +
51C THR* 4.5 13.5 - - + -
62C VAL* 3.9 18.8 - - + -
63C ASP* 1.3 80.3 - - - +
65C THR* 1.3 69.7 + - - +
66C VAL* 4.4 1.3 - - + -
70C PHE* 3.5 28.0 - + + -
86C VAL* 3.6 34.1 - - + -
93C LEU* 4.1 3.1 - - + -
106C TRP* 4.1 29.4 - + - -
108C GLN* 6.1 0.7 - - - -
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Residues in contact with THR 65 (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 ASP* 3.2 19.1 - - + +
48C ASN* 3.0 23.8 + - - +
64C PHE* 1.3 79.4 - - - +
66C VAL* 1.3 77.2 + - - +
67C GLY 3.2 0.3 + - - -
68C VAL* 3.1 44.9 + - + +
70C PHE* 5.4 0.6 - - - -
86C VAL* 4.5 2.4 + - - +
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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