Contacts of the strand formed by residues 71 - 78 (chain F) in PDB entry 2ZNZ
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 ILE 71 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76E ALA* 4.1 8.7 - - + -
77E ILE 3.6 3.6 - - - +
78E ILE* 3.7 18.6 - - + -
33F ILE* 4.9 2.0 - - + -
36F LEU* 4.0 27.4 - - + -
62F ILE* 4.2 4.7 - - + +
65F LEU* 3.2 33.8 + - + -
66F ARG* 3.8 38.6 - - + +
69F GLY* 4.0 4.4 - - - -
70F VAL* 1.3 75.0 - - - +
72F LYS* 1.3 63.2 + - - +
73F LYS* 3.8 21.3 - - - +
74F PHE* 3.8 22.4 - - + -
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Residues in contact with LYS 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ILE* 2.7 32.7 + - + +
78E ILE 3.8 8.7 - - - -
79E ASP* 3.7 32.0 + - + +
80E PRO* 3.6 20.8 - - - +
164E GLU* 5.2 8.7 + - - -
69F GLY* 4.3 12.3 - - - +
70F VAL 3.7 0.8 - - - -
71F ILE* 1.3 73.3 - - - +
73F LYS* 1.3 66.3 + - + +
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Residues in contact with LYS 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E GLN 3.2 10.9 + - - -
38E ASN* 3.7 15.9 + - - +
76E ALA* 3.5 2.9 - - - -
77E ILE* 2.8 44.9 + - + +
165E THR* 4.8 3.4 + - - -
166E THR* 5.1 2.6 + - - +
167E GLU* 2.5 37.0 + - - +
66F ARG* 6.3 0.7 - - - +
71F ILE* 3.3 6.8 - - - +
72F LYS* 1.3 84.4 - - + +
74F PHE* 1.3 79.2 + - - +
75F THR* 3.7 13.9 + - - -
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Residues in contact with PHE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ASP* 3.7 9.6 + - - +
40E GLY* 2.9 17.6 + - - +
41E LYS* 3.4 61.2 - - + +
75E THR 3.4 8.1 - - - -
76E ALA* 3.8 20.4 - - + -
36F LEU* 4.2 23.1 - - + -
40F GLY* 3.8 19.3 - - - -
62F ILE* 4.3 5.2 - - + -
66F ARG* 3.7 38.1 - - - +
71F ILE* 3.8 17.0 - - + -
73F LYS* 1.3 86.0 - - - +
75F THR* 1.3 63.6 + - - +
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Residues in contact with THR 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E LEU 3.7 6.1 - - - -
37E GLN* 2.7 25.3 + - - +
40E GLY* 3.8 6.0 - - - +
74E PHE* 3.3 5.2 - - - +
75E THR* 3.0 43.1 + - + -
77E ILE* 3.8 12.8 - - + -
166E THR* 3.8 14.7 + - - +
167E GLU* 4.7 0.9 - - - +
73F LYS* 3.7 9.9 + - - -
74F PHE* 1.3 77.9 - - - +
76F ALA* 1.3 68.1 + - - +
77F ILE* 3.8 27.3 + - + -
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Residues in contact with ALA 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E LEU* 3.1 34.2 + - + +
37E GLN* 3.7 15.6 + - - +
71E ILE* 3.9 22.0 - - + -
73E LYS 3.5 4.9 - - - -
74E PHE* 3.9 10.5 - - + -
166E THR* 5.1 2.4 + - - +
75F THR* 1.3 83.5 + - - +
77F ILE* 1.3 62.5 + - - +
78F ILE* 3.6 13.3 + - + -
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Residues in contact with ILE 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ILE* 3.5 2.9 - - - -
72E LYS* 2.7 55.7 + - + +
73E LYS* 2.8 32.8 + - + +
75E THR* 3.9 22.0 - - + -
166E THR* 3.8 37.5 - - + +
75F THR* 3.8 16.4 - - + -
76F ALA* 1.3 70.5 - - - +
78F ILE* 1.3 58.5 + - - +
166F THR* 4.0 10.5 - - + +
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Residues in contact with ILE 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ILE* 3.7 24.2 - - + -
37E GLN* 3.4 38.3 - - + +
70E VAL* 3.3 17.7 - - + +
71E ILE* 3.7 29.8 - - + -
72E LYS* 4.0 5.0 - - - +
166E THR 5.5 2.0 + - - -
168E LEU* 3.5 11.1 - - + +
76F ALA* 3.6 14.1 + - + +
77F ILE* 1.3 80.6 - - - +
79F ASP* 1.3 76.1 + - - +
80F PRO* 3.3 8.8 - - - +
83F LEU* 3.9 22.9 - - + -
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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