Contacts of the helix formed by residues 66 - 70 (chain B) in PDB entry 1ZN8
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 SER 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ASP* 3.6 17.7 + - - -
66A SER* 3.8 8.5 - - - -
69A PHE* 3.4 12.6 - - - -
87A ARG* 2.5 34.3 + - - -
64B LEU 3.5 0.9 - - - -
65B ASP* 1.3 85.1 + - - +
67B ARG* 1.3 67.0 + - - +
68B GLY 3.3 2.2 - - - -
69B PHE* 3.1 22.4 + - - +
70B LEU 4.0 0.2 + - - -
88B LYS* 4.3 7.2 - - - +
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Residues in contact with ARG 67 (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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69A PHE* 4.9 1.3 - - + -
85A LEU* 5.9 2.5 - - + -
87A ARG* 2.9 34.8 - - - +
91A LYS* 3.7 27.1 + - - +
26B PHE* 3.7 18.1 - - - -
27B ARG 5.5 0.2 + - - -
29B ILE* 4.6 9.2 - - - -
64B LEU 3.7 0.2 + - - -
65B ASP 3.8 0.2 - - - -
66B SER* 1.3 79.3 + - - +
68B GLY* 1.3 62.8 + - - +
70B LEU* 3.2 37.6 + - + +
71B PHE* 3.5 10.2 - - - -
127B ASP* 4.0 3.3 + - - +
128B ASP* 3.1 33.0 + - + +
1032B AMP 2.8 55.3 + - - +
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Residues in contact with GLY 68 (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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63B GLY* 4.2 1.1 - - - -
64B LEU 2.7 22.0 + - - -
67B ARG* 1.3 66.8 - - - +
69B PHE* 1.3 62.1 + - - +
70B LEU 3.1 2.7 - - - -
71B PHE* 3.1 4.4 + - - -
72B GLY* 2.9 28.6 + - - -
126B VAL* 3.8 18.9 - - - +
127B ASP* 3.2 21.7 + - - -
128B ASP 4.3 0.9 - - - -
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Residues in contact with PHE 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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66A SER* 3.6 24.7 - - - -
67A ARG* 4.9 0.4 - - + -
69A PHE* 3.3 20.4 - - + +
70A LEU* 3.6 32.0 - - + -
63B GLY* 3.5 18.6 - - - -
64B LEU 3.7 7.4 - - - -
65B ASP* 3.5 37.2 - - + -
66B SER* 3.1 17.7 + - - +
68B GLY* 1.3 78.0 - - - +
70B LEU* 1.3 55.9 + - - +
71B PHE 3.2 0.2 - - - -
73B PRO* 3.0 25.3 - - - +
85B LEU* 3.8 16.2 - - + -
86B ILE 4.0 2.0 - - - -
87B ARG* 3.7 36.6 - - + -
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Residues in contact with LEU 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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69A PHE* 3.6 39.9 - - + -
73A PRO* 3.4 41.2 - - + +
85A LEU* 3.7 39.3 - - + -
29B ILE* 4.1 18.2 - - + -
33B LEU* 4.1 8.1 - - + -
39B PHE* 3.6 9.7 - - - -
67B ARG* 3.3 28.3 - - + +
68B GLY 3.1 0.6 - - - -
69B PHE* 1.3 78.4 - - - +
71B PHE* 1.3 67.5 + - + +
73B PRO* 4.6 0.4 - - - +
74B SER* 4.6 1.7 + - - -
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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