Contacts of the helix formed by residues 66 - 78 (chain B) in PDB entry 1ZX1
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 ASN 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A HIS* 5.8 2.9 - - - -
193A GLU* 5.6 4.9 - - - +
232A FAD 3.5 37.7 + - - +
64B VAL* 3.6 9.0 + - + +
65B PHE* 1.3 76.9 - - - +
67B TYR* 1.3 59.0 + - - +
68B GLY* 3.3 14.6 + - - -
69B VAL* 3.4 31.7 + - + +
70B GLU* 3.0 34.8 + - + +
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Residues in contact with TYR 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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11A HIS* 6.0 1.4 - - - -
12A GLN* 3.8 18.4 + - - +
104A TYR* 4.0 6.7 - - - +
232A FAD 3.9 19.3 - - + -
50B ALA* 3.6 33.4 - - + -
51B THR 3.3 12.8 - - - -
54B ASP* 2.5 32.6 + - + +
55B ILE* 4.8 0.2 - - + -
65B PHE* 3.8 29.3 - + + -
66B ASN* 1.3 71.8 + - - +
68B GLY* 1.3 52.5 + - - +
71B THR* 2.7 66.9 + - + +
84B ILE* 4.3 2.1 - - - +
117B ASP 4.1 15.5 - - - -
118B ARG* 3.5 19.2 + - - +
121B CYS* 6.3 1.1 - - + -
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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
----------------------------------------------------------
232A FAD 3.9 21.6 - - - +
233A CB1 5.8 6.3 - - - -
66B ASN* 3.3 6.6 + - - -
67B TYR* 1.3 77.4 - - - +
69B VAL* 1.3 63.0 + - - +
71B THR* 3.4 5.8 + - - -
72B HIS* 3.1 24.9 + - - +
122B GLN* 4.6 9.7 - - - +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B SER* 5.2 7.4 - - - +
61B ASN* 6.4 1.3 - - + -
66B ASN* 3.3 33.3 + - + +
68B GLY* 1.3 74.9 - - - +
70B GLU* 1.3 71.7 + - + +
72B HIS* 3.3 7.0 + - - +
73B GLU* 3.0 32.3 + - + +
122B GLN* 5.9 0.2 - - - -
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 3.8 14.2 - - + +
59B LEU* 3.5 13.8 - - + +
60B SER* 2.7 31.5 + - - -
61B ASN* 2.8 39.2 + - - +
64B VAL 4.8 1.6 - - - +
65B PHE* 3.8 29.4 - - + -
66B ASN* 3.0 23.3 + - + +
67B TYR 4.3 0.4 - - - +
69B VAL* 1.3 81.9 - - + +
71B THR* 1.3 57.0 + - - +
73B GLU* 3.6 4.4 + - - +
74B ALA* 3.0 28.6 + - - +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 4.7 0.7 - - + -
55B ILE* 3.8 13.7 - - + -
67B TYR* 2.7 65.1 + - + +
68B GLY* 3.4 7.3 + - - -
70B GLU* 1.3 73.1 - - - +
72B HIS* 1.3 61.2 + - - +
74B ALA* 3.8 4.8 - - - +
75B TYR* 2.8 31.4 + - - +
80B LEU* 4.1 18.1 - - + +
84B ILE* 5.6 0.4 - - + -
118B ARG 6.0 0.9 - - - +
121B CYS* 4.3 19.8 - - - +
122B GLN 5.4 0.3 + - - -
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Residues in contact with HIS 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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68B GLY 3.1 19.5 + - - +
69B VAL* 3.3 7.3 + - - +
71B THR* 1.3 78.6 + - - +
73B GLU* 1.3 71.3 + - - +
75B TYR* 3.4 1.7 + - - +
76B LYS* 3.2 40.5 + - + +
122B GLN* 3.3 64.5 + - + +
123B GLY* 3.9 7.9 + - - -
127B ASP* 3.9 15.6 + - - -
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B SER* 4.6 22.2 - - - +
69B VAL* 3.0 22.1 + - + +
70B GLU* 4.0 6.3 - - - +
72B HIS* 1.3 88.6 + - - +
74B ALA* 1.3 56.9 + - - +
76B LYS* 3.3 24.7 + - - +
77B GLN* 3.0 47.2 + - + +
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Residues in contact with ALA 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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55B ILE* 3.7 24.2 - - + -
70B GLU 3.0 18.9 + - - +
71B THR 3.8 3.4 - - - +
73B GLU* 1.3 74.0 - - - +
75B TYR* 1.3 60.9 + - - +
77B GLN* 3.3 1.1 + - - -
78B ARG* 2.9 9.2 + - - -
79B SER* 2.8 50.2 + - - +
80B LEU* 3.8 13.8 + - + -
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Residues in contact with TYR 75 (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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71B THR 2.8 21.4 + - - +
72B HIS 3.6 4.7 - - - +
74B ALA* 1.3 71.5 - - - +
76B LYS* 1.3 71.9 + - + +
78B ARG* 3.0 19.5 + - - +
80B LEU* 3.9 11.0 - - + +
88B GLN* 3.6 21.5 - - - -
92B ARG* 3.2 22.7 + - - -
121B CYS* 3.9 16.6 - - - -
122B GLN 4.0 2.5 - - - +
123B GLY* 3.4 30.9 + - - -
124B PHE* 3.5 31.4 - + + -
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Residues in contact with LYS 76 (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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72B HIS* 3.2 36.4 + - + +
73B GLU* 3.3 29.6 + - - +
75B TYR* 1.3 85.5 - - + +
77B GLN* 1.3 66.9 + - - +
78B ARG* 3.6 6.1 + - - +
123B GLY* 5.7 1.3 - - - -
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.0 33.0 + - + +
74B ALA 4.0 3.1 - - - +
75B TYR 3.2 0.2 - - - -
76B LYS* 1.3 83.3 + - - +
78B ARG* 1.3 70.4 + - - +
79B SER* 3.5 13.4 + - - +
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Residues in contact with ARG 78 (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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74B ALA 2.9 5.4 + - - -
75B TYR* 3.0 13.6 + - - +
76B LYS 4.6 4.9 + - - +
77B GLN* 1.3 81.1 + - - +
79B SER* 1.3 59.2 + - - +
80B LEU* 3.6 4.8 + - - +
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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