Contacts of the strand formed by residues 69 - 77 (chain C) in PDB entry 5DO7
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 LEU 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ALA* 5.1 4.0 - - + +
44C SER* 2.3 32.0 + - - +
45C TYR* 2.8 40.3 + - + +
67C GLN 3.1 4.4 + - - +
68C ILE* 1.3 90.2 - - + +
70C LYS* 1.3 56.1 + - - +
72C VAL* 4.5 10.3 - - + -
91C GLY* 4.2 16.4 - - - +
94C THR* 5.0 3.4 - - + -
95C LEU* 3.3 40.4 - - + +
98C ALA* 5.5 2.9 - - + -
266C LEU* 4.3 5.6 - - + -
269C GLY* 3.6 21.1 - - - +
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Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA 3.4 0.4 - - - -
44C SER* 3.2 5.6 - - - +
67C GLN 5.2 7.0 - - - +
68C ILE 5.9 0.2 - - - -
69C LEU* 1.3 74.8 - - - +
71C ASP* 1.3 77.8 + - + +
72C VAL* 2.9 11.8 + - - +
268C PHE 5.9 0.7 - - - +
269C GLY 3.5 11.1 + - - +
270C GLU* 4.0 33.5 + - + +
271C LEU* 4.3 6.8 + - - +
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Residues in contact with ASP 71 (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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42C HIS* 3.4 36.5 - - + +
43C ALA 2.8 16.7 + - - +
44C SER* 3.5 5.2 + - - -
70C LYS* 1.3 77.1 - - + +
72C VAL* 1.3 60.8 + - - +
73C SER* 4.2 0.5 + - - -
110C LEU* 3.6 21.6 - - - +
271C LEU* 4.6 2.8 - - - +
330C LYS* 3.4 27.8 + - - +
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Residues in contact with VAL 72 (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 ILE* 4.2 7.9 - - + +
41C LEU 3.4 1.2 - - - -
42C HIS 2.8 13.2 + - - -
43C ALA* 2.8 39.8 + - + +
69C LEU* 4.5 12.3 - - + -
70C LYS 3.4 16.6 - - - +
71C ASP* 1.3 74.1 - - - +
73C SER* 1.3 70.4 + - - +
74C LEU* 5.0 9.0 - - + -
95C LEU* 5.1 10.1 - - + -
266C LEU* 4.7 10.3 - - + -
269C GLY 3.8 18.6 - - - +
271C LEU* 3.9 32.1 - - + -
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ILE* 3.0 18.4 - - - -
41C LEU* 4.1 8.5 - - - -
42C HIS* 4.0 12.0 + - - -
71C ASP 4.2 0.3 + - - -
72C VAL* 1.3 81.9 - - - +
74C LEU* 1.3 68.9 + - - +
271C LEU* 3.6 22.7 - - - +
274C CYS* 5.3 0.3 - - - +
329C TYR* 4.8 7.4 + - - -
330C LYS* 4.1 13.3 + - - -
338C THR* 5.3 2.0 + - - -
339C LEU* 5.1 14.3 - - - +
342C ILE* 5.8 0.4 - - - -
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU 3.8 1.1 - - - +
39C GLY* 3.0 5.5 - - - -
40C ILE* 2.8 61.0 + - + +
72C VAL* 5.0 6.5 - - + -
73C SER* 1.3 76.2 - - - +
75C TYR* 1.3 62.7 + - - +
76C VAL* 4.6 12.1 - - + -
82C MET* 3.8 31.6 - - + -
84C ILE* 6.0 0.7 - - + -
264C ALA* 4.2 8.5 - - + -
266C LEU* 6.1 1.3 - - + -
271C LEU* 4.8 9.6 - - + -
274C CYS* 4.0 27.1 - - + -
338C THR* 5.3 8.3 - - - -
339C LEU* 6.4 0.9 - - - +
342C ILE* 3.8 6.3 - - - +
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Residues in contact with TYR 75 (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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37C SER* 4.9 1.2 - - - -
38C LEU 3.7 9.2 - - - -
39C GLY* 4.6 0.7 - - - -
74C LEU* 1.3 78.0 - - - +
76C VAL* 1.3 81.5 + - - +
77C GLU* 1.8 44.1 + - + -
80C GLN* 4.7 1.1 - - - +
262C LYS* 3.1 37.9 + - - +
337C LYS* 5.3 2.5 - - - -
338C THR* 4.0 12.0 - - - +
341C ASN* 3.3 50.6 + - + -
342C ILE* 3.8 21.8 - - + -
345C MET* 3.6 31.3 - - + +
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Residues in contact with VAL 76 (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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37C SER* 3.7 2.1 - - - -
38C LEU* 2.8 48.1 + - + +
74C LEU* 4.6 7.0 - - + -
75C TYR* 1.3 85.1 - - - +
77C GLU* 1.3 81.7 + - - +
80C GLN* 3.1 22.2 - - + +
82C MET* 3.3 37.0 - - + -
244C ILE* 3.8 22.9 - - + -
245C VAL 5.3 0.4 - - - +
246C VAL* 5.6 2.5 - - + -
262C LYS* 4.9 2.7 - - + -
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Residues in contact with GLU 77 (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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36C HIS 3.3 10.1 - - - +
37C SER* 5.3 1.1 - - - -
75C TYR* 1.8 62.7 + - + -
76C VAL* 1.3 75.2 - - - +
78C SER* 1.3 72.2 + - - +
80C GLN* 2.2 55.2 + - + +
244C ILE* 3.9 5.9 - - - +
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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