Contacts of the helix formed by residues 71 - 83 (chain A) in PDB entry 5Z66
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 ASP 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A SER* 1.3 75.1 - - - +
72A PRO* 1.3 85.3 - - - +
73A LEU* 3.1 25.8 + - - +
74A MET* 2.9 29.2 + - + +
75A ILE* 2.9 10.6 + - - +
137A TRP* 3.6 30.3 + - + -
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Residues in contact with PRO 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.7 35.4 - - + +
44A LEU* 3.7 18.2 - - + -
68A PRO* 4.5 4.7 - - + -
70A SER 3.2 6.0 - - - +
71A ASP* 1.3 91.0 - - - +
73A LEU* 1.3 53.4 + - - +
75A ILE* 3.7 9.6 - - + +
76A LEU* 2.7 41.2 + - - +
137A TRP* 3.5 39.5 - - + +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASP* 3.1 19.5 + - - +
72A PRO* 1.3 76.3 - - - +
74A MET* 1.3 58.6 + - - +
76A LEU* 3.9 7.7 - - + +
77A ALA* 3.0 29.6 + - + +
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A SER* 3.9 25.4 - - - +
71A ASP* 2.9 19.8 + - + +
73A LEU* 1.3 76.9 - - + +
75A ILE* 1.3 56.4 + - - +
77A ALA* 3.0 6.6 + - - +
78A ASP* 2.6 59.0 + - - +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 4.8 2.7 - - + -
47A LEU* 3.7 27.1 - - + -
68A PRO* 3.7 14.1 - - + -
70A SER* 3.4 37.9 - - - +
71A ASP 2.9 9.0 + - - +
72A PRO* 3.2 10.3 + - + +
74A MET* 1.3 74.4 - - - +
76A LEU* 1.3 52.3 + - - +
78A ASP* 3.6 6.7 - - - +
79A TYR* 2.6 36.7 + - - +
93A PHE* 3.5 14.7 - - + -
97A ASN* 3.6 35.4 - - + +
98A PHE* 3.9 13.9 - - + -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU 3.6 22.4 - - - +
44A LEU* 3.4 31.6 - - + +
45A GLY* 4.6 1.3 - - - +
46A PRO* 4.4 13.7 - - + -
47A LEU* 3.7 25.1 - - + +
72A PRO 2.7 24.5 + - - +
73A LEU* 4.0 7.2 - - + +
75A ILE* 1.3 71.8 - - - +
77A ALA* 1.3 58.0 + - - +
79A TYR* 3.6 8.0 - - + +
80A ARG* 2.8 31.0 + - - +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.0 20.1 + - + +
74A MET* 3.4 7.0 - - - +
76A LEU* 1.3 73.4 - - - +
78A ASP* 1.3 68.6 + - - +
80A ARG* 3.2 6.1 + - - +
81A MET* 3.1 29.7 + - + +
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Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A MET* 2.6 47.0 + - - +
75A ILE* 3.8 5.2 - - - +
77A ALA* 1.3 74.9 - - - +
79A TYR* 1.3 51.9 + - - +
81A MET* 3.3 4.9 + - - +
82A GLN* 2.7 59.4 + - - +
93A PHE* 4.2 7.9 - - + -
97A ASN* 4.7 8.6 - - - +
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Residues in contact with TYR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO* 4.8 6.1 - - + -
47A LEU* 3.8 39.5 - - + -
50A ASP* 2.3 39.0 + - - +
75A ILE 2.6 22.6 + - - +
76A LEU* 3.6 11.7 - - + +
78A ASP* 1.3 73.7 - - - +
80A ARG* 1.3 61.2 + - + +
82A GLN* 4.7 0.2 - - - -
83A HIS* 2.8 56.7 + + + +
88A PHE* 3.6 35.2 - + - -
90A LEU* 4.0 7.6 - - + +
93A PHE* 3.4 26.0 - + + -
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU 2.8 21.7 + - - +
77A ALA* 3.2 6.7 + - - +
79A TYR* 1.3 78.0 - - + +
81A MET* 1.3 68.1 + - + +
83A HIS* 4.2 10.1 + - - +
84A THR* 4.3 13.0 + - - +
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Residues in contact with MET 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA* 3.1 17.5 + - + +
78A ASP* 3.9 4.7 - - - +
80A ARG* 1.3 85.4 - - + +
82A GLN* 1.3 62.6 + - + +
83A HIS 3.4 0.2 - - - -
84A THR* 2.9 23.9 + - - +
85A GLN* 4.3 3.1 + - - +
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Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP* 2.7 42.7 + - - +
79A TYR 4.3 0.4 - - - +
81A MET* 1.3 70.2 - - + +
83A HIS* 1.3 63.9 + - - +
84A THR 3.2 2.2 - - - -
85A GLN* 3.1 22.3 + - + +
88A PHE* 3.2 27.6 - - + -
93A PHE* 3.6 23.1 - - + -
96A MET* 3.8 17.8 - - - +
97A ASN* 5.3 1.0 - - - +
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Residues in contact with HIS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP* 5.1 3.5 + - - -
79A TYR* 2.8 47.4 + + + +
80A ARG* 4.3 7.4 - - - +
81A MET 3.4 0.4 - - - -
82A GLN* 1.3 73.8 - - - +
84A THR* 1.3 65.3 + - + +
85A GLN 3.4 6.4 + - - +
88A PHE* 3.7 33.0 - + + +
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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