Contacts of the helix formed by residues 68 - 74 (chain B) in PDB entry 5DAH
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 CYS 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B CYS* 3.2 11.6 - - - -
47B CYS* 4.0 4.7 - - - -
49B VAL* 4.0 17.0 - - + -
56B TYR* 3.4 13.5 - - + +
66B TRP* 3.5 20.9 - - + -
67B PHE* 1.3 75.4 - - - +
69B ARG* 1.3 62.5 + - - +
70B LYS* 3.1 16.9 + - - -
71B CYS 3.3 14.2 + - - -
72B GLU* 2.9 27.6 + - - +
92B LEU 5.8 2.2 - - - +
302B ZN 2.4 33.9 - - - -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR* 2.8 25.8 + - + +
57B GLY 5.6 3.8 + - - -
59B VAL* 6.1 3.2 - - - +
67B PHE 5.6 1.5 + - - -
68B CYS* 1.3 73.0 - - - +
70B LYS* 1.3 64.4 + - - +
72B GLU* 3.4 34.0 + - - +
73B SER* 3.3 15.1 + - - -
92B LEU 3.9 7.0 - - - +
93B LYS* 3.8 12.0 - - + +
94B ARG* 5.4 2.5 - - + +
100B TRP* 3.4 23.1 - - + -
119B THR* 5.8 2.8 - - - -
121B GLU* 3.0 43.8 + - - +
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B CYS* 5.9 2.5 - - - -
56B TYR* 4.3 1.0 + - - -
68B CYS* 3.1 13.5 - - - -
69B ARG* 1.3 79.0 - - - +
71B CYS* 1.3 71.0 + - - +
73B SER* 3.0 22.1 + - - -
74B GLN 3.8 1.7 + - - -
75B GLU 5.2 0.2 + - - -
80B VAL* 3.3 50.6 + - + +
88B LYS 5.2 6.7 - - - +
89B ASP* 5.9 2.2 - - - -
90B GLY 5.5 3.8 - - - +
92B LEU* 3.9 24.2 + - + +
100B TRP* 4.0 10.8 - - + -
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Residues in contact with CYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B CYS* 3.8 7.6 - - - -
44B GLY* 4.0 9.6 - - - -
45B HIS 5.7 0.9 - - - -
47B CYS* 3.6 18.2 - - - -
67B PHE* 4.3 14.8 - - + -
68B CYS* 3.3 5.3 + - - +
70B LYS* 1.3 85.1 - - - +
72B GLU* 1.3 61.7 + - - +
74B GLN* 3.4 14.9 + - - +
302B ZN 2.4 33.7 - - - -
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PHE* 4.2 23.3 + - + +
68B CYS 2.9 17.8 + - - +
69B ARG* 3.4 37.9 + - - +
71B CYS* 1.3 76.2 - - - +
73B SER* 1.3 64.6 + - - +
74B GLN* 3.4 4.9 + - - +
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG 3.3 13.5 + - - -
70B LYS 3.0 12.4 + - - -
72B GLU* 1.3 79.3 - - - +
74B GLN* 1.3 70.6 + - - +
75B GLU* 3.3 27.7 + - - +
80B VAL* 5.2 4.2 - - - +
94B ARG* 3.4 29.4 - - - +
100B TRP* 4.2 10.6 - - - -
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LYS 3.8 1.8 + - - -
71B CYS 3.4 12.6 + - - +
72B GLU 3.2 6.6 - - - +
73B SER* 1.3 83.6 + - - +
75B GLU* 1.3 59.6 + - - +
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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