Contacts of the helix formed by residues 66 - 79 (chain A) in PDB entry 3F3Z
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.7 4.1 - - - +
65A GLU* 1.3 76.8 - - + +
67A VAL* 1.3 58.1 + - - +
68A ASP* 2.9 26.7 + - - +
69A ARG* 3.0 54.3 + - + +
70A PHE* 3.1 26.2 + - - +
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Residues in contact with VAL 67 (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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64A VAL* 4.0 23.8 - - + +
65A GLU 4.0 2.4 + - - +
66A ASP* 1.3 70.8 + - - +
68A ASP* 1.3 65.3 + - - +
70A PHE* 3.2 5.8 + - + +
71A LYS* 2.8 54.1 + - + +
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Residues in contact with ASP 68 (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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66A ASP* 2.9 10.1 + - - +
67A VAL* 1.3 79.1 - - - +
69A ARG* 1.3 59.4 + - - +
71A LYS* 3.4 21.3 + - - +
72A GLN* 3.0 26.9 + - - +
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Residues in contact with ARG 69 (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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66A ASP* 3.0 49.6 + - + +
68A ASP* 1.3 72.5 - - - +
70A PHE* 1.3 65.6 + - - +
72A GLN* 3.2 8.5 + - - +
73A GLU* 3.0 22.7 + - - +
184A THR* 4.8 15.8 - - - +
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Residues in contact with PHE 70 (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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59A ILE* 4.0 30.7 - - + -
64A VAL* 3.7 25.1 - - + -
66A ASP 3.1 15.8 + - - +
67A VAL* 3.2 10.5 + - + +
69A ARG* 1.3 75.9 - - - +
71A LYS* 1.3 67.7 + - + +
73A GLU* 3.2 26.4 + - - +
74A ILE* 3.1 52.4 + - + +
98A ILE* 3.6 36.3 - - + -
100A LEU* 4.3 6.3 - - + -
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Residues in contact with LYS 71 (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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67A VAL* 2.8 39.7 + - + +
68A ASP* 3.5 20.5 + - - +
70A PHE* 1.3 79.6 - - + +
72A GLN* 1.3 56.0 + - - +
74A ILE* 3.3 6.8 + - - +
75A GLU* 2.9 38.5 + - + +
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Residues in contact with GLN 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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68A ASP 3.0 13.5 + - - +
69A ARG* 3.2 11.6 + - - +
71A LYS* 1.3 75.0 - - - +
73A GLU* 1.3 54.1 + - - +
75A GLU* 3.3 8.3 + - - +
76A ILE* 2.8 50.8 + - + +
173A ALA 5.4 2.0 - - - +
174A ALA* 5.9 0.7 - - - -
175A ARG* 3.4 46.0 - - - +
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Residues in contact with GLU 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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39A TRP* 6.1 0.9 - - - -
57A LYS* 5.6 2.9 + - - -
69A ARG 3.0 12.3 + - - +
70A PHE* 3.2 28.4 + - - +
72A GLN* 1.3 76.8 - - - +
74A ILE* 1.3 77.2 + - + +
76A ILE* 3.4 9.1 + - - +
77A MET* 3.0 32.7 + - + +
100A LEU* 5.3 3.1 - - - +
169A ASP* 5.1 3.5 - - - +
170A PHE* 3.3 30.3 + - + +
171A GLY* 3.6 28.8 + - - +
173A ALA 5.6 1.5 + - - -
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Residues in contact with ILE 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 PHE* 3.1 43.9 + - + +
71A LYS* 3.7 8.1 - - - +
73A GLU* 1.3 86.2 - - + +
75A GLU* 1.3 68.3 - - - +
77A MET* 3.2 11.4 + - - +
78A LYS* 2.9 33.9 + - + +
88A LEU* 3.8 17.7 - - + +
91A THR* 4.4 13.5 - - + -
100A LEU* 3.6 33.4 - - + -
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Residues in contact with GLU 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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71A LYS* 2.9 26.3 + - + +
72A GLN* 3.7 10.1 - - - +
74A ILE* 1.3 79.5 - - - +
76A ILE* 1.3 64.6 + - - +
78A LYS* 2.8 40.9 + - - +
79A SER* 3.2 16.6 + - - -
175A ARG* 3.0 22.6 + - - +
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Residues in contact with ILE 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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72A GLN* 2.8 35.7 + - + +
73A GLU* 3.6 7.4 - - - +
74A ILE 3.3 0.2 - - - -
75A GLU* 1.3 73.0 - - - +
77A MET* 1.3 63.7 + - - +
79A SER* 2.6 21.5 + - - -
80A LEU* 3.3 10.0 - - + +
144A VAL* 3.8 28.3 - - + -
170A PHE* 4.1 19.3 - - + -
173A ALA* 3.6 35.4 - - + +
174A ALA 4.0 1.8 - - - +
175A ARG* 3.4 43.9 - - + +
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Residues in contact with MET 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 GLU* 3.0 25.4 + - - +
74A ILE* 3.4 20.2 - - - +
76A ILE* 1.3 76.6 - - - +
78A LYS* 1.3 62.8 + - - +
80A LEU* 3.2 27.1 + - - +
85A ILE* 5.7 0.5 - - - +
86A ILE* 3.6 38.6 - - + +
88A LEU* 4.1 31.4 + - + +
100A LEU* 4.7 8.5 - - - -
102A MET* 4.0 18.2 - - - +
168A ILE 4.7 3.8 - - - +
169A ASP* 5.8 0.2 - - - -
170A PHE* 3.8 32.5 - - + -
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Residues in contact with LYS 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 ILE* 2.9 22.5 + - + +
75A GLU* 2.8 43.0 + - - +
76A ILE 3.3 0.2 - - - -
77A MET* 1.3 77.2 - - - +
79A SER* 1.3 59.1 + - - +
80A LEU 3.2 5.5 + - - +
88A LEU* 4.1 24.2 - - + +
91A THR* 6.1 2.0 - - + -
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Residues in contact with SER 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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75A GLU 3.2 11.2 + - - -
76A ILE* 2.6 19.6 + - - +
78A LYS* 1.3 75.7 - - - +
80A LEU* 1.3 64.9 + - - +
81A ASP* 4.2 0.5 + - - +
138A TYR* 4.2 1.2 + - - -
142A LEU* 3.7 19.7 - - - +
144A VAL* 4.8 1.0 - - - +
175A ARG* 3.3 27.2 + - - -
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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